tag:blogger.com,1999:blog-84701403421707958012024-03-13T10:23:43.421-07:00Neuroscience BroSome thoughts about neuroscience and other thoughts not about neuroscienceTorbenhttp://www.blogger.com/profile/03586733786614548430noreply@blogger.comBlogger10125tag:blogger.com,1999:blog-8470140342170795801.post-22469126179807525792019-01-23T12:43:00.002-08:002019-01-23T23:04:20.555-08:00Sniffing and Epilepsy...Why?<!--[if gte mso 9]><xml>
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<span style="background: white; color: black; font-family: "arial"; font-size: x-large;">Before I start the post</span><br />
<span style="background: white; color: black; font-family: "arial"; font-size: 10.0pt;"><br /></span>
<span style="background: white; color: black; font-family: "arial";">I put this up last week but my PI, (my boss for you non-scientists),
sent me an urgent text to take it down ASAP. There's this huge issue in
science called 'scooping.' This is where a scientist will see somebody else's
work on a project that is similar to their own and race to publish it first,
taking all of the credit. This happens far more often than you might think,
especially among a group people who are all generally trying to help the world
in some way. It's pretty weird and awful. My PI read the first paragraph
and to her it looked like what I was saying was putting my work, as well as the
other people in our lab, at risk of being scooped. She gave it a full read-through
this weekend and gave it the OK. Most of the science and the methodologies that
I write about here have actually been known and used for a long time. I wanted
to write this thing because I'm really stoked about what we're working on and wanted to
spread the word beyond the small circle of scientists that we interact with at talks
and conferences. It turns out that you should at least ask somebody whether its
alright before you launch their ideas out to wherever they go on the internet. Lesson learned. </span><br />
<span style="background: white; color: black; font-family: "arial";">Now let's talk about this sniffing stuff.</span><span style="color: black; font-family: "arial";"><o:p></o:p></span><br />
<span style="background: white; color: black; font-family: "arial";"><br /></span></div>
<div class="separator" style="clear: both; text-align: center;">
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<span style="background: white; color: black; font-family: "arial"; font-size: x-large;">I spent the last few months applying for a grant through the NIH to
study...<b>sniffing</b>. </span><span style="color: black; font-family: "arial";"><br />
<span style="background: white;"><br />
If all goes as planned, some of your hard-earned tax dollars are going to
directly to <i>me</i> to spend a couple of years investigating <b><i>sniffing</i></b>.
Some scientists study the science of olfaction, or how your brain forms
perceptions of odors from the chemicals that enter your nose. My research isn't
so much about that. I'm literally going to study how people sniff stuff. </span><br />
<br />
<span style="background: white;">If that isn't weird enough for you, I plan to
work with epilepsy patients at Northwestern Hospital and ask them to smell a
bunch of heinous odors while I record electrical signals from their brains and
breathing waveforms from their noses.</span><br />
<br />
<span style="background: white;">So this obviously seems pretty insane. </span><br />
<span style="background: white;"><br />
Neuroscientists should probably work on important problems like Alzheimer's
Disease and MS. What reason could <b><i>ever</i></b> justify this
trash?</span><br />
<span style="background: white;"><br />
My mentor, lab mates, and I believe that the results of this project could
actually have pretty significant implications for understanding and
treating <b>epilepsy</b>. In the rest of this post I'm going to walk you
through our logic and hopefully prove to you that I haven't <b><i>completely</i></b> lost
my mind. I'm going to start by explaining the basics of epilepsy.</span><br />
<span style="background: white;"><br />
<br /><span style="font-size: x-large;">
Epilepsy and SUDEP</span></span><br />
<span style="background: white;"><br />
Epilepsy is a neurological disorder that is characterized by the
recurrent tendency for one to have seizures. Seizures can come in many
forms. For instance, someone having an absence seizure will appear to space out
for a few seconds. These can be so subtle that many people who have
absence seizures don't even realize that they have epilepsy for a long time.
On the other hand, someone having a grand mal seizure will experience violent
convulsions for up to about two minutes.</span><o:p></o:p></span></div>
<div class="MsoNormal">
<span style="background: white; color: black; font-family: "arial";"><br />
If you look someone's brain activity while they have a seizure, you will see
that neurons in one area of the brain will start to fire more rapidly and
synchronously than they ever normally would. In more severe seizures, this
rampant abnormal activity can spread across the brain, sometimes
reaching areas far from where it started. For example, in a grand mal seizure,
the seizure activity reaches the motor cortex, which is responsible for many
aspects of controlling movement. These neurons are mostly silent when you’re
resting. But when you chose to move part of your body, a select group of these
neurons will activate in a complex, finely-tuned pattern, sending signals down
your spinal cord, precisely controlling which muscles to flex. However, when
seizure activity sweeps across the motor cortex, tons of neurons are
simultaneously activated, causing the erratic, unintentional muscle movements
seen in grand mal seizures. </span><span style="color: black; font-family: "arial";"><o:p></o:p></span></div>
<div class="MsoNormal">
<span style="background: white; color: black; font-family: "arial";"><br />
The main takeaway here is that seizures disrupt the neural activity in the
parts of the brain that they spread to and can initiate (or modify) the
processes that neurons in those areas are involved in. </span><span style="color: black; font-family: "arial";"><br />
<span style="background: white;"><br />
Lots of great people are working on understanding seizures and epilepsy. I'm
particularly excited about brain implants that can predict and disrupt seizures.
Few people know that these exist and are actually inside some peoples' heads right now! </span>(seriously awesome right?) My work is related to <b style="font-family: arial;">SUDEP</b>, a fatal
complication of epilepsy that afflicts people with severe,
medication-resistant cases. It is the leading cause of death for people with
severe epilepsy.</span><br />
<span style="color: black; font-family: "arial";"><b><span style="background: white;"><br /></span></b></span>
<span style="color: black; font-family: "arial";">
<b><span style="background: white;">SUDEP</span></b><span style="background: white;"> stands
for <b>S</b>udden <b>U</b>nexpected <b>D</b>eath in <b>EP</b>ilepsy. If
you can guess by the name, we really have no idea how to predict SUDEP and we
have just a vague idea of its cause. This is clearly a huge problem and we want
to make a big dent in it. </span><br />
<span style="background: white;"><br />
My brilliant supervisor had the idea that studying the neurons that
control <b>sniffing</b> might actually help us understand <b>SUDEP</b>,
and hopefully prevent it in the future. </span><br />
<span style="background: white;"><br />
<b>So why in tarnation would anyone think that?</b></span><br />
<br />
<span style="background: white;"><br /><span style="font-size: x-large;">
Epilepsy and Breathing</span></span><br />
<span style="background: white;"><br />
One of the first key clues about the cause of SUDEP is evidence suggesting
that these people may die because they <b>stop breathing</b>, which is soon followed by cardiac arrest<b> </b>[<a href="https://www.ncbi.nlm.nih.gov/pubmed/18805738">1</a>,</span><a href="https://www.ncbi.nlm.nih.gov/pubmed/21783426"><span style="background: white;">2</span></a><span style="background: white;">]. This is a huge step
forward but it is also rather unexpected.</span><br />
<span style="background: white;"><br />
More often than not, seizures begin in the <b>temporal lobes</b> of
the brain, while breathing is controlled by a few small patches of neurons far
away in the <b>brainstem</b>. Therefore, the first big question that
we need to answer is, how would disrupted activity in these epileptic brain
regions trigger neurons in a totally different area of the brain to make
somebody stop breathing?</span></span><br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://2.bp.blogspot.com/-aEmGOeFIDDc/XEjM40NX3VI/AAAAAAAABOQ/R8e0RJSG8ZgI0tYQYD89Qywjp-uJQk3XQCLcBGAs/s1600/brain%2Bschematic.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="1066" data-original-width="1326" height="321" src="https://2.bp.blogspot.com/-aEmGOeFIDDc/XEjM40NX3VI/AAAAAAAABOQ/R8e0RJSG8ZgI0tYQYD89Qywjp-uJQk3XQCLcBGAs/s400/brain%2Bschematic.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: "arial" , "helvetica" , sans-serif;">how tho?</span></td></tr>
</tbody></table>
</div>
<div class="MsoNormal">
<span style="background: white; color: black; font-family: "arial";">Basically, for this to happen, there has to be an anatomical pathway
linking epileptogenic neurons in the temporal lobe to respiratory neurons in
the brainstem. I wasn't taught any such pathways in my neuroscience
education, but that doesn't mean they don't exist. After some research, we came
across some previous work that identified such a pathway in rats [<a href="https://www.ncbi.nlm.nih.gov/pubmed/6204716">3</a>] and non-human
primates [<a href="https://www.ncbi.nlm.nih.gov/pubmed/6171630">4</a>], suggesting
that we may have it in our brains as well. The amygdala, a brain region within
each temporal lobe, contains a subregion called the central nucleus, which
appears to have neurons that directly project to respiratory areas in the
brainstem through the amygdalofugal pathway! Therefore, it seems plausible that
when a seizure propagates to neurons in the central amygdala, this activity may
reach respiratory neurons in the brainstem where it could disrupt — and maybe
halt — ongoing breathing rhythms.</span><span style="color: black; font-family: "arial";"><o:p></o:p></span></div>
<div class="MsoNormal">
<span style="color: black; font-family: "arial";"><br />
<span style="background: white;">Now, anatomical evidence is good but it’s
critical that we to test whether this connection matters. In other words, we
need to experimentally<b> test the hypothesis that activating neurons in
the central amygdala causes people to stop breathing</b>.</span><br />
<span style="background: white;"><br />
Testing this hypothesis is tricky because you can't just go around making
people undergo brain surgery to stick wires in their amygdala and mess with
their neurons. In the face of this completely reasonable constraint, many neuroscientists
choose to do experiments on non-human animals. This is a totally valid approach but there’s
always going to be uncertainty about whether something found in the brain of
another species is going to be present in our brains as well. In the end we’re really going to have to test any hypothesis about humans directly <i>in</i> humans
to be sure. Fortunately, there is actually a rare and special condition where
we can do this. </span></span><br />
<span style="color: black; font-family: "arial";"><span style="background: white;"><span style="font-size: medium;"><br /></span></span></span>
<span style="color: black; font-family: "arial";"><span style="background: white;"><span style="font-size: medium;"><br /><span style="font-size: x-large;">
Doing Neuroscience with Epilepsy Patients</span></span><br />
</span></span></div>
<div class="MsoNormal">
<span style="background: white; color: black; font-family: "arial";"><br /></span>
<br />
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-UHFinyAqNWA/XEjNI_tNuJI/AAAAAAAABOY/ZSkZlSROj2gFSIu87xGrnxBrzfUoQNjBwCLcBGAs/s1600/penfield%2Bsurgery.jpg" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" data-original-height="491" data-original-width="376" height="320" src="https://1.bp.blogspot.com/-UHFinyAqNWA/XEjNI_tNuJI/AAAAAAAABOY/ZSkZlSROj2gFSIu87xGrnxBrzfUoQNjBwCLcBGAs/s320/penfield%2Bsurgery.jpg" width="245" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: "arial" , "helvetica" , sans-serif;">This kind of surgery has been done <br />since the 40's!</span></td></tr>
</tbody></table>
<span style="background: white; color: black; font-family: "arial";">If you have debilitating, treatment-resistant epilepsy,
sometimes neurologists will recommend that you undergo surgery to remove the
part of the brain where your seizures originate. This is a difficult and
involved procedure that can take days and sometimes weeks. During this
treatment, electrodes are surgically implanted in the patient’s
brain. Then, the patient is taken off their anti-seizure drugs and
monitored 24/7, until they experience several clinical seizures. During the
seizures, the electrodes in their brain record data that neurologists and
technicians use to try to figure out where the seizures originate. Using
up to around one hundred contact sites electrodes they create a 3D map of the
epileptogenic site, or the seizure’s starting point, and follow where it
spreads through the brain. Once the neurologists are confident that they have
found the epileptogenic site, they perform another step before surgically
removing it.</span><span style="font-family: "arial";"><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="background: white; color: black; font-family: "arial";">The electrodes implanted in the patient’s brain can stimulate as well as
record. With electrical neurologists can perturb areas around the resection site to test whether
they are responsible for major cognitive functions like language and memory.
This is really important because everybody’s brain is a little different and if
a part of the patient’s brain that is responsible for say, forming new
memories, overlaps with the epileptogenic site, the neurologists can modify the
surgery plan to avoid negatively affecting the patient.</span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="background: white; color: black; font-family: "arial";">Perhaps the craziest part of this process is that these patients have to
be <b><i>awake</i></b> while the neurologists assess these other
cognitive functions with and without stimulation. The only way to be confident
that the patient can still use language after parts of their brain are removed
is to have them perform various tasks that they have to be awake to
do—like reading or talking— while electrically stimulating these areas.</span></div>
<div class="MsoNormal">
<span style="background: white; color: black; font-family: "arial";"><br />
You might think it would be super painful to have a bunch of metal wires
running an electrical current through your brain while you are conscious, but
it actually isn't. We can sense pain in lots of the tissue in our head but the
brain itself doesn't have any pain receptors, so surprisingly, stimulating most
areas isn't painful. I say ‘most’ only because there are just a few areas that
receive signals from neurons that are sensitive to pain, so stimulating these
select areas could actually induce </span><span style="color: black; font-family: "arial";">sensations of pain. It's super interesting and I could go on but we’re quickly getting
off topic.<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="background: white; color: black; font-family: "arial";"><br />
We work closely with lots of neurologists at Northwestern to do experiments
with epilepsy patients. It goes without saying that we are extremely aware of
the ethical considerations we must take with these patients and everything we
do is approved by an internal ethics review board. </span><span style="font-family: "arial";"><o:p></o:p></span></div>
<div class="MsoNormal">
<br />
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-IOcLAsXNmOQ/XEjNivx_6rI/AAAAAAAABOg/Wu2mgWdG1t0lTtLggOV61ltUqxMHR22OgCLcBGAs/s1600/nobisfig.png" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" data-original-height="1144" data-original-width="708" height="400" src="https://1.bp.blogspot.com/-IOcLAsXNmOQ/XEjNivx_6rI/AAAAAAAABOg/Wu2mgWdG1t0lTtLggOV61ltUqxMHR22OgCLcBGAs/s400/nobisfig.png" width="247" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><div style="text-align: left;">
<span style="font-size: 12.8px;"><span style="font-family: "arial" , "helvetica" , sans-serif;">Stimulating the central amygdala (left) but </span></span></div>
<div style="text-align: left;">
<span style="font-size: 12.8px;"><span style="font-family: "arial" , "helvetica" , sans-serif;">not the hippocampus (right) caused patients</span></span></div>
<div style="text-align: left;">
<span style="font-size: 12.8px;"><span style="font-family: "arial" , "helvetica" , sans-serif;">to stop breathing.</span></span></div>
</td></tr>
</tbody></table>
</div>
<div class="MsoNormal">
<span style="background: white; color: black; font-family: "arial";">Members of my lab recently published an </span><span style="color: black; font-family: "arial";"><a href="https://www.ncbi.nlm.nih.gov/pubmed/29420859"><span style="background: white;">experiment</span></a><span style="background: white;"> that they
conducted with epilepsy patients to test this hypothesis—that directly
stimulating the central amygdala causes people to stop breathing. It turns out
that their hypothesis was correct; <b>every single patient that was tested
instantly stopped breathing when the central nucleus of the amygdala was
stimulated</b>. We think this is specific to the central amygdala because
stimulating neighboring regions had no effect on breathing. Interestingly,
breathing only stopped when the patients were instructed to breathe naturally
through their nose, not their mouth. There were several fascinating things we
noticed. For one, patients <b>stopped their breathing for as long as the
stimulus was applied</b> and sometimes longer. However, they were able to
resume breathing during stimulation if they were instructed to. Also,
(anecdotally) <i>all but one of the patients were totally unaware that
they had stopped breathing at all</i>! This is all really exciting and builds on the findings of others [</span><a href="http://www.jneurosci.org/content/35/28/10281"><span style="background: white;">5</span></a><span style="background: white;">] [</span><a href="https://www.ncbi.nlm.nih.gov/pubmed/3681736"><span style="background: white;">6</span></a><span style="background: white;">] but, like most science,
raises more questions than it answers. </span><o:p></o:p></span></div>
<div class="MsoNormal">
<span style="color: black; font-family: "arial"; font-size: 10.0pt;"><br style="mso-special-character: line-break;" />
<!--[if !supportLineBreakNewLine]--><br style="mso-special-character: line-break;" />
<!--[endif]--><o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-size: xx-small;"><br /></span>
<span style="font-size: xx-small;"><br /></span>
<span style="background: white; color: black; font-family: "arial"; font-size: x-large;">The Amygdala and Breathing?</span><span style="color: black; font-family: "arial";"><br />
<br />
<span style="background: white;">The amygdala has been well-defined as a brain
area that is crucial for a lot of emotional processes. If you get rid of
someone's amygdalae (the plural of amygdala that nobody uses), they exhibit
hypoemotionality, or a lack of emotions. These people can recognize if
something is meant to be scary but they don't <i>experience</i> the
fear associated with it or exhibit fear-induced behaviors like sweating or
elevated heart rate. There have been numerous studies that have shown that </span><span style="background-color: white;">people with anxiety disorders, depression, and PTSD all seem to have differences in their amygdalae compared to healthy controls. </span><br />
<br />
<span style="background: white;">So why the heck is this emotional brain region
talking to respiratory areas in the brainstem in the first place? </span><br />
<span style="background: white;"><br />
We know that when we're emotional, we breathe very differently. For example,
laughing and crying are respiratory behaviors that are induced by specific
emotional states. Laughing and crying are both so freaking weird and just get
weirder the more you think about them. I'm sure that you've laughed so hard
that you couldn't breathe, likewise with crying, but hopefully far less often.
But that doesn't answer the question. <i>Why</i> is emotion so tied
to breathing and how would this be helpful at all? <b>If you were building a
brain from scratch, why would you <i>ever</i> give this
emotional brain region the authority to override and halt a vital process that
keeps you alive</b>? </span><o:p></o:p></span></div>
<div class="MsoNormal">
<span style="background: white; color: black; font-family: "arial";"><br />
I wanted to get my head around this brain region a little better so I asked if
I could sit in on my program's neuroanatomy lab. Something I
didn't realize is just how <i>tiny </i>the amygdala is! </span></div>
<div class="MsoNormal">
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://3.bp.blogspot.com/-R7o8u-zxOes/XEjOK1gUscI/AAAAAAAABOo/S7_Rt0iryIg6vB8lIt4KYgkogxzRJn7mgCLcBGAs/s1600/human%2Bamygdala.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="882" data-original-width="1600" height="352" src="https://3.bp.blogspot.com/-R7o8u-zxOes/XEjOK1gUscI/AAAAAAAABOo/S7_Rt0iryIg6vB8lIt4KYgkogxzRJn7mgCLcBGAs/s640/human%2Bamygdala.png" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><div style="text-align: left;">
<span style="font-family: "arial" , "helvetica" , sans-serif;">In the picture on the left, I'm holding a section of a medical donor's right temporal lobe, which </span><span style="font-family: "arial" , "helvetica" , sans-serif; font-size: 12.8px;">I have sliced coronally. (or at least attempted to)</span></div>
<div style="text-align: left;">
<span style="font-family: "arial" , "helvetica" , sans-serif;">In picture on the right you can see that the amygdala is only visible in two of these ~1 cm slices.</span> </div>
</td></tr>
</tbody></table>
<span style="background: white; color: black; font-family: "arial";"><br />
Why does this glob of cells, that is roughly the size and shape of an almond, have so much control when we have one of
the largest brains in the animal kingdom?</span><span style="color: black; font-family: "arial";"><o:p></o:p></span></div>
<div class="MsoNormal">
<span style="background: white; color: black; font-family: "arial";"><br style="mso-special-character: line-break;" /></span></div>
<div class="MsoNormal">
<span style="color: black; font-family: "arial";">
<span style="background: white;">It’s possible that this connection between the
amygdala and breathing is some vestigial circuit leftover from evolution or
development. A colleague suggested that pausing breathing could help you avoid being detected by a predator, which is very plausable. But maybe, just maybe, the reason that this connection exists might
have something to do with <b>smell</b>.</span><br />
<br />
<span style="background: white;"><br /><span style="font-size: x-large;">More About The Amygdala and Also Sniffing</span></span><br />
<span style="background: white;"><br />
"The amygdala is the emotion part of the brain", is a platitude that
I've read more times than I can remember. While this is mostly true, I think
that the amygdala may be more accurately described as the brain region
responsible for determining the hedonic value of stimuli and triggering
adaptive responses. In English, that means that when you sense something, your
amygdala determines whether it is good for you or bad for you. If you
present people with pleasant stimuli, their amygdalae activate. If you
show them images of landscapes, or play simple tones, the amygdala doesn't do
much. If you show people scary images, their amygdalae go nuts. The
amygdala has bidirectional connections with tons of brain areas including
the sensory cortices, prefrontal cortex, hippocampus, basal ganglia,
hypothalamus, brainstem, and other areas as well. It is like your own
personal Central Intelligence Agency that is always gathering intel from all
over the brain and monitoring whether things are OK. If your amygdala detects
a threat, it sends signals to activate areas of the brain that do things like
potentiating reflexes and releasing hormones, which help you react quickly and
avoid most kinds of immediate danger [<a href="https://www.ncbi.nlm.nih.gov/pubmed/9720596">7</a>].</span><o:p></o:p></span></div>
<div class="MsoNormal">
<span style="color: black; font-family: "arial";"><br />
<span style="background: white;">Something that few people know about the
amygdala is that it receives extensive, direct input from the olfactory bulb -
which is the first area in the brain that processes information about odors.
When you smell something awful your amygdala activates like it would if you saw
or heard something aversive. However, <b>if you smell something unpleasant
you also reflexively stop sniffing</b> [</span><a href="https://www.physiology.org/doi/full/10.1152/jn.00115.2003"><span style="background: white;">8</span></a><span style="background: white;">] [</span><a href="https://www.ncbi.nlm.nih.gov/pubmed/12576116"><span style="background: white;">9</span></a><span style="background: white;">]. Most things that smell bad
are also harmful to you, like rotten food or noxious gasses. Rapidly halting
your nasal breathing when you detect potentially dangerous chemicals in your
nose prevents you from breathing them into your lungs, where they could be
absorbed into your body and harm you. <b>This reflex is key because it demonstrates
that olfactory information can rapidly halt ongoing breathing rhythms.</b> This
reflex is extremely fast, which has led some researchers to hypothesize the
existence of an 'olfactomotor' circuit ('olfacto' meaning olfaction and
'motor' referring to respiratory motor neurons) [</span><a href="https://www.ncbi.nlm.nih.gov/pubmed/16339268"><span style="background: white;">10</span></a><span style="background: white;">]. The anatomy of the
olfactomotor circuit not been investigated yet but I'm bringing this up here
because this behavior has amygdala written all over it.</span><span style="background: white;"><br style="mso-special-character: line-break;" />
<!--[if !supportLineBreakNewLine]--><br style="mso-special-character: line-break;" />
<!--[endif]--></span><o:p></o:p></span></div>
<div class="MsoNormal" style="background: white;">
<span style="color: black; font-family: "arial";">Now I feel like I need to recap what I've told
you so far because I've introduced a bunch of pretty tricky ideas in
neuroscience that relate to each other in ways that I maybe didn't chain
together as well as I could have.<o:p></o:p></span></div>
<div class="MsoNormal" style="background: white;">
<br />
<br /></div>
<div class="MsoNormal">
<span style="background: white; color: black; font-family: "arial"; font-size: x-large;">The Story So Far</span></div>
<ol start="1" type="1">
<li class="MsoNormal" style="color: black; mso-list: l0 level1 lfo1; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; tab-stops: list .5in;"><span style="background: white; color: black; font-family: "arial";">People with severe epilepsy can die from SUDEP.</span><span style="color: black; font-family: "arial";"><o:p></o:p></span></li>
<li class="MsoNormal" style="color: black; mso-list: l0 level1 lfo1; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; tab-stops: list .5in;"><span style="background: white; color: black; font-family: "arial";">SUDEP seems to be caused largely by fatal
cessation of breathing.</span><span style="color: black; font-family: "arial";"><o:p></o:p></span></li>
<li class="MsoNormal" style="color: black; mso-list: l0 level1 lfo1; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; tab-stops: list .5in;"><span style="color: black; font-family: "arial";">For a
seizure to cause changes in breathing, it must affect the activity of
neurons in the respiratory areas of the brainstem.<o:p></o:p></span></li>
<li class="MsoNormal" style="color: black; mso-list: l0 level1 lfo1; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; tab-stops: list .5in;"><span style="color: black; font-family: "arial";">The
central amygdala is located in the temporal lobe, where seizures resulting
in SUDEP tend to originate, and directly connects to neurons in the
brainstem that control breathing.<o:p></o:p></span></li>
<li class="MsoNormal" style="color: black; mso-list: l0 level1 lfo1; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; tab-stops: list .5in;"><span style="color: black; font-family: "arial";">Activating
neurons in the central amygdala, both with direct electrical stimulation
and seizure activity, causes people with epilepsy to stop breathing.<o:p></o:p></span></li>
<li class="MsoNormal" style="color: black; mso-list: l0 level1 lfo1; mso-margin-bottom-alt: auto; mso-margin-top-alt: auto; tab-stops: list .5in;"><span style="color: black; font-family: "arial";">We
have a circuit that links information about olfactory hedonic value to
respiratory control but its location is unknown.<o:p></o:p></span></li>
</ol>
<div class="MsoNormal">
<span style="background: white; color: black; font-family: "arial";"><br />
<b>Here's is the kicker</b>: it seems like the central nucleus of the
amygdala is poised to be a key node in this olfactomotor circuit. If this
is true, the reason that people stop breathing during a seizure could be
because the seizure reaches the central nucleus of the amygdala, activating the
olfactomotor circuit, which disrupts nasal breathing. </span><span style="color: black; font-family: "arial";"><br />
<span style="background: white;"><br />
So in an ironic and deeply dark way, it could be the case that the
circuit that protects us from breathing in harmful chemicals
by halting our nasal breathing can be '<b>hijacked</b>' by a seizure,
causing breathing to stop for as long as the seizure persists - <b>potentially
leading to SUDEP</b>. </span><br />
<span style="background: white;"><br />
<b>It's important to point out that these last two statements are theories, not
facts.</b> It would be so awesome if we could prevent SUDEP by
electrically suppressing activity in the central amygdala. Preventing
SUDEP could even be as simple as telling someone who is having a seizure to
just breathe through their mouth. However, when you do science, your ideas are
wrong <i>far</i> more often than they are right. In fact, it's kind
of incredible that we're ever right. Nature is confusing as hell and we're just
this weird, emotional primate species trying to figure it all out. The
best way to test whether a theory is correct is, un-intuitively, to
conduct experiments designed to prove that your theory is <i>wrong</i>. In
other words, my research is all about investigating these ideas but every day
at work my lab mates and I try to prove ourselves wrong.</span><br />
<br />
<span style="background: white;">These days we're running experiments to see if
the central amygdala is <b>not</b> part of the olfactomotor circuit.
Specifically, we're trying to identify what chemosensory properties of
odors activate this circuit, whether activating the central amygdala
actually leads to activation of the brainstem respiratory groups, and how the
trigeminal system (something I haven't even mentioned here) might participate
in these processes as well. If we successfully fail at proving ourselves wrong,
the next steps will be working on treatments for how to use this knowledge to
intervene and hopefully prevent SUDEP altogether.</span></span><br />
<span style="color: black; font-family: "arial";"><br /></span>
<span style="color: black; font-family: "arial";"><br /><span style="background: white; font-size: x-large;">Final Thoughts</span><br />
<span style="background: white;"><br />
I came into grad school almost exclusively interested in brain-computer
interfaces, the benefits of which are incredible and obvious. But three years
in, I find myself in the hospital, wearing a lab coat, politely
asking people undergoing epilepsy surgery to smell a bunch of disgusting odors
for me. It's certainly not what I had expected to be doing but I think that I'm
a lot happier doing this compared to just about anything else. I think these
ideas are fascinating, important, and worth a whole lot of my time to work on,
even if I someday have the misfortune of proving all of them wrong. </span><br />
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...I also really hope that whoever is reading my 64 page grant right now
agrees. </span><br />
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Thanks for reading and I hope that the rest of your day is filled with deep,
healthy sniffs of exclusively pleasant odors.</span><span style="font-size: 10pt;"><o:p></o:p></span></span></div>
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<!--EndFragment--><br />Torbenhttp://www.blogger.com/profile/03586733786614548430noreply@blogger.com44tag:blogger.com,1999:blog-8470140342170795801.post-80236980543320453522017-07-25T11:12:00.001-07:002017-08-01T09:32:18.228-07:00The Creator's Game: Lacrosse and The Brain<div class="separator" style="clear: both; text-align: left;">
<span style="font-family: "arial" , "helvetica" , sans-serif;">I've had a hard time putting my finger on exactly what makes me love lacrosse so much but I think I've figured it out. I love lacrosse because this game is all about the brain. From the outside it looks like manchildren running around hitting each other with sticks...and it is, but <b>to play this game well requires a broad and deep level of cognitive abilities unlike just about every other sport or activity.</b></span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Here I'm going to argue that lacrosse is both intellectual and spiritual. This is something all experienced lacrosse players know to be true, but this idea isn't taken seriously anywhere else. <b>The Iroquois, who invented this game nearly a millennium ago, were getting at something special about human thought.</b> This game and the mental framework it cultivates is something that I use to think about how our brains work almost every day.</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Last weekend I was at the Lake Tahoe Lacrosse Tournament with roughly over a thousand other people who have been playing this game since they were kids but just can't seem to put their sticks down. I'm not aware of any other sport that draws so many people to train and compete after the glory of high school and college is long gone. (But actually, is there any other sport that does this kind of stuff?) Tournaments like this, of which there are dozens, often have masters divisions (for people over 30), some have grandmasters (50+), and one even has a <a href="http://vaillacrosse.com/mens-zenmasters/" target="_blank">zenmasters division for 60 year olds+ (!!!)</a>. I'm convinced that there is something really special about this game and I'm starting to put together why that might be.</span><span style="font-family: "arial" , "helvetica" , sans-serif;"> </span></div>
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<tr><td class="tr-caption" style="font-size: 12.8px;"><span style="font-family: "arial" , "helvetica" , sans-serif;">My Squad</span><br />
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<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: "arial" , "helvetica" , sans-serif;">My squad in 40 years</span></td></tr>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><br /></span><span style="font-family: "arial" , "helvetica" , sans-serif;">I played at a competitive level in college and I think that I know something about how brains work, but unfortunately I am a mere sub-sub-sub-zenmaster at lacrosse and I certainly don't completely understand how our brains work. My experience </span><span style="font-family: "arial" , "helvetica" , sans-serif;">playing lacrosse has facilitated thinking about my own mental processes and other peoples' in new, invaluable ways. This post is going to be half '</span><i style="font-family: arial, helvetica, sans-serif;">my gushing love letter to lacrosse'</i><span style="font-family: "arial" , "helvetica" , sans-serif;"> and half '</span><i style="font-family: arial, helvetica, sans-serif;">all brain scientists must play lacrosse if they want to understand how our brains work'</i><span style="font-family: "arial" , "helvetica" , sans-serif;">. <b>Team sports, and especially lacrosse, aren't taken seriously in academia and most scientists I know didn't really play team sports.</b> I hope that maybe one person who</span><span style="font-family: "arial" , "helvetica" , sans-serif;"> </span><span style="font-family: "arial" , "helvetica" , sans-serif;">reads this and </span><span style="font-family: "arial" , "helvetica" , sans-serif;">becomes a teacher won't roll their eyes when student athletes have to miss class for sports - something I've experienced my share of.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Lacrosse is the Creator's game </span></h3>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Last weekend a teammate told me to read the origin story of lacrosse, something I had never been exposed to in roughly 15 years of playing. When I read it, many of my feelings towards lacrosse fell into place. </span><span style="font-family: "arial" , "helvetica" , sans-serif;">Lacrosse was invented by the Iroquois tribe somewhere around what is now upstate New York and sometime around 1100 AD. Some sources say it was invented to prepare young men for war but the way the Iroquois describe it characterizes lacrosse as <b>something much more spiritual that connects them to their minds, nature, and each other</b>. There's a beautiful origin story of lacrosse </span><span style="font-family: "arial" , "helvetica" , sans-serif;">that you can read <a href="http://iroquoisnationals.org/the-iroquois/the-story-of-lacrosse/" target="_blank">here</a> </span><span style="font-family: "arial" , "helvetica" , sans-serif;">(http://iroquoisnationals.org/the-iroquois/the-story-of-lacrosse/), or you can read my little oversimplification</span><span style="font-family: "arial" , "helvetica" , sans-serif;"> below. </span><span style="font-family: "arial" , "helvetica" , sans-serif;">Also, </span><b style="font-family: arial, helvetica, sans-serif;">what other sport has a mythology?</b><span style="font-family: "arial" , "helvetica" , sans-serif;"> How f**cking cool is that?</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><br />The first legendary game of lacrosse was a competition between the four-legged animals and the winged birds. The Bear, The Deer, and The Turtle were the captains of the four-legged animals. The Bear was strong and could overpower any opponent physically, The Deer was quick and could cover long distances, and The Turtle was strong and could withstand blows from any opponent and still advance the ball forward. The Owl, The </span><span style="font-family: "arial" , "helvetica" , sans-serif;">Eagle</span><span style="font-family: "arial" , "helvetica" , sans-serif;">, and The Hawk, were the captains of the winged birds. The Owl could keep track of the ball, while The Eagle and Hawk were swift and agile. The four-legged animals shunned The Mouse and The Squirrel because they were small but the birds recognized their unique value and added them to their roster. And beautiful, epic, long story short - while the four-legged animals were physically stronger, the birds won the first game of lacrosse with the help of their new teammates by appreciating each other's skills and working together.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="font-family: "arial" , "helvetica" , sans-serif;"><b>Lacrosse was not designed for war and victory, but to</b></span><span style="font-family: "arial" , "helvetica" , sans-serif;"><b> recognize each individual's gifts and for a group to use their skills together to achieve a common goal.</b> In Iroquois mythology </span><span style="font-family: "arial" , "helvetica" , sans-serif;">The Creator made lacrosse so that he could watch all of his children enjoy the game. </span></span><span style="font-family: "arial" , "helvetica" , sans-serif;">I can vouch that it is certainly fun to play and its easy to imagine a Creator proudly watching his children playing with literally the best toy ever made. The Creator also invented lacrosse as</span><span style="font-family: "arial" , "helvetica" , sans-serif;"> a 'medicine game' they could use to heal. I can also attest to the healing aspect to this game but it is hard to explain without experiencing it. Obviously the physical exercise involved in lacrosse is good for you but there is a substantial mental health component to this game. </span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">The four-legged animals represent the physical nature of the game but the winged animals, the more successful team, use a subtle, harmonizing collection of mental skills to succeed. <b>Playing this game well requires one to think critically about his own abilities, develop the understanding that </b></span><span style="font-family: "arial" , "helvetica" , sans-serif;"><b>other players' skills are often different than his, and that we can create beautiful things by combining our unique abilities together. </b></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Other team sports become algorithmic. <b>I'd argue that lacrosse is a much, much higher entropy game than any other team sport.</b> </span><span style="font-family: "arial" , "helvetica" , sans-serif;">Clear strategies, with few degrees of freedom, emerge in basketball, where you pretty much have to be tall and football, where you pretty much have to be a freak athlete ...or a kicker.</span><span style="font-family: "arial" , "helvetica" , sans-serif;"> Soccer is a creative game, but lacrosse is like a parent class or superset of soccer. The fields are the same size and you can kick the ball in both, but lacrosse adds many more elements like tools and more contact which allow much more creativity. </span><span style="font-family: "arial" , "helvetica" , sans-serif;"><b>In lacrosse there are multitudes of viable strategies that different phenotypes of players can use - even Mouse and Squirrel can play</b>.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">In playing such an open ended, creative game, participants have to engage in an always updating process of self reflection as well as evaluation of other players' ideas and strategies. Psychology calls this idea of attributing mental states to others 'theory of mind.' I don't have data to prove this but <b>thinking about how I and others think while solving flurries of novel physical and mental challenges makes me feel like I'm expanding my own cognitive toolbox.</b></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="font-family: "arial" , "helvetica" , sans-serif;">That's all pretty abstract but here's an example. In lacrosse, an ironclad strategy has been to throw the ball with both hands on your stick ...obviously. Conversely, defensive players are taught to force attackers' hands off of their sticks so they can't pass or shoot. This is Mark Matthews. This friggin guy figured out how to do just about everything with only one hand on his stick - which totally changes how defenders have to face him. Also, by having only one hand on his stick he can score goals when his body is <i>behind the goal</i> by using the extra length the one-handed strategy affords him. But by doing this, he has to string his stick in an unorthodox way that limits other aspects of his game and changes how he fits into an offense. Both offensive and defensive players have to adapt their strategies to interact with a player like this. While Matthews found a pretty rare strategy, players constantly create and innovate on this game. Over the course of a game, players learn the habits of their opponents so they have to adapt and create if they want to win. The importance (or salience) of different features of the game </span></span><span style="font-family: "arial" , "helvetica" , sans-serif;">are</span><span style="font-family: "arial" , "helvetica" , sans-serif;"> constantly shuffled </span><span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="font-family: "arial" , "helvetica" , sans-serif;">in the </span></span><span style="font-family: "arial" , "helvetica" , sans-serif;">players'</span><span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="font-family: "arial" , "helvetica" , sans-serif;"> </span></span><span style="font-family: "arial" , "helvetica" , sans-serif;">cognitive landscape. </span><span style="font-family: "arial" , "helvetica" , sans-serif;"> <b>The mind of a good lacrosse player has to actively resonate with the game.</b></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Brain Sciences and Lacrosse - Experience Matters</span></h3>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">I missed a little bit of class in college because of lacrosse commitments, but I'd argue that I was using my brain more than my classmates with that time. I was exercising different cognitive skills that I don't normally get to use in school regurgitating the answers to contrived science exams or writing boilerplate five paragraph essays for english class.<br /><br /><br />In neuroscience, psychology, and cognitive science, we study brains by observing what they do and we try to reverse engineer how it might have worked. In lacrosse you're presented with rich, complex experiences of high-level brain function but in neuroscience we simplify these kinds of complicated mental phenomena and study their components. The difference is that in lacrosse, players have to exercise almost all of their cognitive abilities: sensory decoding and integration, motor coordination, language, tool/body schema interactions, emotional regulation, planning and prediction, awareness of time - I'm having trouble thinking of something our brains can do that <i>isn't</i> a critical component of lacrosse. In a neuroscience experiment, you pretty much have to choose part of just one <i>winged-bird </i>skill to study.</span><span style="font-family: "arial" , "helvetica" , sans-serif;"> </span><span style="font-family: "arial" , "helvetica" , sans-serif;">Not so surprisingly, the foundational work describing how our brains can connect the location where a sound originates from to an eye movement towards that location, was all found by studying juvenile owl brains. Thanks Owl. </span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Thanks Owl</span></div>
<span style="font-family: "arial" , "helvetica" , sans-serif;">see here for more if you have access: https://www.ncbi.nlm.nih.gov/pubmed/12015612</span></td></tr>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="font-family: "arial" , "helvetica" , sans-serif;">When I play lacrosse, I can feel each of these cognitive components churning together in my sensorium. </span><span style="font-family: "arial" , "helvetica" , sans-serif;">I'm using my entire brain at once and learning about it as I engage with the game. My thoughts are on fire and it feels awesome. </span><span style="font-family: "arial" , "helvetica" , sans-serif;">My neurons churn through ATP, carefully modulating circuits that keep my mental representation of everything on the field updated. I use my long-term memory knowledge of the game and modify it with novel aspects of the current context. I have to regulate my emotions towards blatantly incorrect, unjust, and stupid calls from the ref. I'm constantly trying to read my opponent's mind and predict what will happen next in the game, while he knows I'm doing this and is actively trying to trick me. Then I integrate all of this information and more into multitudes of small decisions and actions that impact the game in this giant, complex, recursive, loop that I'm a part of. <b>It's not like I'm not some sort of brainiac, I'm just one of twenty people on the field who also all have brains doing the exact same thing but with each metallization flavored like a different kind of ice cream. A good lacrosse game is like a free-for-all at a Baskin Robbins. </b></span></span></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="font-family: "arial" , "helvetica" , sans-serif;">This presents a catch-22 for me where I can have these rich experiences of combining many mental processes playing lacrosse that I've learned to intuit but I want to understand mechanistically. </span><span style="font-family: "arial" , "helvetica" , sans-serif;">And the only way we know how to study how our brains do such cool shit is to simplify and isolate these complex, interacting systems and study them in artificial laboratory environments. </span>Rigorous, detailed science is necessary to understand the brain but we lose the 'lacrosse-ness' of our cognitive abilities by studying them in pristine experiments in labs with simple circuits of neurons and explain our ideas to each other using diagrams and powerpoint slides. </span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><br />Do you think that a blind person will ever be able to fully comprehend vision even if a scientifically complete explanation of it is available to them? Seriously. I really don't think so. <b>There is something fundamental to the <i>experience</i> of a cognitive phenomenon compared to analyzing data about it.</b> </span><span style="font-family: "arial" , "helvetica" , sans-serif;">Taking this a step further, <b>I'd argue that someone who spends time engaging and pushing their mental faculties at a high level in an evolving, dynamic, natural environment might have a better intuition for studying the system scientifically than someone who only studies it in a lab.</b> I read somewhere that as you learn new words, your mental representations of the concepts they refer to become more detailed and complex. I believe that playing lacrosse might have a similar ability to expand conceptual space.</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;"><br /><br />This is a strong assertion and I don't have evidence to support it besides my obviously biased experience. Focused, </span><span style="font-family: "arial" , "helvetica" , sans-serif;">detailed</span><span style="font-family: "arial" , "helvetica" , sans-serif;"> research into neural circuits is necessary to understand the brain </span><span style="font-family: "arial" , "helvetica" , sans-serif;">but there is something about playing lacrosse or otherwise, fully engaging with other people using their mental skills at their limits - that facilitates gaining deep insights into cognition. </span><span style="font-family: "arial" , "helvetica" , sans-serif;"><b>Each time I play, I learn a little more about each of these processes and whether they worked in the specific situation that I used them.</b> I want other brain scientists to share these experiences and learn from their perspectives.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Lax vs. The Creator's Game</span></h3>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Like every mention of lacrosse, its important to note its place in contemporary culture as a caricature of elite, east coast, overprivileged, private school, white, male culture - which is just such a bizarre contrast to its origins. I'm conflicted because <b>I'm not sure if I would have been exposed to neuroscience otherwise</b>. A significant admissions bump from the lacrosse coach separated me from swaths of applicants and got me into an elite college with a great neuroscience program that I was only starting to get interested in. Lacrosse has pushed me</span><span style="font-family: "arial" , "helvetica" , sans-serif;">, and continues to push me,</span><span style="font-family: "arial" , "helvetica" , sans-serif;"> to think in new ways. It has given me a rich bank of experiences I use to think about how our brains work every day at work</span><span style="font-family: "arial" , "helvetica" , sans-serif;">. </span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Lacrosse culture is strange and sometimes disappointing but I find myself constantly inspired by the incredible things people do with this game. <b>It's definitely easier to be good at lacrosse if you start out as a Bear or a Deer but I see Squirrels outplay them all of the time by engaging their mind - learning, practicing, and understanding their own gifts.</b></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">I hope I get to see this kid out at an open tournament some day. <b>I bet even the zenmasters might even have something to learn from him.</b></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Lacrosse is Both Intellectual and Spiritual</span></h3>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">I guess that the conclusion of this whole thing is that lacrosse is special to me and it is deeply intertwined with my professional work of studying our brains.<b> </b></span><span style="font-family: "arial" , "helvetica" , sans-serif;"><b>I spend most of my time with people who live their lives in their head and forget that it is connected to a body that is optimized to do a lot more than pipette solutions into test tubes and press computer keys.</b> I, and I'm sure most of my lacrosse friends, are met with furrowed brows when we say we're traveling across the country for an extended weekend to play a game </span><span style="font-family: "arial" , "helvetica" , sans-serif;">that </span><span style="font-family: "arial" , "helvetica" , sans-serif;">we're obviously too old for </span><span style="font-family: "arial" , "helvetica" , sans-serif;">with other manchildren</span><span style="font-family: "arial" , "helvetica" , sans-serif;">. They don't understand why this experience is so special. </span><span style="font-family: "arial" , "helvetica" , sans-serif;"><b>The Iroquois discovered a game that is so damn good at pushing our human cognitive abilities that coaches and players constantly find new spaces and edges in this game that break traditions and redefine the game nearly a millennium after it was created.</b></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">He does everything that's hard about using a lacrosse stick except it's also upside-down and backwards and there's this whole other team trying to put him on the ground.</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><b>Not only is lacrosse highly intellectual, it just might just be <i>the most</i> intellectual thing to do.</b> Unlike any singular activity I can think of right now, it requires that one develop, flexibly modify, and rapidly deploy this huge breadth of cognitive functions. </span><span style="font-family: "arial" , "helvetica" , sans-serif;">I want people who study brain sciences to have these kinds of experiences and not just read about them. <b>Using your brain is different than reading about brains.</b> I think I've beat this point into the ground but the last point I want to make is that this game is just as spiritual as it is cognitive. </span><span style="font-family: "arial" , "helvetica" , sans-serif;">I'm a pretty strident atheist and I have difficulty connecting with most religious ideas but learning this game with my teammates has a spiritual component that I can understand. Not to say that this is something magical, <b>lacrosse just sometimes feels like a group meditation more than a game.</b></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><b>I'm happy that I found lacrosse and that it led me to think about the ideas that got me interested in neuroscience. </b></span><span style="font-family: "arial" , "helvetica" , sans-serif;">Lacrosse played an invaluable role in finding my self and I love seeing other players use lacrosse to discover their own abilities and apply them to their lives in a unique way. I don't understand this game the same way that the Iroquois, the zenmasters, and lots of people at my level do. <b>This is the unique but shared perspective I bring to the game, and I think that's what lacrosse all about.</b></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><br /><br /><br /><br /><span style="font-size: xx-small;">Thanks to Evan Xanthos, Derrick Kravitz, Alex Moffit, and everyone at Tahoe for the feedback and ideas!</span></span><br />
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Torbenhttp://www.blogger.com/profile/03586733786614548430noreply@blogger.com0tag:blogger.com,1999:blog-8470140342170795801.post-37053200429479204572017-04-09T21:56:00.003-07:002017-04-18T08:18:12.217-07:00Turning Pictures Into Music<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: center;">
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<span style="white-space: pre-wrap;"><span style="font-family: "arial" , "helvetica" , sans-serif;">Some people use their spring break to go on vacation to New York or publish a science paper. I chose to spend mine making some bullshit on my computer and resurrecting my blog that I haven't posted on in months. </span></span><br />
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<span style="white-space: pre-wrap;"><span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="font-family: "arial" , "helvetica" , sans-serif; vertical-align: baseline;">Anyways I’m back with some more nonsense. And it’s some unusually big-time nonsense. No neuroscience here, not really data science, you won't be inspired.</span><span style="font-family: "arial" , "helvetica" , sans-serif; white-space: pre-wrap;"> T</span><span style="font-family: "arial" , "helvetica" , sans-serif; white-space: pre-wrap;">here is literally no real purpose for this project except that we thought it would be cool. </span></span></span><br />
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</span><span style="font-family: "arial" , "helvetica" , sans-serif; white-space: pre-wrap;"><b>To fully experience this post, you'll need to be able to have sound playing out of your device and be without fear of being judged by those around you. </b></span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif; white-space: pre-wrap;"><b>Also I'm using this weird video format so you'll have to turn up the volume on the sketchy videos.</b></span><br />
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<b style="font-weight: normal;"><img alt="Image result for days since last nonsense" height="312" src="https://lh4.googleusercontent.com/RikpMKLPXDNswTOhuF5SwnTmB-l8jjYAWgLZVuO5Jre8Be7Y0faXCzdLj6D3FcL-kS-t8wCGB6RJqYPzDCc4bTSPzjXbEYGHx20nbuXM2g8otL6KDlK13wHN8kqbB97hCicJKa8D" style="border: none; font-family: arial, helvetica, sans-serif; font-weight: normal; transform: rotate(0rad); white-space: pre-wrap;" width="416" /></b><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="white-space: pre-wrap;">My friend and fellow graduate student, Vivek and I made a little algorithm that turns pictures into songs. For instance, I can give our algorithm a picture like this handsome logo for the Northwestern University Interdepartmental Neuroscience Program:</span></span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><a href="http://1.bp.blogspot.com/-wC_QzlxR7f4/WOsCeYSmSJI/AAAAAAAAAz0/uTkiCavs3_0ZMMs1SJiSzaDiLgwtO1xJwCK4B/s1600/nuin_logo.png" imageanchor="1" style="white-space: pre-wrap;"><img border="0" height="76" src="https://1.bp.blogspot.com/-wC_QzlxR7f4/WOsCeYSmSJI/AAAAAAAAAz0/uTkiCavs3_0ZMMs1SJiSzaDiLgwtO1xJwCK4B/s200/nuin_logo.png" width="200" /></a><span style="white-space: pre-wrap;"> </span></span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="white-space: pre-wrap;">and it'll make a nice little song like this:</span></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="white-space: pre-wrap;">Yup. That's about it. Dozens of hours of work...</span></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="white-space: pre-wrap;">If you're still with me, this post will explain how we came up with this idea, show you some weird youtube videos, provide some examples of what our thing can do, then explain how it works. If all goes as planned, this should all amount to a substantial waste of time for both you and me. I am confident that we can achieve this goal.</span></span><br />
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<span style="background-color: transparent; font-family: "arial" , "helvetica" , sans-serif; font-style: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Inspiration</span><br />
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<span style="background-color: transparent; font-family: "arial" , "helvetica" , sans-serif; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">A few weeks ago I was talking with Vivek about levels of meaning in music. When you listen to a song you can just enjoy the nice sounds but it’s so much cooler when you know something about what’s going on behind the curtain. If you know about music theory, or the artist who wrote the music, or the context that a song was written or performed in, it just makes the experience a little richer. For example, when you learn something like how Dark Side of the Moon synchronizes with The Wizard of Oz, or that Closing Time by Semisonic is not about a bar but about the singer's son’s birth - it just adds this whole new layer of meaning to a song that you already liked. And we thought that was an interesting concept.</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif; text-indent: 36pt; white-space: pre-wrap;">I stumbled onto some really interesting youtube videos that demonstrate this idea of embedding meaning into a song in this totally new and fascinating way. In the following videos, the artists have put visual pictures into their music. </span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif; text-indent: 36pt; white-space: pre-wrap;">This group engineered their music so that when it is played through an oscilloscope it makes pictures that go along with the music (~3:20 is especially cool IMO):</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif; white-space: pre-wrap;">Shrooms by Jerobeam Fenderson</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif; text-indent: 36pt; vertical-align: baseline;"><span style="white-space: pre-wrap;">So what you’re seeing in this video is literally the waveform of what is being played out of your speakers. Most songs would look like indiscernible noise if played through an oscilloscope, but they made this music with the purpose of the actual waveform being interpretable visually. I am kept perpetually amazed by the things that engineers can do. Details here:</span></span><a href="http://www.jerobeamfenderson.net/post/101351329308/how-it-works" style="font-family: Arial, Helvetica, sans-serif; text-decoration-line: none; text-indent: 36pt;"><span style="vertical-align: baseline; white-space: pre-wrap;"> </span><span style="vertical-align: baseline; white-space: pre-wrap;">http://www.jerobeamfenderson.net/post/101351329308/how-it-works</span></a></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif; text-indent: 36pt; vertical-align: baseline; white-space: pre-wrap;">Here’s another one where the artist inserted a picture of his face into the spectrogram of the music. And music has a very loose definition here. I don't find this 'song' to be particularly musical. But the important thing here is that he somehow engineered the song to play a series of tones at the specific amplitudes and frequencies in the middle of the song that made this picture </span><span style="font-family: "arial" , "helvetica" , sans-serif; text-align: center; text-indent: 36pt; white-space: pre-wrap;">(Skip to 5:30 for the face)</span><span style="font-family: "arial" , "helvetica" , sans-serif; text-indent: 36pt; white-space: pre-wrap;">:</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="text-indent: 36pt; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 14.6667px;">Equation by </span>Aphex Twin </span><span style="text-indent: 36pt; vertical-align: baseline; white-space: pre-wrap;"><a href="https://www.youtube.com/watch?v=M9xMuPWAZW8" style="text-decoration: none;"> </a></span></span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif; vertical-align: baseline; white-space: pre-wrap;">Also I just now remembered seeing this super weird piece of sheet music that someone left in the jazz band room in high school:</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">It's kind of the same idea of embedding visual aspects in music. Not super relevant, but whatever. It's neat and worth sharing. Don't yuck my yum.</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">(Info here: http://socks-studio.com/2012/05/19/the-unplayable-score-faeries-aire-and-death-waltz-john-stump/)</span><br />
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<span style="background-color: transparent; font-family: "arial" , "helvetica" , sans-serif; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Then while I was working super hard in lab and not browsing reddit I found this meme where people were making midi files out of pictures. In other words, people will take a simple line image and turn the lines into notes to put into music software like GarageBand, where the horizontal spacing is the timing of the notes and the vertical spacing is the pitch of the notes.</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="text-indent: 36pt; vertical-align: baseline; white-space: pre-wrap;">Drawing pictures with music</span><span style="text-decoration: none; text-indent: 36pt; vertical-align: baseline; white-space: pre-wrap;"><a href="https://www.youtube.com/watch?v=lVybwjl_GI0&t=104s" style="text-decoration: none; text-indent: 36pt;"> </a>- Andrew Huang</span></span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif; text-indent: 36pt; vertical-align: baseline; white-space: pre-wrap;">To do this, the guy in this video printed out the image he wanted, manually traced it by hand into the music production software on his computer and adjusted the notes to make it sound nice. As people who understand a small amount about computers and music theory, Vivek and I thought this was cool but realized that we could do this ~algorithmically~ </span><span style="font-family: "arial" , "helvetica" , sans-serif; font-size: large; font-weight: 700; text-indent: 36pt; white-space: pre-wrap;">because what the world needs right now is an algorithm that saves the precious time of artists who make pictures of unicorns into music. So we chose to bear this great burden. You're welcome world.</span></div>
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<span style="background-color: transparent; font-family: "arial" , "helvetica" , sans-serif; font-style: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Results</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif; text-indent: 36pt; vertical-align: baseline; white-space: pre-wrap;"><br class="Apple-interchange-newline" />We did it. </span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif; text-indent: 36pt; white-space: pre-wrap;">And not only can we process an image into a song, we can tweak features of the image to make it sound a little nicer. For instance, this is what the NUIN logo sounds like if we don't edit it:</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><b style="font-weight: normal;">This sounds pretty bad. But you can improve bad things and make them better, like me at doing grad school. In the image above, we're playing so many notes at a time and there is no organization to the tonal quality so it sounds like shit. It's like pressing random adjacent chunks of keys on a piano erratically over time. But we can fix that. </b></span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;"><b style="font-weight: normal;"><br class="Apple-interchange-newline" />Here's what the NUIN logo sounds like if we shift all of the notes to notes in D# major and play them with a more forgiving instrument:</b></span><br />
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<iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.blogger.com/video.g?token=AD6v5dwK_DLku1sxfEjOaR9SzgyajU_k42Z2PMP-_HNmWoiUz7eACK8kzmVDbjyXZZDOZJtHjkI0JUZlYRECuls6Wg' class='b-hbp-video b-uploaded' frameborder='0'></iframe></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><b style="font-weight: normal;"><span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="font-weight: normal;"><br /></span></span><span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="font-weight: normal;">And we can add chord changes so that for every 16 beats, we switch to a new key in pattern. Dare I say that this sounds almost kind of good?</span></span></b></span><br />
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<iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.blogger.com/video.g?token=AD6v5dwrPK51KPQUR1_Zr51BX4u3v6xR8-HJmlY97NRdcz1XakVDArqeELS3ctWb4j64--YzhNJ-ZSCaM6YX3S_U' class='b-hbp-video b-uploaded' frameborder='0'></iframe></div>
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<span style="background-color: transparent; font-family: "arial" , "helvetica" , sans-serif; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span><span style="background-color: transparent; font-family: "arial" , "helvetica" , sans-serif; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><b>Here are some Examples:</b></span></div>
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<span style="background-color: transparent; font-family: "arial" , "helvetica" , sans-serif; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Lax in C# Major.</span><br />
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<span style="background-color: transparent; font-family: "arial" , "helvetica" , sans-serif; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><a href="http://1.bp.blogspot.com/-0PuG7TVm6fo/WOsAiOab4VI/AAAAAAAAAzQ/0LNGvLbbhacN-oJu3wc0IqMnq7iEq5FHgCK4B/s1600/lax.jpg" imageanchor="1"><img border="0" height="190" src="https://1.bp.blogspot.com/-0PuG7TVm6fo/WOsAiOab4VI/AAAAAAAAAzQ/0LNGvLbbhacN-oJu3wc0IqMnq7iEq5FHgCK4B/s200/lax.jpg" width="200" /></a></span></div>
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<span style="background-color: transparent; font-family: "arial" , "helvetica" , sans-serif; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Doge Blues (I tried running this on a a picture that wasn't a line drawing. It wasn't great at getting the important features in the image but sounds pretty cool.)</span>
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<span style="background-color: transparent; font-family: "arial" , "helvetica" , sans-serif; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><a href="http://3.bp.blogspot.com/--uLHiq4n8ks/WOsKafvAKGI/AAAAAAAAA0M/m0fFaeknBQg0s4xfnEIYIM1Pqo8unDSeQCK4B/s1600/doge.jpeg" imageanchor="1" style="clear: left; font-family: Times; margin-bottom: 1em; margin-right: 1em; white-space: normal;"><span style="color: black;"></span></a></span><br />
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<a href="https://3.bp.blogspot.com/--uLHiq4n8ks/WOsKafvAKGI/AAAAAAAAA0M/m0fFaeknBQg0s4xfnEIYIM1Pqo8unDSeQCK4B/s1600/doge.jpeg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="196" src="https://3.bp.blogspot.com/--uLHiq4n8ks/WOsKafvAKGI/AAAAAAAAA0M/m0fFaeknBQg0s4xfnEIYIM1Pqo8unDSeQCK4B/s200/doge.jpeg" width="200" /></a><iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.blogger.com/video.g?token=AD6v5dwaYzg8ISCKxvzq9_cfbWRu13CZ_ZpnGOGGJ9bqZ7YhGFO_KFTTir1nYc-ajIpgxRnm3xL_brX9po2s2RHjxg' class='b-hbp-video b-uploaded' frameborder='0'></iframe></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif; white-space: pre-wrap;">Northwestern Wildcats Electronic Odyssey.</span><br />
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<a href="https://2.bp.blogspot.com/-Cyk3aHM4EZQ/WOsAXrGGlKI/AAAAAAAAAzI/BtnQJzafQVYm5QYjBTZUpvh8POKHg0TxgCK4B/s1600/northwestern-wildcats.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="105" src="https://2.bp.blogspot.com/-Cyk3aHM4EZQ/WOsAXrGGlKI/AAAAAAAAAzI/BtnQJzafQVYm5QYjBTZUpvh8POKHg0TxgCK4B/s200/northwestern-wildcats.png" width="200" /></a><iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.blogger.com/video.g?token=AD6v5dz7E3NEciOnbtGU9E9StUFUW-TUaJJuuUDPKJXPYRVZHm0gC8N5Jkv5MctrIV_vmMZZRAfcAUsQXbRo-tuw9w' class='b-hbp-video b-uploaded' frameborder='0'></iframe></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Powerhouse of the cell for bass</span><br />
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<a href="https://1.bp.blogspot.com/-aNqM7_w0Xoo/WOsADa6yW-I/AAAAAAAAAzA/HdJ2B2UAj9AQeGRbad5vqHVUzf6O_cCLACK4B/s1600/mitochondria.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="126" src="https://1.bp.blogspot.com/-aNqM7_w0Xoo/WOsADa6yW-I/AAAAAAAAAzA/HdJ2B2UAj9AQeGRbad5vqHVUzf6O_cCLACK4B/s200/mitochondria.jpg" width="200" /></a><iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.blogger.com/video.g?token=AD6v5dw3Vd1J11nJBFfPCnl7zShEsS3QULKHLnaY1Wj5S0IoC4X38rGFZuehBsUPA6fyMhCJBnjVxd4lmu5wzqSuhg' class='b-hbp-video b-uploaded' frameborder='0'></iframe></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif; text-align: center; white-space: pre-wrap;">Poop in C Major for Trumpet Ensemble</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="clear: left; color: black; font-family: "arial" , "helvetica" , sans-serif; margin-bottom: 1em; margin-right: 1em;"><a href="http://2.bp.blogspot.com/-eLnh8KX1Cz8/WOsA-Jn8QGI/AAAAAAAAAzg/kWIU0y97fkcR3sm-atHrt7BkyZ-9IJ-wQCK4B/s1600/poop_emoji.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="100" src="https://2.bp.blogspot.com/-eLnh8KX1Cz8/WOsA-Jn8QGI/AAAAAAAAAzg/kWIU0y97fkcR3sm-atHrt7BkyZ-9IJ-wQCK4B/s200/poop_emoji.jpg" width="200" /></a> </span><iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.blogger.com/video.g?token=AD6v5dzNvdl7GgqGtsqVV6wQmSBNKAxak9raBWM_X5kDALp2RF0IfGqkmwPBthryOiEbLFnovkUKdeWOYsIgxsaIyg' class='b-hbp-video b-uploaded' frameborder='0'></iframe></span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">This:</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.blogger.com/video.g?token=AD6v5dwBbht_zhhnUOZ4Gt2Dom6yJk78gTc0tywU27NLs6_sHQRBKo9B11SBF5EYd42qyZJsXHEBydogRQUoRHz9bw' class='b-hbp-video b-uploaded' frameborder='0'></iframe></span></div>
<span style="font-family: "arial" , "helvetica" , sans-serif;">And this:</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Also this:</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.blogger.com/video.g?token=AD6v5dwtM7D0JxfDGLZ_dIpQjqgXQ9uGejw6SvqE0aT3aBli7RqHLBUmxVKrHfYlqp22sFYwgq4zu0by73ep8j-jiA' class='b-hbp-video b-uploaded' frameborder='0'></iframe></span></div>
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<b style="font-weight: normal;"><span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="font-family: "times";"><span style="font-family: "arial" , "helvetica" , sans-serif;">OK that's enough of that. </span></span></span></b><br />
<b style="font-weight: normal;"><span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="font-family: "times";"><span style="font-family: "arial" , "helvetica" , sans-serif;"><br /></span></span></span></b>
<b style="font-weight: normal;"><span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="font-family: "times";"><span style="font-family: "arial" , "helvetica" , sans-serif;">Let me know if there are any images that you're dying to hear and I will consider making it for you! (or just use cool open source <a href="https://github.com/torbenator/prettysounds" style="text-indent: 48px; white-space: pre-wrap;" target="_blank">algorithm</a><span style="white-space: pre-wrap;"> </span>we made)</span></span></span></b><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="background-color: transparent; font-style: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Methods </span></span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif; white-space: pre-wrap;">(All code was written in Python and can be downloaded from github at </span><span style="font-family: "arial" , "helvetica" , sans-serif; white-space: pre-wrap;">https://github.com/torbenator/prettysounds</span><span style="font-family: "arial" , "helvetica" , sans-serif; white-space: pre-wrap;">)</span></div>
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<span style="background-color: transparent; font-family: "arial" , "helvetica" , sans-serif; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">This project seemed complicated at first but we made it easier by splitting it into just a few discrete, not-too-hard parts: </span><br />
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<span style="background-color: transparent; font-family: "arial" , "helvetica" , sans-serif; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">1) Get the important parts out of an image and turn it into a matrix.</span></div>
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<span style="background-color: transparent; font-family: "arial" , "helvetica" , sans-serif; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">2) Manipulate the matrix to clean up the picture and make the corresponding notes sound nice.</span></div>
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<span style="background-color: transparent; font-family: "arial" , "helvetica" , sans-serif; font-style: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">3) Turn the matrix into a midi file that can be played by a music program.</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="white-space: pre-wrap;">1) </span></span><span style="font-family: "arial" , "helvetica" , sans-serif; white-space: pre-wrap;">It is easy to take an image and turn it into a 3d matrix of RGB values for each pixel using the sk-image library. But you can imagine that if we 'played' an image like this it would sound totally noisy and crazy because there would be values at every pixel that would correspond to notes. We chose to filter the image for any prominent edges that it has and only include these in the matrix. We did this using a Sobel filter. I don't know how it works, but it does work and it works pretty well. This outputs a 2d matrix where edge intensity is coded for by a value between 0 and 1. So faint edges play softer notes, like the second half of the brain in the NUIN logo and the second N in NUIN. Also it had a little trouble with the U for some reason. We also built some parameter tuning functions into our code so that we could threshold which edges to include. I had to play with this a lot to get the doge to work. That was time well spent.</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="vertical-align: baseline; white-space: pre-wrap;">2) </span></span><span style="font-family: "arial" , "helvetica" , sans-serif; white-space: pre-wrap;">The next challenge was to take a matrix and manipulate it such that it maintains the visual picture, but sounds a little bit better. First we built simple functions to resize and pad the x and y dimensions of the image using scipy.signal.resample. In this way we could choose how many beats we wanted the image to play for and the range of notes that would be used to play it. The more interesting methods we made could determine the starting note and the key of the song and these could be called repeatedly to make chord changes. </span><span style="font-family: "arial" , "helvetica" , sans-serif;"> </span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="vertical-align: baseline;"><span style="white-space: pre-wrap;">3) </span></span></span><span style="font-family: "arial" , "helvetica" , sans-serif; white-space: pre-wrap;">Lastly, we found a library that writes notes to MIDI files - a file format that is pretty much a piece of sheet music for an electronic instrument (or soundfont) to play. We could just use this function as we iterated through the picture/music matrix that we made and dump it into a midi file with a function that we wrote.</span><span style="font-family: "arial" , "helvetica" , sans-serif;">
</span><span style="font-family: "arial" , "helvetica" , sans-serif; white-space: pre-wrap;">Then we just dropped the MIDI into GarageBand to play the 'song.' There's probably a fancier way to programmatically make videos of the MIDI being played but whatever. We tried to do this and we started to write some fancier algorithms to change more things about the picture and music but then we realized that we had spent way, way, too much time on this 'project' and it was time to stop.</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="vertical-align: baseline; white-space: pre-wrap;"><br class="Apple-interchange-newline" />All of our code is written in Python and can be found here: </span></span><span style="font-family: "arial" , "helvetica" , sans-serif; white-space: pre-wrap;"><a href="https://github.com/torbenator/prettysounds">https://github.com/torbenator/prettysounds</a></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif; white-space: pre-wrap;"><br /></span><span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="font-weight: normal;"></span></span><span style="font-family: "arial" , "helvetica" , sans-serif; white-space: pre-wrap;">Feel free to use any of it but if you somehow find a way to make money with this then please give us some.</span><br />
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<b>What did we learn?</b>
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<span style="background-color: transparent; font-family: "arial" , "helvetica" , sans-serif; font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Absolutely nothing. But I hope that you had fun and that someone you want to impress didn't see you listening to the song made by the poop emoji.
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<b>Bonus:</b></span><br />
<span style="background-color: transparent; font-family: "arial" , "helvetica" , sans-serif; font-style: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Since I posted this, a few people have pointed out other media that is related:
This is a piece called Pictures at An Exhibition written by </span><span style="font-family: "arial" , "helvetica" , sans-serif; white-space: pre-wrap;">a Russian composer named </span><span style="font-family: "arial" , "helvetica" , sans-serif; white-space: pre-wrap;">Mussorgsky. He wrote this song after being inspired by an art exhibit. There are several movements in this work that each represent a work of art from the exhibit.
(Thanks Sean McWeeny!)</span><br />
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The results of this algorithm have been likened to the work of La Monte Young, who has been called one of the greatest living composers today and who's work called into question the nature and definition of music. (Thanks Claire Chambers)
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Torbenhttp://www.blogger.com/profile/03586733786614548430noreply@blogger.com0tag:blogger.com,1999:blog-8470140342170795801.post-36130499397846020722016-06-03T12:56:00.001-07:002016-06-03T13:00:03.878-07:00Studying Fake Busses With Science!<span style="font-family: "arial" , "helvetica" , sans-serif;">My last post was about my experience at this </span><a href="http://smartcityhackathon.io/" style="font-family: arial, helvetica, sans-serif;" target="_blank">cool hackathon</a><span style="font-family: "arial" , "helvetica" , sans-serif;"> I went to. This post is about what I actually did there. </span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">All of the code that I used is written in Python and is on my github <a href="https://github.com/torbenator/sdsmartcityhackathon" target="_blank">[Here]</a>. I'd like to think it's pretty readable. You can also run all of the code and reproduce all of my figures in Binder without even having to download anything!</span><br />
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<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: "arial" , "helvetica" , sans-serif;">Look its that thing we made</span></td></tr>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">For the hackathon we came up with the idea of using the city's public data to improve bus usage in San Diego. We noticed that certain bus routes were either overused, underused, or had surge times. During commute times in San Diego people actually wait in line for the bus. They get to the bus stop and some of the people don't get to even board the bus when it comes because there are too many people. This phenomenon is whack and presents lots of space for improvement. </span><br />
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<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: "arial" , "helvetica" , sans-serif;">Whack bus line somewhere thats not in San Diego</span></td></tr>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="font-size: x-large;">The Plan</span></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Here's what we set out to do:<br />* Build an app that the city to use to visualize and analyze bus usage data</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">* Identify overused, underused, and surging bus lines.</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">* Explore ways we could partner with rideshare companies to make busses great again (sorry)<br /><br />We learned that the city of San Diego just started started installing infrared sensors on the doors to the bus to count how many people get on and off bus at each stop. This seemed like a great place to start... but we couldn't get our hands on that data over the weekend with 0 hours notice. Crap. </span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Well </span><span style="font-family: "arial" , "helvetica" , sans-serif;">in neuroscience if you want to study something that there is no data for, the best thing you can do is to build a simulation. And by simulation I mean a big 'ol math equation. This math equation will output realistic data by making certain assumptions about the underlying processes that generate it Then you can analyze the simulated data while you tweak the parameters to see what happens. </span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Here's what I decided were the important features of one day in the life of a bus line:</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">1. Number of stops</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">2. Max capacity of the bus</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">3. How many passengers get on at each stop</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">4. The stops where the bus fills up</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">5. Number of surges in the bus line</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">6. When the surges happen</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">This seems like a lot of stuff to stuff into a math equation but it's actually not too bad if we assume bus demand is governed by A: some combination of random noise (riders randomly get on and off stops irrespective of the time) and B: oscillations (rider demand increases and decreases over time). I whipped up a simulation of this [<a href="https://github.com/torbenator/sdsmartcityhackathon/blob/master/Simulating%20and%20characterizing%20bus%20rider%20data%20-%20clean%20demo.ipynb" target="_blank">here</a>] but if that's not your thing then I guess you can just take my word for it.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="font-size: x-large;">Fake Busses</span></span>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Using my algorithm I could create daily bus routes and change different things about them. Here are some examples: (blue line is the number of passengers on the bus at each stop, red dots are where the bus reaches capacity of 40)</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">If I make ridership completely random it looks like this:</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">And if I make ridership completely oscillatory</span><span style="font-family: "arial" , "helvetica" , sans-serif;"> it looks like this:</span></div>
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<a href="https://1.bp.blogspot.com/-o6jE4wWRwYY/V1ElmKLW-rI/AAAAAAAAAlk/iiNwGUMVFkU8OkIZZe_Mwav1hc3IU0lyQCLcB/s1600/bus_two_surge_no_noise.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="120" src="https://1.bp.blogspot.com/-o6jE4wWRwYY/V1ElmKLW-rI/AAAAAAAAAlk/iiNwGUMVFkU8OkIZZe_Mwav1hc3IU0lyQCLcB/s640/bus_two_surge_no_noise.jpg" width="640" /></a></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Both of those look kind of artificial but if I find the happy medium between noise and oscillations it looks a little more realistic.</span><br />
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<a href="https://4.bp.blogspot.com/-ZDgjUBFT1hc/V1Elmo6zxRI/AAAAAAAAAl0/8SDNkiqUkzkCo8cW4ZEg4pNpZrWpL3zeACLcB/s1600/two_surge_noise.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="120" src="https://4.bp.blogspot.com/-ZDgjUBFT1hc/V1Elmo6zxRI/AAAAAAAAAl0/8SDNkiqUkzkCo8cW4ZEg4pNpZrWpL3zeACLcB/s640/two_surge_noise.jpg" width="640" /></a></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">The previous models all have the same number of times that they fill up. I can also change the overall demand without changing the timing of demand. </span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">High demand:</span><br />
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<a href="https://2.bp.blogspot.com/-icGNhfmrVIA/V1Ellze9SOI/AAAAAAAAAlc/E71yRkl9h846Rvggeup73mSmFWu2qIShQCLcB/s1600/high_demand_bus.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="120" src="https://2.bp.blogspot.com/-icGNhfmrVIA/V1Ellze9SOI/AAAAAAAAAlc/E71yRkl9h846Rvggeup73mSmFWu2qIShQCLcB/s640/high_demand_bus.jpg" width="640" /></a></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Low demand:</span><span style="text-align: start;"> </span></div>
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<a href="https://3.bp.blogspot.com/-aZxuQbpWCOg/V1ElmUmlJTI/AAAAAAAAAls/xGElPo4m_rIMAI54pVp853b3nXP1SYU0ACLcB/s1600/low_demand_bus.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="120" src="https://3.bp.blogspot.com/-aZxuQbpWCOg/V1ElmUmlJTI/AAAAAAAAAls/xGElPo4m_rIMAI54pVp853b3nXP1SYU0ACLcB/s640/low_demand_bus.jpg" width="640" /></a></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><br /><br />Cool. Now we have a bunch of fake buses... Why did we do that again? </span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">We made these so that we can use them as templates for figuring out how to analyze them. If we only have the data, and we don't have access to the parameters that generated it, can we infer them? In other words, is there a way that I can give you numbers that characterize the noisiness, 'surginess', and demand of a bus line?</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif; font-size: x-large;">Demand</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Demand is easiest so I'll talk about it first. If we want to know the total passengers who got on a bus in a given day, we just have to find the integral of the number of passengers on the route over time. There is a handy function for that called sum().</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">The more important feature of demand is how many times the bus filled up. If a bus line has lots of demand but doesn't fill up then thats perfect. I want to know when the bus is too full. I did this by set a threshold at the max capacity in for the bus and each time the amount of passengers on the bus reaches that number I record the times. It looks something like this:<br /><br /><a href="http://4.bp.blogspot.com/-svpb7dN7Y2M/V1G8xdzbvPI/AAAAAAAAAmc/kN4dv3A8nCgPfjU7z_aCJAvOd7hVdCYrACK4B/s1600/noisy_vs_surge_bus.jpg" imageanchor="1"><img border="0" height="400" src="https://4.bp.blogspot.com/-svpb7dN7Y2M/V1G8xdzbvPI/AAAAAAAAAmc/kN4dv3A8nCgPfjU7z_aCJAvOd7hVdCYrACK4B/s640/noisy_vs_surge_bus.jpg" width="640" /></a></span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">These are two bus routes that both filled up 20 times but the way they filled up over time is totally different. The blue one filled up randomly, but the red one filled up in bursts. It's obvious to a human which is which but if we had 1000 bus lines that we didn't want to manually comb through, could we write an algorithm that would tell us if a bus line is noisy or surgey automatically?<br /><br /><br /><span style="font-size: x-large;">Noise</span></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Yes we can. Some neuroscientists were faced with a similar problem in analyzing spike times in neurons and figured out you can quantify 'burstiness' using the coefficient of variation of the inter-spike intervals (CV).</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Check it out. If I take a purely surging bus line and iteratively add a little bit of noise, CV tracks this change pretty well - before it gets too noisy.</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;"><a href="http://3.bp.blogspot.com/-5CqkstZQYwI/V1G_Jc7aZ-I/AAAAAAAAAmo/JgvkEKyc36c1ZpCdmFWRqNG8eJSiKve2ACK4B/s1600/cv_analysis.jpg" imageanchor="1"><img border="0" height="400" src="https://3.bp.blogspot.com/-5CqkstZQYwI/V1G_Jc7aZ-I/AAAAAAAAAmo/JgvkEKyc36c1ZpCdmFWRqNG8eJSiKve2ACK4B/s640/cv_analysis.jpg" width="640" /></a></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif; font-size: x-large;">Surges</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Cool. Now we can use CV automatically tell us how noisy and surgey busy bus lines are. But wouldn't it be helpful to know how many surges there are and when they happen? It would, dear reader, and we can do that pretty well using k-means clustering. If you look through my code you'll see that I tried the traditional approach of finding the optimal k using the elbow method but I couldn't get that to work so I made up my own thing. </span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Here's an example of my method identifying the surge times in a bus line:</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;"><a href="http://4.bp.blogspot.com/-HhEcjLtNy0o/V1HNaB1gkXI/AAAAAAAAAng/cHJSrm6tZ6cHpt5cemi1fjRland4i824gCK4B/s1600/kmeans_example.jpg" imageanchor="1"><img border="0" height="320" src="https://4.bp.blogspot.com/-HhEcjLtNy0o/V1HNaB1gkXI/AAAAAAAAAng/cHJSrm6tZ6cHpt5cemi1fjRland4i824gCK4B/s640/kmeans_example.jpg" width="640" /></a></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">It looks like it works but I totally could have lied so here's a little more proof - here's how it does on bus lines with between 1 and 5 surges and 50% noise:</span><br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://2.bp.blogspot.com/-MocwOAz-lT8/V1HNJOmCmHI/AAAAAAAAAnY/IVkIq8oS3fQp3THUr5qDIq0V5BMWu9b0ACK4B/s1600/validating_kmeans.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="320" src="https://2.bp.blogspot.com/-MocwOAz-lT8/V1HNJOmCmHI/AAAAAAAAAnY/IVkIq8oS3fQp3THUr5qDIq0V5BMWu9b0ACK4B/s640/validating_kmeans.png" width="640" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: "arial" , "helvetica" , sans-serif;">Dope</span></td></tr>
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<span style="font-family: "arial" , "helvetica" , sans-serif; font-size: x-large;">Summary, Problems, Caveats, and Future Directions</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Overall I did a pretty good job. I was successfully able to quantify demand, noisiness, and surges in simulated MTS data. By doing this, I could take large amounts of ambiguous 1's and 0's and turned it into actionable information someone can use to understand and hopefully improve the system. </span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">However, there are some important things to acknowledge. First of all, my simulation is definitely still a little artificial. Bus surges are probably not totally sinusoidal and I don't think surges ever happen at 3:30 AM. This feature shouldn't really affect the way I analyzed the data but it makes the simulations seem a little less genuine. Moreover, as the real data comes in, it might turn out that noise/oscillations are not the best way we can describe demand. </span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">CV is also a pretty finicky measure. It is highly sensitive to both the length of time being analyzed and the total number of points where the busses fill up. I didn't think this would happen and I have been using this measure in real science code so I gotta go make sure it really makes sense.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">There are much more sophisticated ways to characterize peaks in the presence of noise, (somebody might even publish an algorithm that does just this for neural oscillations someday). There are also several other machine learning algorithms one could use to analyze bus ridership that I didn't get to</span><span style="font-family: "arial" , "helvetica" , sans-serif;"> for the sake of time. For instance, longitudinal ridership could </span><span style="font-family: "arial" , "helvetica" , sans-serif;">be clustered over weeks and months, and we could do outlier detection for unusual surges. </span><br />
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<a href="http://4.bp.blogspot.com/-OtXUdiWO-GI/V1HN0ohqG7I/AAAAAAAAAno/oK5lxqVMvf8WRW8Kgwn0UzPOpjfCAM6dACK4B/s1600/200_s.gif" imageanchor="1"><img border="0" height="160" src="https://4.bp.blogspot.com/-OtXUdiWO-GI/V1HN0ohqG7I/AAAAAAAAAno/oK5lxqVMvf8WRW8Kgwn0UzPOpjfCAM6dACK4B/s400/200_s.gif" width="400" /></a><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Feel free to mess around the <a href="https://github.com/torbenator/sdsmartcityhackathon/blob/master/Simulating%20and%20characterizing%20bus%20rider%20data%20-%20clean%20demo.ipynb" target="_blank">code</a> and let me know if I made any mistakes!</span>
<span style="font-family: "arial" , "helvetica" , sans-serif;"><br /></span>Torbenhttp://www.blogger.com/profile/03586733786614548430noreply@blogger.com0tag:blogger.com,1999:blog-8470140342170795801.post-83982597112914247982016-05-23T01:01:00.002-07:002016-06-10T09:25:06.811-07:00My First Hackathon<span style="font-family: "arial" , "helvetica" , sans-serif;">I went to my first hackathon, <a href="http://www.smartcityhackathon.io/">The San Diego SmartCity Hackathon</a>, this weekend and it was absolutely incredible. </span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">If you're interested in the actual project I did, click <a href="http://neurosciencebro.blogspot.com/2016/06/studying-fake-busses-with-science.html" target="_blank">here</a> and the code for it is <a href="https://github.com/torbenator/sdsmartcityhackathon" target="_blank">here</a>.<br />This post is more about the actual experience of attending, which I found to be really meaningful.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Here are the takeaways:</span></div>
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<li><span style="font-family: "arial" , "helvetica" , sans-serif;">GO TO A HACKATHON. This entire post will be mostly be a demonstration of why you have got to go to one of these things no matter how technically incompetent you think you are.</span></li>
<li><span style="font-family: "arial" , "helvetica" , sans-serif;">I thought I would be intimidated but the environment was extremely supportive and inclusive</span></li>
<li><span style="font-family: "arial" , "helvetica" , sans-serif;">Wizards are real and they are at hackathons.</span></li>
<li><span style="font-family: "arial" , "helvetica" , sans-serif;">I joined a team, made some friends, and contributed to <a href="http://devpost.com/software/a-data-driven-analysis-of-high-congestion-mts-routes">a project that I'm really proud of</a>.</span></li>
<li><span style="font-family: "arial" , "helvetica" , sans-serif;">We didn't win but it was still super worth it.</span></li>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">I almost didn't go to my first hackathon this weekend.</span></h3>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">On Friday afternoon I remembered that I had registered to go to some "hackaton" thing on campus that evening. The keynote speaker was someone I had heard about and I was hoping there would be free snacks and coffee. I was tired from the week and wanted to just go party but I thought I might as well check it out because I had a ticket. </span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">If you aren't familiar with the term, a "hackathon" is an event where nerds amass to spend a weekend building tech projects together. I had heard legendary stories of people who conceived of an idea </span><span style="font-family: "arial" , "helvetica" , sans-serif;">at a hackathon in San Francisco, </span><span style="font-family: "arial" , "helvetica" , sans-serif;">worked on it all weekend, </span><span style="font-family: "arial" , "helvetica" , sans-serif;">and got hired to work on it full time before Monday. I didn't think this kind of thing was real.</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">I had no intention to participate. I just wanted to consume the coffee, snacks, and free entertainment that I was entitled to. I get to the room where this guy is going to speak and there was free beer and tons of hor d'oeuvres. Nice beer and legit hor d'oeuvres too. Nice. I stood in the corner, stuffed my face, and just kind of observed. The room was full of about 100 people, </span><span style="font-family: "arial" , "helvetica" , sans-serif;">90 dudes, </span><span style="font-family: "arial" , "helvetica" , sans-serif;">125 computers (some desktop boxes that people must have lugged from home), 10 cameras, 20 pieces of technology that I couldn't quite identify, and </span><span style="font-family: "arial" , "helvetica" , sans-serif;">one big virtual reality setup taking up a corner</span><span style="font-family: "arial" , "helvetica" , sans-serif;">. I started chatting with some dude as we were all ushered to the auditorium. </span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">This dude, Rushil, had been to a couple of these</span><span style="font-family: "arial" , "helvetica" , sans-serif;"> things and programs mobile apps for fun. As we walk to the auditorium, some older guy in a suit overhears our conversation about data visualization and starts telling us about his tech company. After a few minutes, he gave us his card and offered us summer internships on the spot. Woah.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Joining the hackathon</span></h3>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">The featured speakers talk for a little bit and it's pretty cool. Then the director of the hackathon invites any teams who want to pick up additional members to present their projects. A couple people get up and talk about what they plan to work on. </span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">The theme of the hackathon is to help San Diego come up with ideas for how to deliver on it's Climate Action Plan. It turns out that California has a shit load of environmental problems, believe it or not. The city just released a ton of infrastructure data to the public and was interested in whether these kinds of data could somehow be used to ameliorate some of the city's environmental problems. It also turns out that people who are highly technically competent like to solve these kinds of problems just for fun on a weekend, basically for free.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">The project presentations begin. They range from, "We're pretty much an early stage startup trying to build a website to gamify environmentalism and looking for anyone who wants to join", to "Wildfires are a problem. Maybe we can use drones or sensors or something?"</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Rushil and I start to talk about what is good and bad about certain ideas. He's all fired up to join a team and win this thing. I'm embarrassingly buzzed from my Stone IPA and entertaining the idea of hovering around a team and checking out what this is all about.<br /><br />After the presentations, we introduce ourselves to the leaders of the groups we're interested in joining. We talk to the drones/something/wildfires guy, whose name is Victor and start talking about how we could work on this. Then we start bouncing other ideas off of each other. We come up with some pretty cool projects but realize we have to think about what kinds of projects we could do with our specific skills.</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">These are our skills:</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Rushil: </span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">* Has completely programmed dozens of mobile apps</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">* Well-versed in business, economics, and tech entrepeneurship</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Victor:</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">* Experienced freelance full-stack web developer who can build literally anything on a computer</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">* Made the website for the event</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">* Is friends with all of the organizers and seems to know the whole SD tech community</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Torben:<br />* Claims to be a "neuroscientist" and "data scientist"</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">* Has no idea what's going on</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">* Still kind of buzzed from one beer<br /><br />Seems like we're all about the same level. Nice.</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Hacking</span></h3>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">So I guess we're a team now and we head into the coding room to work on ideas together. </span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Holy crap. More free stuff. T-shirts, Sandwiches, pizza, high-quality granola bars, Red Bull, soda, and chips. I switch from beer to Red Bull and we start to talk about what to work on. </span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">We try to solve forest fires. Forest fires are complicated and none of us know how to do hardware engineering. Crap. Next we get really excited about making a fitbit for your house. You'll get points for using less energy, water, and waste. Then you can post that shit on Facebook and brag to your friends. Victor and Rushil can build it and I can do stuff with the data. Crap somebody already made that. Ugh. We think about making an online game that would optimize recycling bin locations and joke about how funny it would be if we could trick people into picking up trash off the ground to get points. Suddenly it's</span><span style="font-family: "arial" , "helvetica" , sans-serif;"> 12:30 AM and we have no solid idea. I'm thinking of quitting my new team. </span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Then we think about if there's any way we can use the city's data to improve the bus system and maybe partner public transit with ride-sharing services like Uber or Lyft. I'm not super excited about it but I can't prove to them that it's a dumb idea not worth our time. We head out a little after 1 AM, add each other on Facebook, and message each other til about 2 AM.<br /><br />I wake up to my phone alarm at 7 AM on Saturday. We had planned on meeting at 8 AM.<br />"What am I doing awake right now? Am I really going to go back to this thing? I don't even really know these people, our idea is super fucking dumb, and we came up with it in the middle of the night."</span><span style="font-family: "arial" , "helvetica" , sans-serif;">I somehow convince myself to get up and head back.</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">When I get there, I see people who seem like they had been there all night. There are people programming the crap out of some complicated looking stuff and all we have is a weak idea. Somehow the magic happens and we start to get this project rolling. Rushil and Victor start building the backend of a website we can use to visualize bus usage data. I start modeling bus use data and coming up with analyses we use to characterize it. We absolutely crush work for most of the day, not even stopping for lunch.</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><br />We meet again in the morning and put on some finishing touches. The 'finishing touches' take way longer than we expect. We frantically finish up our project and barely make the deadline - coding until the second the judges arrive to evaluate us. </span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Presenting the project</span></h3>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="font-family: "arial" , "helvetica" , sans-serif;">Our final project kicks ass. It's a dashboard that a city controller can use to visualize bus usage on all of the city's bus routes using the new passenger counter sensors they're adding to busses. We can algorithmically label high-load and surging bus routes (<a href="http://neurosciencebro.blogspot.com/2016/06/studying-fake-busses-with-science.html" target="_blank">post about this</a>, <a href="https://github.com/torbenator/sdsmartcityhackathon" target="_blank">code I wrote to do this</a>). We have economic value models explaining how a partnership with Lyft could help with bus use surges to make public transit more reliable. The app looks nice.</span></span></div>
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The first judge comes over. Rushil gives the elevator pitch. Victor shows off his web platform. I begin to speak on the caveats of modeling surges in bus demand at length. I'm cut off quickly. I didn't even get to brag about clever math I used because we only have 4 minutes total to present. This is not a science conference.<br /><br />Our pitch becomes better with each judge and by the end we sound pretty darn smart.<br /><br />While the judges deliberate, I look at a couple of the projects and they're unreal. I was completely in awe of what these people could make in a weekend. One group was using sensors to optimize water efficiency when watering plants with hydroponics. One group had the idea of displaying the city's water supply on the treasury building using LED's so the building would look like a giant, kind of empty, cup of water.</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><br />The finalists were announced. Unfortunately, we were not chosen but the ones that were chosen were pretty awesome. Remember when I said we were joking on Friday night about making a game out of throwing trash away? The group with the virtual reality setup made a game where you throw objects either into the trash or recycling in virtual reality. They got picked. It actually looked pretty rad. Damn it. One group built a low-cost sensor that could be put in forests to detect forest fires and instantly communicate with the fire department. These sensors could also be repurposed to help 911 identify your location when you call far from a cell tower. They were not even finalists. </span><span style="font-family: "arial" , "helvetica" , sans-serif;">One group received</span><span style="font-family: "arial" , "helvetica" , sans-serif;"> an honorable mention</span><span style="font-family: "arial" , "helvetica" , sans-serif;"> and was publicly offered a job with the city.</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">We didn't move on to the next round, but we received a lot of positive feedback about our project and we talked to a few people about what our next steps could be. We'll see what happens.</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Go to a hackathon</span></h3>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Before I got there I was worried that I would be laughed out of the room for not knowing anything about tech. I was accepted with open arms and I found that I had a niche set of skills that were necessary to make our project work. Not many engineers have the skills that scientists do! Moreover, many projects were in dire need of non-techy skilled individuals like design specialists and people who could come up with projects and keep them on track.</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Every person there seemed to be genuinely interested in helping other people out. Staff members and participants were frequently helping out with each other's projects. I heard the following conversation dozens of times: "Oh you're trying to do <i>this</i>? I know all about <i>this</i>. You should use <i>that</i>! Here's how you do it...(technical jargon for 5 minutes to half-an-hour)"</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><br /></span><span style="font-family: "arial" , "helvetica" , sans-serif;">This was one of the best events I've ever been to. </span><span style="font-family: "arial" , "helvetica" , sans-serif;">The breadth and diversity of technical knowledge at this small room could rival the entire Annual Society for Neuroscience Conference. </span><span style="font-family: "arial" , "helvetica" , sans-serif;">The encouraging, friendly, and positive atmosphere could probably outdo most music festivals. I found myself in a group with two new friends and we built something in a day that I couldn't have done in a year on my own. </span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">I got a whole lot more out of this experience than the snacks, coffee, and lecture that I came for.</span><span style="font-family: "arial" , "helvetica" , sans-serif;"><br /></span></div>
Torbenhttp://www.blogger.com/profile/03586733786614548430noreply@blogger.com1tag:blogger.com,1999:blog-8470140342170795801.post-61839160921128841592016-03-11T15:08:00.001-08:002016-03-16T12:47:59.212-07:00Trying Electrophysiological Analyses on Stock Market Data<span style="font-family: "arial" , "helvetica" , sans-serif;">In this post I'm going to analyze data from the stock market using some of the techniques that I typically use to understand brain data. I can't think of a very good reason for why this makes sense or why it should work... but I'm going to do it anyways and you can't tell me what to do.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">What you get when you google "crazy stock market people"</span></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">A lot of the neuroscience analyses that I do involve analyzing how a signal changes over time. Specifically I look at what voltage does inside or next to brains. Basically, I investigate how different parts of the brain interact with each other based on how their local voltages change over time</span><span style="font-family: "arial" , "helvetica" , sans-serif;">.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">This lead me of think of how different stocks in the stock market might interact. Like voltage recordings in a brain, stock prices move up and down over time and they are spread out over a wide range of industries in the economy. It also seems pretty likely that they might interact with each other in interesting ways that I might be able to characterize using certain analyses. Let's see if I can do that.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Like always, my code for these analyses is on my github here: </span><span style="font-family: "arial" , "helvetica" , sans-serif;">https://github.com/torbenator/ephys-for-stocks</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif; font-size: large;"><b>Getting historical stock market data:</b></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">I found this helpful website for how to algorithmically download historical stock market data here:</span><span style="font-family: "arial" , "helvetica" , sans-serif;"> http://www.quantshare.com/sa-43-10-ways-to-download-historical-stock-quotes-data-for-free</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">Unfortunately, I couldn't get any of the techniques that they described to work except for one, so that was nice.</span><br />
<span style="font-size: large;"><span style="font-family: "arial" , "helvetica" , sans-serif;"><br /></span><span style="font-family: "arial" , "helvetica" , sans-serif;"><b>First problem: What data do I analyze?</b></span></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">There are lots of stocks and I don't know anything about stocks. But I saw a commercial for this thing called sector spiders </span><span style="font-family: "arial" , "helvetica" , sans-serif;">http://www.sectorspdr.com/sectorspdr/ </span><span style="font-family: "arial" , "helvetica" , sans-serif;">when I was watching lacrosse once. From what I understand, this company organizes stocks into categories as a way of diversifying your portfolio. This seems like a reasonable way to split the data into a stock market version of "functional networks". I picked 5 random stocks from each category as a small sample to analyze. I could have picked more but I got tired of googling their tickers and wanted to get going. Of the 50 I tried to download I got 41. Certain stocks had different names in the past year and made my parsing method fail. Also I could only download 1 year of data using my scraping method. Such is data science.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">It's time for a picture. Here's what the data looks like:</span><br />
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<a href="https://1.bp.blogspot.com/-mzmgjhbKLU4/VuNHnGOulmI/AAAAAAAAAh8/oAobR1j5XO82xO6reZKhw-eJKTZGFLzTg/s1600/Screen%2BShot%2B2016-03-11%2Bat%2B2.32.30%2BPM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="color: black;"><img border="0" height="260" src="https://1.bp.blogspot.com/-mzmgjhbKLU4/VuNHnGOulmI/AAAAAAAAAh8/oAobR1j5XO82xO6reZKhw-eJKTZGFLzTg/s640/Screen%2BShot%2B2016-03-11%2Bat%2B2.32.30%2BPM.png" width="640" /></span></a></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif; font-size: large;"><b>First Analysis: How do stocks correlate with each other? </b></span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">i.e. when one stock moves up, does another one reliably move down?</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">If we correlate all the data we get this:</span><br />
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<a href="https://3.bp.blogspot.com/-rTmIdlUtCs8/VuMX6eiP5XI/AAAAAAAAAgQ/RQE2wzRtcbsxNMtZ-3N21R6LtmJ23TzKw/s1600/Screen%2BShot%2B2016-03-11%2Bat%2B11.08.49%2BAM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="color: black;"><img border="0" height="564" src="https://3.bp.blogspot.com/-rTmIdlUtCs8/VuMX6eiP5XI/AAAAAAAAAgQ/RQE2wzRtcbsxNMtZ-3N21R6LtmJ23TzKw/s640/Screen%2BShot%2B2016-03-11%2Bat%2B11.08.49%2BAM.png" width="640" /></span></a></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">From this visualization I can see that most stocks correlate positively with each other. This means that most stocks tend to move together - when one goes up, the other goes up as well. But, for some reason, some stocks seem to have really negative correlations across the board.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="font-family: "arial" , "helvetica" , sans-serif;"><span style="text-align: center;">Here's another (better) way of visualizing the same data but squeezing the y-axis down:</span><br />Side-note for python users: There are some ridiculous colors built into matplotlib (</span>http://stackoverflow.com/questions/22408237/named-colors-in-matplotlib)<br />Colors I used in this plot included 'lemonchiffon','peachpuff', and 'papayawhip'.</span><br />
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<a href="https://1.bp.blogspot.com/-kwSPlEjgp0U/VuMbgsrzRoI/AAAAAAAAAgc/iJBVOoS_uVUhpvq2KA6oXKh7MSxP3SbSA/s1600/Screen%2BShot%2B2016-03-11%2Bat%2B11.24.19%2BAM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="color: black;"><img border="0" height="472" src="https://1.bp.blogspot.com/-kwSPlEjgp0U/VuMbgsrzRoI/AAAAAAAAAgc/iJBVOoS_uVUhpvq2KA6oXKh7MSxP3SbSA/s640/Screen%2BShot%2B2016-03-11%2Bat%2B11.24.19%2BAM.png" style="cursor: move;" width="640" /></span></a></div>
<span style="font-family: "arial" , "helvetica" , sans-serif;">When I sort the stocks by their mean correlation with all other stocks, I can find the stocks that have the highest correlation with all other stocks.</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">The five stocks with the highest mean correlations are (in order):</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Dentsply, Republic Services, Facebook, Nasdaq, and Northrup Grumman</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Because they correlate the highest with all other stocks in my sample, it means that they are the best indicators of general stock market activity. In other words, these stocks are the best at speaking for the general trend in the sample. Something like Nasdac makes sense here because its a reflection of a huge chunk of the economy but who would have thought that Dentsply, <i>a dental prosthetics company,</i> would be the best indicator of market activity in this sample?</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;"><br />Conversely - what's up with those stocks that correlate negatively with everything?</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">The five stocks with the lowest mean correlations are (in order):</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Nisource, Exxon, Newmont Mining, Cigna, and Phillips 66</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">I remember my finance friends telling me that gas prices were generally indicative of a growing economy; when people buy more gas it means they're building, manufacturing, and traveling. But this analysis shows exactly the opposite. When stock in gas companies goes <i>up</i>, values of most other stocks go <i>down</i>. Weird!</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">Perhaps this is due to my tiny sample size of stocks and extremely short time window. I bet with more data this would get cleaned up. </span><span style="font-family: "arial" , "helvetica" , sans-serif;">Moving on.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif; font-size: large;"><b>Next question: What are the relationships between stocks within categories?</b></span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">i.e. are technology stocks all highly correlated with each other while materials stocks aren't?</span><br />
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<a href="https://3.bp.blogspot.com/-2HbWgzphPxQ/VuMdZPuR7kI/AAAAAAAAAgo/6foVZUa3GJYx7AXnfjZA41IWMf2ECjc_Q/s1600/Screen%2BShot%2B2016-03-11%2Bat%2B11.31.37%2BAM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="color: black;"><img border="0" height="449" src="https://3.bp.blogspot.com/-2HbWgzphPxQ/VuMdZPuR7kI/AAAAAAAAAgo/6foVZUa3GJYx7AXnfjZA41IWMf2ECjc_Q/s640/Screen%2BShot%2B2016-03-11%2Bat%2B11.31.37%2BAM.png" width="640" /></span></a></div>
<span style="font-family: "arial" , "helvetica" , sans-serif;"><br /></span><span style="font-family: "arial" , "helvetica" , sans-serif;">This figure is pretty similar to the last one but you'll notice that the correlations are generally higher.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Utilities, Financial Services and Energy were by far the least consistent, while Technology, Consumer Discretionary, and Real Estate were the most consistent. Nothing too crazy here but I guess it's pretty neat.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><b><span style="font-size: large;">Now onto some </span><span style="font-size: x-large;">~fancier~</span><span style="font-size: large;"> analyses:</span></b></span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><b>What does the power spectrum of stock data look like?</b></span></span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">Spectral analyses are things that nerds use to understand periodic signals. And they're fucking rad. If you want a brief explanation of spectral analyses, go here: </span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">https://github.com/voytekresearch/tutorials/blob/master/Power%20Spectral%20Density%20and%20Sampling%20Tutorial.ipynb</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">This section might not make much sense if you aren't familiar with frequency domains.</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;"><br /></span><span style="font-family: "arial" , "helvetica" , sans-serif;">The power spectra of one year of all my stock data look like this:</span><br />
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<a href="https://2.bp.blogspot.com/-IIOwqGeL_DQ/VuMiHQDli_I/AAAAAAAAAhE/ErJ2omDFh90GIwlBq7MMafsQ4AS0WTYPw/s1600/Screen%2BShot%2B2016-03-11%2Bat%2B11.52.41%2BAM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="color: black;"><img border="0" height="520" src="https://2.bp.blogspot.com/-IIOwqGeL_DQ/VuMiHQDli_I/AAAAAAAAAhE/ErJ2omDFh90GIwlBq7MMafsQ4AS0WTYPw/s640/Screen%2BShot%2B2016-03-11%2Bat%2B11.52.41%2BAM.png" width="640" /></span></a></div>
<span style="font-family: "arial" , "helvetica" , sans-serif;">Power in the signal is distributed towards the low frequency oscillations and has a 1/f slope. (Look up 1/f slopes if you don't know what those are. They are <i>very</i> cool). However there is also a spike at the high end. This means that all of the stocks in my sample generally change over large time windows, but day to day fluctuations are also very important. The fact that these peaks are on either end of my frequency domain means that there is lots of information at scales that I don't have access to. Clearly a lot goes on within each day to influence a stock's value but all of that information gets clumped into the tail here. Likewise, fluctuations of a stock's value over a multi-decade window would provide better estimates of power at larger time windows.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Personally, I can conceptualize this observation better with the following figure where I (unorthodoxly for neuroscience) flipped the x axis. To me this makes these time windows a little more intuitive.</span><br />
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<a href="https://2.bp.blogspot.com/-0PCSFu75CRg/VuMiHa2dnqI/AAAAAAAAAhI/jbGLxlJVTSw6Se690ow9GyilvrZ_hGQHg/s1600/Screen%2BShot%2B2016-03-11%2Bat%2B11.52.45%2BAM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="color: black;"><img border="0" height="608" src="https://2.bp.blogspot.com/-0PCSFu75CRg/VuMiHa2dnqI/AAAAAAAAAhI/jbGLxlJVTSw6Se690ow9GyilvrZ_hGQHg/s640/Screen%2BShot%2B2016-03-11%2Bat%2B11.52.45%2BAM.png" width="640" /></span></a></div>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">After looking at the spectra of all of the data, its clear that there is a lot of variation in the 1/f slope of the data. Some stocks are flatter and some are steeper. This has real meaning because it tells us how much of a stocks change in value occurs over different ranges of time. Steeper slopes indicate that a stock is a more stable investment but flatter slopes indicate that it is more volatile. I happen to have worked on an algorithm that automatically calculates 1/f slope in these kinds of data in neuroscience so I ran it on this because I guess that's the point of this post.</span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif; font-size: large;"><b>Exponents of 1/f slopes in stock data </b></span><br />
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<a href="https://2.bp.blogspot.com/-oRQFpeKbLrs/VuMmReI-hBI/AAAAAAAAAhY/-BtmAKzeh3cS2PItEGFwRw9yKfQqxvwKw/s1600/Screen%2BShot%2B2016-03-11%2Bat%2B12.10.14%2BPM.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><span style="color: black;"><img border="0" height="183" src="https://2.bp.blogspot.com/-oRQFpeKbLrs/VuMmReI-hBI/AAAAAAAAAhY/-BtmAKzeh3cS2PItEGFwRw9yKfQqxvwKw/s640/Screen%2BShot%2B2016-03-11%2Bat%2B12.10.14%2BPM.png" width="640" /></span></a></div>
<span style="font-family: "arial" , "helvetica" , sans-serif;">Here we can clearly see that stocks have a wide range of slopes. Furthermore, there seem to be trends within certain stock categories. Consumer Discretionary stocks tend towards steeper slopes, indicating stability, while Utility stocks seem to have flatter slopes, indicating volatility.</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;"><b>Phase amplitude coupling in the stock market</b></span></span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">Phase amplitude coupling is an analysis you can do on electrophysiological data to see how oscillations of different frequencies interact. </span><span style="font-family: "arial" , "helvetica" , sans-serif;">Specifically, you can see how the phase of a slow oscillation</span><span style="font-family: "arial" , "helvetica" , sans-serif;"> influences the amplitude of a fast oscillation. </span><span style="font-family: "arial" , "helvetica" , sans-serif;">(see https://github.com/voytekresearch/tutorials/blob/master/Phase%20Amplitude%20Coupling%20Tutorial.ipynb) </span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">We have pretty good reasons to believe why this makes sense to study in brains. I have no idea why this should make any sense for stock market data but it makes pretty-looking figures. Here is the mean comodulogram (calculating phase amplitude coupling for many phases and amplitudes) of all of the stocks:</span><br />
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<a href="https://3.bp.blogspot.com/-LooQZuWUtNM/VuMrEabme6I/AAAAAAAAAhs/J5lYa42J2nArkk4HEgpDMoX6kHFTFG7wQ/s1600/Screen%2BShot%2B2016-03-11%2Bat%2B12.30.42%2BPM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="color: black;"><img border="0" height="550" src="https://3.bp.blogspot.com/-LooQZuWUtNM/VuMrEabme6I/AAAAAAAAAhs/J5lYa42J2nArkk4HEgpDMoX6kHFTFG7wQ/s640/Screen%2BShot%2B2016-03-11%2Bat%2B12.30.42%2BPM.png" width="640" /></span></a></div>
<span style="font-family: "arial" , "helvetica" , sans-serif;">Interestingly, there seems to be a some phase amplitude coupling in the stock market! The amplitude of 2-3 month oscillations interacts really strongly with the phase of three-quarter year oscillations. I have no intention for why this would happen in reality. This probably happened because I duplicated </span><span style="font-family: "arial" , "helvetica" , sans-serif;">(and left-right flipped) </span><span style="font-family: "arial" , "helvetica" , sans-serif;">the data in order to have enough samples to run this analysis. I don't believe this graph but I think it looks pretty cool.</span><br />
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<b style="font-family: arial, helvetica, sans-serif;">Conclusions and Future Directions</b></span><br />
<span style="font-family: "arial" , "helvetica" , sans-serif;">Do not take anything I did here seriously. Please. I do not claim to be a digital signal processing, financial, or even neuroscience expert. I ran a handful of hacky analyses on an extremely limited amount of data. This was mostly a proof of concept to see if I could find anything at all. That being said, </span><span style="font-family: "arial" , "helvetica" , sans-serif;">there's something here and these analyses could be helpful jumping-off points. One year of data of only 41 stocks simply isn't enough to characterize much but it's clear that we can use neuroscience inspired analyses to identify:</span><br />
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<li><span style="font-family: "arial" , "helvetica" , sans-serif;">Stocks that are markers or outliers of general market or category activity </span></li>
<li><span style="font-family: "arial" , "helvetica" , sans-serif;">Consistency among stocks within and between categories</span></li>
<li><span style="font-family: "arial" , "helvetica" , sans-serif;">The stability of a stock's value over time using spectral analyses</span></li>
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<span style="font-family: "arial" , "helvetica" , sans-serif;">I am interested in pursuing this a little further. Does anyone know how to get more historical stock data without paying? Does anyone reading this know anything about finance and would you be willing to educate me on how to improve the nonsense that I ran here?</span><br />
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<span style="font-family: "arial" , "helvetica" , sans-serif;">Again all data and scripts that I used to run this analysis are on my github here: https://github.com/torbenator/ephys-for-stocks</span>Torbenhttp://www.blogger.com/profile/03586733786614548430noreply@blogger.com1tag:blogger.com,1999:blog-8470140342170795801.post-21946968815523814712016-01-05T10:56:00.002-08:002016-01-05T15:08:50.365-08:00Self-Consistent and Coexisting Spatial Scales in Spongebob Squarepants<span style="font-family: Arial, Helvetica, sans-serif;">Sometimes things initially don't make sense but upon closer investigation, they actually do make sense. </span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><br />This is the case with Spongebob Squarepants. If you this does not interest you, it would be best if you stopped reading <u>now</u>. I warned you.</span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;">For those of you who don't know, Spongebob Squarepants is a cartoon about a kitchen sponge and his wacky undersea adventures. He lives in a pineapple and works for a crab at a fast food restaurant in a treasure chest and does all sorts of other stuff too. Because its a cartoon for children, those kind of creative liberties are allowed. However, there is one critical aspect of Spongebob's universe that I found to be deeply unsettling. </span><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
<span style="font-family: Arial, Helvetica, sans-serif;">How can all of Spongebob's friends hang out when their sizes range over orders of magnitude? Pearl the whale is friends with Plankton the plankton and spongebob the sponge but most whales are at least 8 meters long, many plankton are about 20 micrometers, and kitchen sponges range from about 5-7 inches in length. How can this be?</span><br />
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<a href="http://2.bp.blogspot.com/-TpAFB4xloW8/VonenMxSUtI/AAAAAAAAAak/AkjlSFS4d30/s1600/Slide1.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="font-family: Arial, Helvetica, sans-serif;"><img border="0" height="480" src="http://2.bp.blogspot.com/-TpAFB4xloW8/VonenMxSUtI/AAAAAAAAAak/AkjlSFS4d30/s640/Slide1.jpg" width="640" /></span></a></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Unacceptable.</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">After rigorous investigation of this seemingly inexplicable phenomenon, I have deduced that the Spongebob Squarepants universe exists on three self-consistent and coexisting spatial scales. </span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;">There are three classes of articles in the herein purported multi-scalar meta-space where Spongebob takes place: characters, buildings, and non-building objects (NBO's). </span><span style="font-family: Arial, Helvetica, sans-serif;">Each undergoes a different transformation from real space (R) to spongebob space (SS). </span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><br />Characters are the most interesting class. When you look at the sizes of the characters in R, it looks like this: </span><br />
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<a href="http://3.bp.blogspot.com/-1Q6zd7-NpFA/Votrnza-B5I/AAAAAAAAAbw/zPmLl2cqu5w/s1600/spongebob_realspace.tif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="236" src="http://3.bp.blogspot.com/-1Q6zd7-NpFA/Votrnza-B5I/AAAAAAAAAbw/zPmLl2cqu5w/s640/spongebob_realspace.tif" width="640" /></a></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">But when those same characters in SS, their sizes look like this: </span><br />
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<a href="http://4.bp.blogspot.com/-0TXAeDTTKiY/VotsUMb9KJI/AAAAAAAAAb4/GeNYVNZFVbs/s1600/spongebob_spongespace.tif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="242" src="http://4.bp.blogspot.com/-0TXAeDTTKiY/VotsUMb9KJI/AAAAAAAAAb4/GeNYVNZFVbs/s640/spongebob_spongespace.tif" width="640" /></a></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span><span style="font-family: Arial, Helvetica, sans-serif;">Is there a mathematical function that we can use to transform a real-space object into spongebob space? Let's find out.</span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;">Here's what we start with:</span><br />
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<a href="http://2.bp.blogspot.com/-P1N4jHytols/VotvKBC_tCI/AAAAAAAAAcc/jrQWflkJX1w/s1600/real_vs_sb_raw.tif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="480" src="http://2.bp.blogspot.com/-P1N4jHytols/VotvKBC_tCI/AAAAAAAAAcc/jrQWflkJX1w/s640/real_vs_sb_raw.tif" width="640" /></a></div>
<span style="font-family: Arial, Helvetica, sans-serif;"><br /><br /><br />We want to know exactly what to do to the size of each real object to make it the size that it should be in spongebob space. This means if we perform the correct operation on the size of an object in R and plot against the size of that object in SS, it should be completely linear.</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">Let's find the function that would achieve that goal.<br /><br />Because those numbers vary so much in size, lets see what would happen if we take the log of the size of real objects:</span><a href="http://4.bp.blogspot.com/-hQ-lnjyoobw/VotvDcHP2mI/AAAAAAAAAcE/WqmhhZYjKDk/s1600/log_spongebob.tif" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" height="480" src="http://4.bp.blogspot.com/-hQ-lnjyoobw/VotvDcHP2mI/AAAAAAAAAcE/WqmhhZYjKDk/s640/log_spongebob.tif" width="640" /></a><span style="font-family: Arial, Helvetica, sans-serif;"><br />Better. It looks like spongebob characters exist in a log-normalized version of real space! Cool. Now if we fit a linear equation to the log-normalized data we get this:</span><br />
<a href="http://1.bp.blogspot.com/-0z3VQnnxAJg/VotvJJY8-0I/AAAAAAAAAcU/h7wSyY8OThY/s1600/log_spongebob2.tif" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" height="596" src="http://1.bp.blogspot.com/-0z3VQnnxAJg/VotvJJY8-0I/AAAAAAAAAcU/h7wSyY8OThY/s640/log_spongebob2.tif" width="640" /></a><span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">We could also use a higher order polynomial to fit the data a little more accurately like this:</span><br />
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<a href="http://4.bp.blogspot.com/-PRtOu93p950/Votx1gHBsbI/AAAAAAAAAco/XDBUr91_z48/s1600/log_spongebob_overfit1.tif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="596" src="http://4.bp.blogspot.com/-PRtOu93p950/Votx1gHBsbI/AAAAAAAAAco/XDBUr91_z48/s640/log_spongebob_overfit1.tif" width="640" /></a></div>
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<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span><span style="font-family: Arial, Helvetica, sans-serif;">I prefer the linear fit because while it isn't the most accurate, it has a consistent upward trend unlike the cubic fit. By applying the linear transformation to the log normalized data we make the residuals pretty small:</span><br />
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<a href="http://2.bp.blogspot.com/-0XS22dPO6hc/VotvGXCwQGI/AAAAAAAAAcM/p2Qzei0VPRY/s1600/accuracy_equation_fit.tif" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" height="512" src="http://2.bp.blogspot.com/-0XS22dPO6hc/VotvGXCwQGI/AAAAAAAAAcM/p2Qzei0VPRY/s640/accuracy_equation_fit.tif" width="640" /></a><br />
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<span style="font-family: Arial, Helvetica, sans-serif;">Hooray! A pretty good function for transforming an object from R into SS is:</span></div>
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<a href="http://3.bp.blogspot.com/-L67Yx3iDrZY/VowLhZmcvFI/AAAAAAAAAc4/7AyZLDsd-1c/s1600/Screen%2BShot%2B2016-01-05%2Bat%2B10.29.11%2BAM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="71" src="http://3.bp.blogspot.com/-L67Yx3iDrZY/VowLhZmcvFI/AAAAAAAAAc4/7AyZLDsd-1c/s200/Screen%2BShot%2B2016-01-05%2Bat%2B10.29.11%2BAM.png" width="200" /></a></div>
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span> <span style="font-family: Arial, Helvetica, sans-serif;"><br />With this helpful function, we can take any everyday object and approximate how big it would be in Spongebob assuming it follows the same rules as the other characters.</span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;">The best fit of the equations that transform buildings and non-building objects from R into SS are probably two linear functions. Some objects undergo one linear transformation to become buildings (Pineapple, Krusty Krab treasure chest etc.), while other objects undergo a different transformation to become non-building objects (Spongebob's pants, Squidward's clarinet, etc.) Maybe I'll figure out those at some point but at this point I've definitely wasted enough time on this 'project'.</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span><span style="font-family: Arial, Helvetica, sans-serif;">I guess the only important thing that we learned here is that initially Spongebob space appears to be nonsensical and random but it is actually quite principled and logical! I definitely didn't cherry pick the characters that I used or the sizes that I assigned them. </span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;">All done. Spongebob is completely reasonable. Problem solved. </span></div>
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<a href="http://4.bp.blogspot.com/-xoiBSBfGI2M/Voonb1v5LlI/AAAAAAAAAbU/ge2qwPXSWfc/s1600/Screen%2BShot%2B2015-12-29%2Bat%2B8.29.41%2BPM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="244" src="http://4.bp.blogspot.com/-xoiBSBfGI2M/Voonb1v5LlI/AAAAAAAAAbU/ge2qwPXSWfc/s320/Screen%2BShot%2B2015-12-29%2Bat%2B8.29.41%2BPM.png" width="320" /></a></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">Sources:</span></div>
<table border="1" cellpadding="0" cellspacing="0" dir="ltr" style="border-collapse: collapse; border: 1px solid #ccc; font-family: arial,sans,sans-serif; font-size: 13px; table-layout: fixed;"><colgroup><col width="100"></col><col width="100"></col><col width="100"></col><col width="100"></col><col width="100"></col></colgroup><tbody>
<tr style="height: 21px;"><td data-sheets-value="[null,2,"Species"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; vertical-align: bottom; white-space: nowrap;">Species</td><td data-sheets-value="[null,2,"Size (cm)"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; vertical-align: bottom; white-space: nowrap;">Size (cm)</td><td data-sheets-value="[null,2,"Source"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; vertical-align: bottom; white-space: nowrap;">Source</td><td data-sheets-value="[null,2,"Size (su)"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; vertical-align: bottom; white-space: nowrap;">Size (su)</td><td data-sheets-value="[null,2,"Source"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; vertical-align: bottom; white-space: nowrap;">Source</td></tr>
<tr style="height: 21px;"><td data-sheets-value="[null,2,"Kitchen Sponge"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; vertical-align: bottom; white-space: nowrap;">Kitchen Sponge</td><td data-sheets-value="[null,3,null,12.7]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-align: right; vertical-align: bottom; white-space: nowrap;">12.7</td><td data-sheets-value="[null,2,"http://www.shop3m.com/3m-commercial-size-sponge-c41-7-5-in-x-4-375-in-x-2-06-in.html"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-decoration: underline; vertical-align: bottom; white-space: nowrap;"><a class="in-cell-link" href="http://www.shop3m.com/3m-commercial-size-sponge-c41-7-5-in-x-4-375-in-x-2-06-in.html" target="_blank">http://www.shop3m.com/3m-commercial-size-sponge-c41-7-5-in-x-4-375-in-x-2-06-in.html</a></td><td data-sheets-value="[null,3,null,1]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-align: right; vertical-align: bottom; white-space: nowrap;">1</td><td data-sheets-value="[null,2,"http://www.amazon.com/Best-Sellers-Home-Kitchen-Household-Cleaning-Sponges/zgbs/home-garden/15754811"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-decoration: underline; vertical-align: bottom; white-space: nowrap;"><a class="in-cell-link" href="http://www.amazon.com/Best-Sellers-Home-Kitchen-Household-Cleaning-Sponges/zgbs/home-garden/15754811" target="_blank">http://www.amazon.com/Best-Sellers-Home-Kitchen-Household-Cleaning-Sponges/zgbs/home-garden/15754811</a></td></tr>
<tr style="height: 21px;"><td data-sheets-value="[null,2,"Planktin"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; vertical-align: bottom; white-space: nowrap;">Plankton</td><td data-sheets-value="[null,3,null,0.002]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-align: right; vertical-align: bottom; white-space: nowrap;">0.002</td><td data-sheets-value="[null,2,"https://en.wikipedia.org/wiki/Plankton"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-decoration: underline; vertical-align: bottom; white-space: nowrap;"><a class="in-cell-link" href="https://en.wikipedia.org/wiki/Plankton" target="_blank">https://en.wikipedia.org/wiki/Plankton</a></td><td data-sheets-value="[null,3,null,0.3]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-align: right; vertical-align: bottom; white-space: nowrap;">0.3</td><td data-sheets-value="[null,2,"http://cinema.theiapolis.com/movie-2RXE/the-spongebob-squarepants-movie/gallery/spongebob-and-plankton-1101946.html"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-decoration: underline; vertical-align: bottom; white-space: nowrap;"><a class="in-cell-link" href="http://cinema.theiapolis.com/movie-2RXE/the-spongebob-squarepants-movie/gallery/spongebob-and-plankton-1101946.html" target="_blank">http://cinema.theiapolis.com/movie-2RXE/the-spongebob-squarepants-movie/gallery/spongebob-and-plankton-1101946.html</a></td></tr>
<tr style="height: 21px;"><td data-sheets-value="[null,2,"Squid"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; vertical-align: bottom; white-space: nowrap;">Squid</td><td data-sheets-value="[null,2,"20-60"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; vertical-align: bottom; white-space: nowrap;">20-60</td><td data-sheets-value="[null,2,"http://a-z-animals.com/animals/squid/"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-decoration: underline; vertical-align: bottom; white-space: nowrap;"><a class="in-cell-link" href="http://a-z-animals.com/animals/squid/" target="_blank">http://a-z-animals.com/animals/squid/</a></td><td data-sheets-value="[null,3,null,1.4]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-align: right; vertical-align: bottom; white-space: nowrap;">1.4</td><td data-sheets-value="[null,2,"http://spongebob.wikia.com/wiki/File:Pat_s._spongebob_s._squidward_t..jpg"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-decoration: underline; vertical-align: bottom; white-space: nowrap;"><a class="in-cell-link" href="http://spongebob.wikia.com/wiki/File:Pat_s._spongebob_s._squidward_t..jpg" target="_blank">http://spongebob.wikia.com/wiki/File:Pat_s._spongebob_s._squidward_t..jpg</a></td></tr>
<tr style="height: 21px;"><td data-sheets-value="[null,2,"Starfish"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; vertical-align: bottom; white-space: nowrap;">Starfish</td><td data-sheets-value="[null,2,"12.7-25.4"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; vertical-align: bottom; white-space: nowrap;">12.7-25.4</td><td data-sheets-value="[null,2,"http://www.softschools.com/facts/animals/starfish_facts/85/"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-decoration: underline; vertical-align: bottom; white-space: nowrap;"><a class="in-cell-link" href="http://www.softschools.com/facts/animals/starfish_facts/85/" target="_blank">http://www.softschools.com/facts/animals/starfish_facts/85/</a></td><td data-sheets-value="[null,3,null,1.3]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-align: right; vertical-align: bottom; white-space: nowrap;">1.3</td><td data-sheets-value="[null,2,"http://spongebob.wikia.com/wiki/File:Pat_s._spongebob_s._squidward_t..jpg"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-decoration: underline; vertical-align: bottom; white-space: nowrap;"><a class="in-cell-link" href="http://spongebob.wikia.com/wiki/File:Pat_s._spongebob_s._squidward_t..jpg" target="_blank">http://spongebob.wikia.com/wiki/File:Pat_s._spongebob_s._squidward_t..jpg</a></td></tr>
<tr style="height: 21px;"><td data-sheets-value="[null,2,"Whale"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; vertical-align: bottom; white-space: nowrap;">Whale</td><td data-sheets-value="[null,2,"396.24 -3048"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; vertical-align: bottom; white-space: nowrap;">396.24 -3048</td><td data-sheets-value="[null,2,"http://frontiersofzoology.blogspot.com/2012/02/whale-scale.html"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-decoration: underline; vertical-align: bottom; white-space: nowrap;"><a class="in-cell-link" href="http://frontiersofzoology.blogspot.com/2012/02/whale-scale.html" target="_blank">http://frontiersofzoology.blogspot.com/2012/02/whale-scale.html</a></td><td data-sheets-value="[null,3,null,1.9]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-align: right; vertical-align: bottom; white-space: nowrap;">1.9</td><td data-sheets-value="[null,2,"http://spongebob.wikia.com/wiki/SpongeBob-Pearl_Relationship"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-decoration: underline; vertical-align: bottom; white-space: nowrap;"><a class="in-cell-link" href="http://spongebob.wikia.com/wiki/SpongeBob-Pearl_Relationship" target="_blank">http://spongebob.wikia.com/wiki/SpongeBob-Pearl_Relationship</a></td></tr>
<tr style="height: 21px;"><td data-sheets-value="[null,2,"Sea Snail"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; vertical-align: bottom; white-space: nowrap;">Sea Snail</td><td data-sheets-value="[null,2,"<12"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; vertical-align: bottom; white-space: nowrap;"><12</td><td data-sheets-value="[null,2,"http://www.snail-world.com/"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-decoration: underline; vertical-align: bottom; white-space: nowrap;"><a class="in-cell-link" href="http://www.snail-world.com/" target="_blank">http://www.snail-world.com/</a></td><td data-sheets-value="[null,3,null,0.4]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-align: right; vertical-align: bottom; white-space: nowrap;">0.4</td><td data-sheets-value="[null,2,"http://spongebob.wikia.com/wiki/File:Patrick_SpongeBob_and_Gary_Opposite_Day.png"]" style="font-family: Calibri; font-size: 120%; padding: 2px 3px; text-decoration: underline; vertical-align: bottom; white-space: nowrap;"><a class="in-cell-link" href="http://spongebob.wikia.com/wiki/File:Patrick_SpongeBob_and_Gary_Opposite_Day.png" target="_blank">http://spongebob.wikia.com/wiki/File:Patrick_SpongeBob_and_Gary_Opposite_Day.png</a></td></tr>
</tbody></table>
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<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span><span style="font-family: Arial, Helvetica, sans-serif; text-align: center;"><br /></span><br />
<span style="font-family: Arial, Helvetica, sans-serif; text-align: center;">I need to stop drinking so much coffee.</span>
Torbenhttp://www.blogger.com/profile/03586733786614548430noreply@blogger.com2tag:blogger.com,1999:blog-8470140342170795801.post-63644433764379141052015-12-03T19:19:00.000-08:002016-06-13T17:29:15.692-07:00Is Online Brain Training Real?<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="color: black; font-family: "arial"; font-size: 14.6667px; line-height: 1.38; white-space: pre-wrap;">Almost every morning I hear an advertisement for an online 'brain training' service called Lumosity on the radio. As someone who is pretty interested in brains, training, and pretend words - I decided to look into Lumosity and see what it's all about. </span><span style="color: black; font-family: "arial"; font-size: 14.6667px; line-height: 20.24px; white-space: pre-wrap;">Here's what I found:</span><br />
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><b>First of all, brain training is nothing new</b></span><br />
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><b><br /></b></span></div>
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<span style="color: black; font-family: "arial"; font-size: 14.6667px; line-height: 1.38; white-space: pre-wrap;">Since our ancestors discovered writing, math, and science, we have been interested in improving how we think. And we've gotten good at it. We've learned that people who practice certain mental skills tend to get better at those skills than people who don't. If you practice reading, you'll be able to read more complicated books. If you practice solving math equations, you'll be able to solve more complicated problems. If you practice guitar, you'll be able to play more complicated songs. And if you write a bunch of shitty blog posts, hopefully you'll eventually figure out how to write some good ones. </span><br />
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<span style="color: black; font-family: "arial"; font-size: 14.6667px; line-height: 1.38; white-space: pre-wrap;">Just about everyone has an opinion on what kinds of activities enrich you mind or rot your brain but I think that it's important that we examine our intuitions methodologically. It is contentious whether we can objectively measure what activities can make somebody smarter but I think we know enough that we can rule out activities that definitely don't. In the last couple of years more and more people are using neuroscience and psychology to justify products for cognitive enhancement. Here are just a few:</span></div>
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<li><span style="font-family: "arial";"><span style="font-size: 14.6667px; line-height: 20.24px; white-space: pre-wrap;"><span style="font-size: 14.6667px; line-height: 20.24px;">http://www.</span>lumosity.com</span></span></li>
<li><span style="font-family: "arial";"><span style="font-size: 14.6667px; line-height: 20.24px; white-space: pre-wrap;">http://www.neuronation.com/</span></span></li>
<li><span style="font-family: "arial";"><span style="font-size: 14.6667px; line-height: 20.24px; white-space: pre-wrap;">http://brainage.nintendo.com/</span></span></li>
<li><span style="font-family: "arial";"><span style="font-size: 14.6667px; line-height: 20.24px; white-space: pre-wrap;">http://www.brainmetrix.com/</span></span></li>
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<span style="color: black; font-family: "arial"; font-size: 14.6667px; line-height: 1.38; white-space: pre-wrap;">My concern is that while these approaches might have good intentions, it’s important to take a step back and critically examine whether they actually work.</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><b style="font-size: 14.6667px; line-height: 1.38;">TLDR: The biggest issue with new-age brain training services is that they haven’t been validated </b></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">When someone come up with a new method in science, somebody has to make sure that it works the way that we think it does. If you come up with a new treatment for ADHD we would like to know that it actually reduces the symptoms. If you discover a new species of octopus, we need to make sure that you didn't re-discover one that we already know about. If you come up with a brain training service and you sell it for $50 a year to people worried about their mental health...you should make sure that it works.
Good science is full of sanity checks and re-dos. The history of science is littered with mistakes and assumptions from well-meaning people who didn't check their work well enough. The best way to make sure that we take more steps forwards than backwards is to constantly make sure we know what we think we know. Doing this requires validation. None of the popular marketed brain training services have been appropriately validated to show that they work.</span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> This is a tricky point to get across so I think that the best way to explain what I mean is to just walk you through an example: </span><br />
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><b style="font-size: 14.6667px; line-height: 1.38;"><br /></b></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><b style="font-size: 14.6667px; line-height: 1.38;">The Example</b></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">This is the flanker task:</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><img alt="i1.png" height="219px;" src="https://lh5.googleusercontent.com/vUKrDVJFcucvAKG1gZXaImTUjBa0gbVtfNrlmbQPI2ZQgDRJ2IOdU7vxTcqgxD9QO6puzjsx38Z9TmcmtXZNfGtvPrzWkI--bPZKWXkyPEv0hWES_36bFkK-y6Ac0qoHuw6Iafw" style="-webkit-transform: rotate(0.00rad); border: none; transform: rotate(0.00rad);" width="400px;" /></span></div>
<b id="docs-internal-guid-27652032-cfc3-8402-f55b-352ced24680e" style="font-weight: normal;"><br /></b>
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<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">If you sign up to participate in a psychology experiment in college, this might be a task that the experimenter will ask you to do. You’ll sit at a computer and a bunch of arrows will pop up on the screen, maybe in different patterns. And you are told to use the use the arrow keys on the computer to indicate which direction the central most arrow is pointing as quickly as you can. This task is interesting to neuroscientists and cognitive psychologists because it’s pretty good at measuring how well people can filter out distracting information. That is to say - if you can ignore the arrows that aren't important and notice the one that is important, you have to be using attention of some sort. </span></div>
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<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Now this is one of Lumosity’s games that claims to train "attention and response inhibition", called ‘Lost in Migration’:</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><img alt="screenshot-lumosity-3.jpg" height="320px;" src="https://lh3.googleusercontent.com/bXWfi17w1ZfQDsccplIfJr_leIEk6HqFlCRHjQYUan6NOtzP7oRZibfNwNR1bXjlyqMMy5BEZmwY3hLYamODvBq1t-N8HI3F2B6pz3bezBbfnIQJD-SK2r2bPffH8pNUFrU3CwE" style="-webkit-transform: rotate(0.00rad); border: none; transform: rotate(0.00rad);" width="431px;" /></span></div>
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<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">In this game, players use the arrow keys to indicate which direction the central-most bird is pointing without being distracted by the other birds - as quickly as they can. They pop up in different patterns in different locations on the screen. </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Can you notice any similarities between the Flanker Task and Lost in Migration?
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">
Clearly these tasks are nearly identical. It seems like most of Lumosity's games are designed to closely resemble a neuropsychological task. Cognitive psychologists have come up with lots of games like the Flanker task that are thought to measure different parts of your cognitive processes such as memory, response inhibition, spatial processing and pattern recognition. </span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">The idea behind a lot of lumosity’s games is to ‘gamify’ these psychology tasks. If the only purpose of Lumosity was to practice and play games that are similar to neuropsychological tasks, I'd say that they do a pretty good job. But I don't think that's why many of the 70 Million (!!!) people use Lumosity. </span><br />
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<span style="color: black; font-family: "arial"; font-size: 14.6667px; line-height: 1.38; white-space: pre-wrap;">The more important question is whether practicing these games should measurably <i>improve</i> your cognitive abilities.</span><br />
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Lumosity never overtly claims that playing their games will improve your cognitive abilities but it is implied. Oh boy is it implied.</span><br />
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Here is a figure that pops up the first time you play Lost in Migration:</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><img height="313px;" src="https://lh3.googleusercontent.com/Reo_a4vILZes12jdsuwj84B8IH9fBsXlLpYTkGxBU6FZnvwfsUpJosZPUny1m6Gt2r-d_0kOUC5P6ZLGQHvjveOFs026iyYFwmmaxMY1GWKEsQlcgj1F7pax9dPns5Q8F-3npKTl" style="-webkit-transform: rotate(0.00rad); border: none; transform: rotate(0.00rad);" width="624px;" /></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Let’s look at that graph. It looks like brain performance gets better with a month of training! </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Awesome! </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">While it's one issue that they deceitfully tiptoe around not saying "this will help improve your attention". There’s a </span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">huge</span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> problem with this graph. Can you figure out what is wrong here?</span></div>
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<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">One issue is that we have no idea where that data is coming from but let’s assume that this is really some global average of everybody who does this task and that everybody actually improves over a month of training. My biggest issue here is with the y axis. What units are we measuring ‘Brain Performance’ in? What the hell is brain performance? In >5 years of studying neuroscience, I’ve never encountered the term ‘brain performance’ in any lecture or academic paper. What units do you measure 'brain performance' in? </span><br />
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(Side note- Potential units of brain performance: RAM? "lumositrons"? pico-Elon's? hmmm...)</span></div>
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<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">What they’re really showing on the y-axis of this graph is your performance on this task. They're showing that if you practice that task, you’ll get better at it. </span><br />
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Does that mean your attention improved? </span><b style="color: black; font-family: arial; font-size: 14.6667px; line-height: 20.24px; white-space: pre-wrap;">No. No. No. This is the most important part.</b></div>
<span style="font-family: "arial";"><span style="font-size: 14.6667px; line-height: 20.24px; white-space: pre-wrap;"><br /></span></span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Humans improve at almost everything that they practice! Everybody knows that if you practice at something you tend to get better at it. If you practice Lost in Migration or the Flanker task a bunch of times, you will get faster and more accurate. Does that really mean that you improved your ability to prevent yourself from being distracted, or did you just get better at the game? Or did you get better at doing a repetitive task over and over again? ...Or did you improve one small aspect of attention?...Or did you just get better at using a computer? ...Or did you just get more confident in yourself? ...Or did you actually get better at attention? What even<i> is</i> attention?</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">It’s totally unclear which of these effects underlies improvement on this task over time but my guess is that people are probably just getting better at the games. </span><br />
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<span style="color: black; font-family: "arial"; font-size: 14.6667px; line-height: 1.38; white-space: pre-wrap;"><b>What does the research say?</b></span></div>
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<span style="font-family: "arial"; font-size: 14.6667px; line-height: 1.38; white-space: pre-wrap;"><b><br /></b></span></div>
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">If Lumosity's attention training works, we would expect to see training improve everyday usage of attention or at least a few neuropsychological measures of attention. Lumosity provides absolutely </span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><u>no</u></span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> evidence that improvement in these games generalizes to everyday experiences or even to other attentional measures. To me, this is the very first thing that they should have tested and proven. And this is a really big problem - especially because they have an in house lab and claim to have connections to 40 university collaborators. </span></div>
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<b style="font-weight: normal;"><span style="color: black; font-family: "arial"; font-size: 14.6667px; line-height: 20.24px; white-space: pre-wrap;">They have done some research though. Some of their work shows that shows when aging or cognitively impaired people play a Lumosity game (Lost in Migration), it improves their abilities to perform on the corresponding or highly similar psychological task (flanker task). This is like showing practicing playing checkers with black and red pieces makes you better at playing checkers with blue and yellow pieces. It doesn’t mean that playing checkers will make you better at chess or improve your SAT score or make you more confident to approach girls at middle school dances; you just learned how to play a game and there is no evidence to think what you learned will extend beyond that.</span></b><br />
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<b style="line-height: 1.38;"><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">While I haven't found any evidence for the arrow-bird-game-practice-improves-real-cognition narrative, there is some evidence against it. One critical piece of evidence is that a group at FSU </span></b><b style="line-height: 1.38;"><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">split undergraduate participants into two groups. One group played commercial action/puzzle video game (Portal 2) and the other played Lumosity's games for 8 hours. Both groups were tested before and after training in problem solving, spatial skill, and persistence. The group that played the video game improved at all of these measures while the group that played Lumosity's games improved at </span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><u>none</u></span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span></b><span style="font-weight: normal;"><b style="line-height: 1.38;"><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(</span></b><span style="font-family: "arial";"><span style="color: black; font-size: 14.6667px; line-height: 20.24px; white-space: pre-wrap;">http://myweb.fsu.edu/vshute/pdf/portal1.pdf</span></span><b style="line-height: 1.38;"><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">). While this is only one study, it's starting to seem less and less likely that Lumosity's games make you better at anything besides the games themselves.</span></b></span></div>
<b style="font-weight: normal;"><b style="line-height: 1.38;"><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></b></b>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Surprisingly, some of Lumosity's research has been published to real peer-reviewed journals. But none of this research provides evidence that their method actually works. They show some evidence that these games can accurately </span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">measure</span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> cognitive abilities in aging adults, which is different but actually pretty interesting. </span></div>
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">While I have been pretty critical of Lumosity's false promises of cognitive enhancement, the silver lining is that they have just conducted the largest neurobehavioral assay of all time. They have data from millions of people, men and women, of all ages, from different parts of the world performing dozens of tasks that measure their cognitive abilities. This is really cool because we might be able to find patterns in age related cognitive decline and identify populations that are resilient to cognitive decline at an unprecedented scale. This is really valuable data and has the potential to move science forward but with some serious ethical 'is it worth it' considerations.</span><br />
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<span style="font-family: "arial"; font-size: 14.6667px; line-height: normal; white-space: pre-wrap;"><br /></span><span style="color: black; font-family: "arial"; font-size: 14.6667px; line-height: 20.24px; white-space: pre-wrap;">I'm really only worried about this because I’m sure that the vast majority of their users believe that these games are actually making them smarter and I wouldn’t be surprised if most of their users are older adults and/or people who are worried about their mental health. It seems likely that they are taking advantage of a vulnerable group of people who are suffering from real cognitive impairments such as dementia and Alzheimer’s Disease. If this is true, then they are being intentionally deceitful by using the smoke and mirrors of 'neuroscience' to claim that this is a product that might really help people. Frankly, they are snake-oil salesmen. They are selling a sham product that they have no reason to think will help anybody as something akin to psychoactive medicine.</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Also, while most of Lumosity’s games mirror real cognitive psychological assays, some of the Lumosity games appear to be completely made up with seemingly no psychological basis at all! </span><br />
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Here is one where you play the role of someone in a kitchen who is supposed to match faces of cartoon characters to food orders they place. In this scenario, you must help this Mark Zuckerburg looking fellow get himself a juicy little cheeseburger. </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><img height="372px;" src="https://lh3.googleusercontent.com/X-3UvMe_BJ4PBs_OYOt-rvemj-JfCrY4yEUWxMVZ9cSCiQu88_e_My7KKBTcP7MafpWT9jrZu1RR_tfXvHGnS0JWFR_6JDzWAg1L3_Wry3dzfh6C2bOkXokWISoiVs7tGMhBLhEE" style="-webkit-transform: rotate(0.00rad); border: none; transform: rotate(0.00rad);" width="624px;" /></span></div>
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<span style="font-family: "arial";"><span style="font-size: 14.6667px; line-height: 20.24px; white-space: pre-wrap;">What. the. fuck. is. this?</span></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><b>Cognitive Enhancement through brain training games might be possible after all</b></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Ignoring the aforementioned neuromarketing schemes, there are a few groups studying brain training correctly. For instance, there is a group at UCSF showing cognitive enhancement through video game training and they are doing it really, really well (</span><a href="http://gazzaleylab.ucsf.edu/neuroscience-projects/neuroracer/" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">http://gazzaleylab.ucsf.edu/neuroscience-projects/neuroracer/</span></a><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">). After publishing a finding that their training </span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><b>works</b></span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><b>and generalizes</b></span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> in a top peer-reviewed science journal, Nature, they are going through clinical trials to get their neurofeedback training approved through the FDA as a possible treatment for ADHD. They are different from Lumosity because they are going through a rigorous process of demonstrating that their method might actually help people with disabilities while making sure that their users don’t have any adverse side effects like video game addiction. Moreover this could actually revolutionize how we treat people with attention problems. Instead of prescribing drugs that act on the entire brain, with these cognitive training tasks we have the potential to train the specific pathological networks. We just have to be sure that it works.</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 14.6667px; line-height: 20.24px; white-space: pre-wrap;"><b>What did we learn?</b></span></span></div>
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Cognitive improvement through commercial brain-training games hasn't been proven (yet). Someday somebody might come out with a report providing tons of evidence that these games work, but until that day, I remain very skeptical. The other issue at hand is that we don't really evaluate many of the ways that we teach and learn. We don't know the most efficient ways to train our mental capacities yet besides the same basic formula we've done in schools for over a century. I think it's a great idea to experiment with cognitive enhancement methodologies but it's important that we know if these techniques work before moving forward. </span><br />
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 14.6667px; line-height: 20.24px; white-space: pre-wrap;"><b>In three sentences</b></span></span></div>
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Don't buy Lumosity</span><span style="color: black; font-family: "arial"; font-size: 14.6667px; line-height: 1.38; white-space: pre-wrap;">. Sometimes people will do bad science to mislead you. We should challenge ourselves to t</span><span style="color: black; font-family: "arial"; font-size: 14.6667px; line-height: 1.38; white-space: pre-wrap;">hink critically about how we teach and learn. </span></div>
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<span style="color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;"><br /></span>Torbenhttp://www.blogger.com/profile/03586733786614548430noreply@blogger.com0tag:blogger.com,1999:blog-8470140342170795801.post-22053966307747987082015-10-15T19:13:00.000-07:002015-10-15T19:15:25.396-07:00The automation and ‘datification’ of neuroscience.<br />
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<span style="font-family: Arial; font-size: 14.6667px; font-style: italic; white-space: pre-wrap;">Are experimental neuroscience studies becoming algorithm fodder?</span></div>
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<span id="docs-internal-guid-1ee85724-6e5c-4bef-a4c9-e3a014bc151a"><span style="font-family: Arial; font-size: 14.6667px; font-style: italic; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: Arial; font-size: 14.6667px; font-style: italic; vertical-align: baseline; white-space: pre-wrap;"><br /></span></span></span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">What are you talking about?</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">A few months ago I was in San Francisco. I grabbed a trendy vegetarian brunch (complete with $8 cold pressed juice) with an old friend. He works at a tech consulting firm that is currently interested in how ‘datification’ will disrupt certain industries. ‘Datification’ is a silly pretend word but it represents the idea that many aspects of our everyday lives are now available as computerized data. Imagine (if you can) the olden days when you couldn’t search and sort through your list of friends or look at your phone to see how many calories you had burned that day. There are now many services that turn aspects of your life into data. ‘Datafication’ produces opportunities to analyze previously unavailable information to gain novel insights to the processes that produce it. </span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">The tricky part is figuring out how to analyze this kind of data and how to integrate multiple analyses in a way that best suits your needs. This is an emerging field becoming known as data science. Some services that involve applying data science to newly available data are services such as online reputation management and digital marketing using social media data, and data-driven public health policy for large-scale health data. When Netflix recommends a move or an Uber driver picks you up, your data is being gathered and analyzed by some clever algorithms. Most of this data is so sparse and distributed that it will never be the Orwellian, fascist nightmare some people think it will; but this process, for better or worse, provides us new ways for us to interact with the world around us. Since its emergence, it has become clear that this process of ‘datafication’ and applications of data science have transformed how we live and how many businesses work.</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Ironically, one of the few fields that has been slow to apply data science, is academic research. It is safe to bet that just as data science has changed many industries,</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> data science will also change how we do research in the information era. </span></div>
<span style="font-family: Arial; font-size: 14.6667px; font-style: italic; vertical-align: baseline; white-space: pre-wrap;"><b id="docs-internal-guid-1ee85724-6e5c-a297-cda5-aea4821b0b85" style="font-weight: normal;"><br /></b></span>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Can we ‘datify’ neuroscience?</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Neuroscience, as a formal study, has been going on for about 100 years now. In that time there have been lots of great studies that link the complex biology of our brains to mental processes. By the nature of the scientific method, most experiments study how one variable affects another. For example, I just saw an experiment where there was a difference in activation in certain parts of the brain between depressed people and healthy people - the variables here being (1) depression and (2) activity in certain brain regions. </span></div>
<span style="font-family: Arial; font-size: 14.6667px; font-style: italic; vertical-align: baseline; white-space: pre-wrap;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> Alone this study doesn’t tell us much. It tells us an important link between depression, brain regions but that’s not enough to say anything </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">meaningful</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> about depression, brain regions or their interaction. However, when we synthesize many studies together, we can start to tell a coherent story about how our brains work and how they break using many many pieces of evidence like how Robert Supolsky does here:
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<span style="font-family: Arial; font-size: 14.6667px; font-style: italic; vertical-align: baseline; white-space: pre-wrap;"><iframe allowfullscreen="" class="YOUTUBE-iframe-video" data-thumbnail-src="https://i.ytimg.com/vi/NOAgplgTxfc/0.jpg" frameborder="0" height="266" src="https://www.youtube.com/embed/NOAgplgTxfc?feature=player_embedded" width="320"></iframe></span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">The process of fitting a study into a larger story is very hard. It takes years of research to find meaningful papers and an unmeasurable amount of creativity to piece it all together and develop new understandings of the how our brains work. A google scholar search of papers about depression returns a little less than </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">3 million</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> results. Robert Supolsky, the guy in that video, has spent his entire life working very hard to develop explanations of how mental disorders like depression work. Those of us new to the field are in trouble. Every day thousands of new pubMed articles are published. If I want to be a thorough scientist, do I have to read all of the neuroscience papers every day in addition to reading to catch up on 100 years of neuroscience? I really hope not.</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Technology has taught us that there are often easier ways of combing through >3 million sources of data than doing it individually by hand. Search engines provide a crude way of doing this. Search engines keep track of where things are on the internet and give us the data that it thinks is most relevant to our searches. However, search engines only give us hints for where to find the info that we want. I want a </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">knowledge engine</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> for academia. I don’t want to search for something and find </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">where</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> it is, I want to know </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">what</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> it is.</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">It turns out that’s pretty hard for computers. It’s easy to make computers do math and perform tasks repeatedly but it’s hard to make them think ‘creatively’, tell stories, and explain things in a way that humans can understand. We’re a long ways away from making a computer think creatively but there are some clever algorithms that are ‘hacking’ this problem.</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">A case study in hacking neuroscience</span></div>
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<span id="docs-internal-guid-1ee85724-6e5e-a228-1e8f-2bcc16a21001"><br /><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> When you go on a social media site like LinkedIn, it recommends friends that you might know. My boss’s project, BrainScanr analyzes neuroscience data in a similar way. With this tool, you can search for a neuroscienc-ey word like ‘depression’ or ‘dopamine’ and it scours the literature to find what other neuroscience terms are associated with yours. For example, we’ve known for a long time that people with Parkinson’s disease have lower levels of dopamine in the substantia nigra. If we search for Parkinson’s Disease on brain Scanr, we get this: </span></span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">This web shows us all of the terms found in the literature that are found in the same papers as the words ‘Parkinson’s Disease’. We can see the strong links between dopamine, Parkinson’s Disease, and the basal ganglia - that is nothing special. The bigger story here is comes from the terms that we </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">didn’t </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">expect to see. I didn’t expect to see hallucinations on this figure. I wasn’t aware that hallucinations had anything to do with Parkinson’s but after a quick google search, it turns out some people with Parkinson’s disease sometimes have hallucinations and this is well documented in the literature. Maybe I should have studied harder in Dr. Koven’s cognitive psychology class - sorry Nancy. However, upon further inspection of this figure, I noticed that </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">none of the brain regions involved in Parkinson’s disease are strongly linked to hallucinations</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">! I wouldn’t have known this no matter how many times I tried to memorize the textbook.</span></div>
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<span id="docs-internal-guid-1ee85724-6e5f-3895-7753-ca562d95c758"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Everybody who’s anybody knows that Parkinson’s disease has a lot to do with a malfunctioning dopamine circuit linking a couple of brain regions. However, the hallucinations Parkinsonian patients get don’t appear to be involved in the same Brain ScanR network. This means that either 1) hallucinations are related to</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> these networks </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">and we don’t see a link because nobody is studying it and publishing papers noting their interaction </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">or, </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">2) Parkinsonian hallucinations come from a </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">different problem</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> in the brain that hasn’t been associated with Parkinson’s disease in the literature. In both cases, this indicates a gap in the research that should be filled.</span></span></div>
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<span id="docs-internal-guid-1ee85724-6e5f-4f10-fd2d-fa1cc465ae0f"><span style="font-family: Arial; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;"><img height="456px;" src="https://docs.google.com/drawings/d/sC0srJPhikiA-QKvSpPWINg/image?w=620&h=456&rev=126&ac=1" style="-webkit-transform: rotate(0.00rad); border: none; transform: rotate(0.00rad);" width="620px;" /></span></span></div>
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<span style="font-family: Arial; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">This kind of analysis isn’t possible in a typical literature search - typing some words into the google scholar search bar. This kind of analysis tells us </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">what to search</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> for and what we should study. This computational algorithm was the means to providing a </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">novel</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> insight using data that has </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">existed for years</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. Again, there are often thousands of papers published about any topic in neuroscience. This algorithm provides a way by which we can use the collective intelligence of the corpus of neuroscience research to produce unbiased research directions.</span></div>
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<b id="docs-internal-guid-1ee85724-6e5f-745d-8994-6b23a8c0e35d" style="font-weight: normal;"><br /></b></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Other meta-analytical algorithms </span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Brain scanR is not the only project using data science in neuroscience. There are a few groups doing this kind of work and developing tools to do this kind of work. Most of these tools are in their infancy but it will be exciting to watch them develop.</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Here are a few:
<b id="docs-internal-guid-1ee85724-6e5f-a0cd-1104-565bbb01c887" style="font-weight: normal;"><br /></b></span></div>
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<table style="border-collapse: collapse; border: none; width: 624px;"><colgroup><col width="*"></col><col width="*"></col><col width="*"></col><col width="*"></col></colgroup><tbody>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Project</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Description</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Link</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Paper</span></div>
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<tr style="height: 0px;"><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">NeuroSynth</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Meta-analysis of what terms are associated with specific </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">fMRI</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> activation</span></div>
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<a href="http://neurosynth.org/" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">http://neurosynth.org/</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span></div>
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<a href="http://www.nature.com/nmeth/journal/v8/n8/fig_tab/nmeth.1635_F1.html" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">http://www.nature.com/nmeth/journal/v8/n8/fig_tab/nmeth.1635_F1.html</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span></div>
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<tr style="height: 0px;"><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Allen Brain Atlas</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Genome-scale profiling of </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">gene expression</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> in human and rat brains.</span></div>
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<a href="http://alleninstitute.org/" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">http://alleninstitute.org/</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span></div>
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<a href="http://alleninstitute.org/our-research/scientific-publications/" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">http://alleninstitute.org/our-research/scientific-publications/</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span></div>
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<tr style="height: 0px;"><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">NeuroElectro</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Meta-analysis of brain-wide differences in </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">neuron physiologies</span></div>
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<a href="http://www.neuroelectro.org/" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">http://www.neuroelectro.org/</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">in press </span></div>
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<tr style="height: 0px;"><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">DAVID</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Gene classification</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> via multiple-databases</span></div>
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<a href="https://david.ncifcrf.gov/" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">https://david.ncifcrf.gov/</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span></div>
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<a href="http://www.ncbi.nlm.nih.gov/pubmed/19131956?dopt=Abstract" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">http://www.ncbi.nlm.nih.gov/pubmed/19131956?dopt=Abstract</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span></div>
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<span style="background-color: transparent; font-size: 14.6667px; line-height: 17.6px; vertical-align: baseline; white-space: pre-wrap;"><span style="color: #1155cc; font-family: Arial;"><u>https://github.com/voytekresearch/laxbro/blob/master/Nsaba_Demonstration.ipynb</u></span></span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Do we need this?</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">We are currently facing a problem concerning ‘overflow’ in the scientific literature </span><a href="http://www.ncbi.nlm.nih.gov/pubmed/26365552?dopt=Abstract" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">http://www.ncbi.nlm.nih.gov/pubmed/26365552?dopt=Abstract</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> . Too much research is being published for anyone to keep up with. There are many possible solutions but I think the most attractive is automated meta-analysis. I think that automatic hypothesis generation is the next step in the scientific method. For all of human history, we have been limited by our own creativity and the time it takes to test our hypotheses. For the first time ever, technology now allows computational meta-analyses to algorithmically produce novel hypotheses and perform coarse tests on them. This is especially useful in neuroscience where we have to integrate a huge amount of knowledge across domains. A complete understanding of brains must span biochemistry to neural networks to psychology and it is unlikely that anyone, alone, will be able to understand the corpus of research in any of these domains. Most neuroscientists focus on one feature of one sub-domain. Computers allow us to build the scaffolding to connect the work of these researchers to build a self-consistent but multi-domain explanation of how brains work.</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Scientific advancement doesn’t happen linearly, it happens in leaps in bounds (http://www.powells.com/biblio/62-9780226458120-0). This kind of analysis affords us the possibility of exponentially increasing the rate of scientific discovery by rapidly and iteratively producing hypotheses and testing them. Automation is the next logical step in the scientific method and we are just now witnessing the first generation of these tools.</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Are experimental studies becoming algorithm fodder?</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">No, and sorry if I click-bait-ed you with this title. Experimental studies are definitely not only algorithm fodder. Experimental neuroscience is still producing tons of fruitful results on its own. Most importantly, we don’t know how to perform meta-analyses very well. While all of the tools I’ve mentioned do a pretty good job, they are nowhere near having the complexity required to do much without human supervision. Computational analyses can logically guide our thinking but they are nowhere close to replacing the human thinking required to keep science moving forward. Moreover, any hypotheses derived from computational analyses should be replicated with real experiments. Meta-analytical tools produce hypotheses, not answers. And any good scientist knows how important it is to challenge and test hypotheses. </span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">What’s the point?</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">In research, like many other things, the whole is greater than the sum of its parts. The more we synthesize the work we do and the work that we have done, the more we can fill in the bigger picture together. Algorithmic neuroscience meta-analysis is in its nascency but as we’ve seen with industry, combinatorial data analytics has a tendency to produce unpredictable and epic possibilities to explore. The idea that this technique might have similar effects on science is itself, a hypothesis that we don’t have an answer for but I certainly hope there are lots of people excited to test this out as I am.</span></div>
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Torbenhttp://www.blogger.com/profile/03586733786614548430noreply@blogger.com0tag:blogger.com,1999:blog-8470140342170795801.post-46576147307209498282015-09-17T09:38:00.000-07:002016-06-19T14:39:48.662-07:00The 2014 CNS Annual meeting should be called: ‘The Meeting for Memory and Also Some Other Things’<div style="text-align: center;">
<span style="color: black; font-family: "arial"; line-height: 1.38; white-space: pre-wrap;">AKA: Nobody knows what “Oscillation People” are talking about</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">The way we talk about science is really important. If someone has a good idea, he or she has to be able to communicate it to other people. This is critically affected by the words that we choose to use. If you present at a neuroscience conference, you write an abstract that shows up with everybody else’s in the program. The goal of your abstract is to explain the gist of what you're working on and why it matters to someone who studies something different. Poster abstracts afford a great opportunity to see how science is communicated. This is especially important in neuroscience where people study the many different but highly interrelated features of brains. I presented some of my work at the Cognitive Neuroscience Society meeting a few months ago and when I got there I was handed a couple-hundred page program with information about all of the the talks and posters that would be there. I was curious how much information I could gather just from the words that were used in the abstracts so I started playing around with it.</span></div>
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<span style="color: black; font-family: "arial"; line-height: 22.08px; white-space: pre-wrap;">In this post I’m going to walk through my process of getting CNS poster abstract data from the internet, how I analyzed it, and what this kind of analysis can tell us. Along the way we will laugh. we will cry. And we will learn some data science.</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Here’s what I did:</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Scraping and cleaning the data. </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">This part is for nerds. Skip ahead to the pictures for the interesting stuff. First, I downloaded the program for the CNS 2015 annual meeting from here: </span><a href="http://www.cogneurosociety.org/wordpress2015/wp-content/uploads/2015/03/CNS_2015_Program.pdf" style="line-height: 1.38; text-align: center; text-decoration: none;"><span style="font-family: "arial"; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">http://www.cogneurosociety.org/wordpress2015/wp-content/uploads/2015/03/CNS_2015_Program.pdf</span></a><span style="font-family: "arial"; line-height: 1.38; text-align: center; vertical-align: baseline; white-space: pre-wrap;"> </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">This is a PDF file. PDF files are assholes.</span><span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">I used a python module, PDFMiner's, PDF2Txt.py function to pull all of the text from the pdf file and put it in a text file.</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Then I loaded the text file into python and took a look. I wanted the text from the abstracts but there was tons of irrelevant information I didn’t want like glossaries, announcements, and advertisements in there as well. Furthermore, there were all sorts of line breaks and hyphens that randomly split some of the words that I did want. And for some reason that I can’t explain, every time there was a ‘fi’ or ‘fl’ in the text, PDF2Txt injected a space in the middle of the word. It was gross. I found where in the text the posters started and deleted everything outside that range. Then I used the titles of the poster sessions (A1 - G131) to index the beginning of an abstract and some characteristic whitespace to find the end. I looped through all of the posters and saved each poster to its own text file for safekeeping. I also had to remove some page numbers and the helpful “COGNITIVE NEUROSCIENCE SOCIETY” footer sporadically littered throughout the text. Those were dark times. Some good data was lost in the process. But I came out of the cleaning process with 902 of the 912 conferences abstracts mostly cleaned up.</span><br />
<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Here’s what one of the abstracts looked like after my process. Note that weird ‘fi’/’fl’ thing: </span></div>
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<span style="font-size: xx-small;"><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">G101 SPECTRAL WHITENING INFLUENCES OSCILLATORY DYNAMICS AND </span></span></div>
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<span style="font-size: xx-small;"><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">BEHAVIOR IN HUMANS Torben Noto1 , Bradley Voytek2 ; 1 UCSD, 2 UCSD —</span></span></div>
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<span style="font-size: xx-small;"><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Neural oscillations play a critical role in many brain functions, including </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">perception, memory, executive functioning, and emotion. The scale over </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">which neural oscillations operate spans the microscale local fi</span><span style="background-color: yellow; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">eld potential </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(LFP) of a local neuronal population to the macroscale electrocorticogram </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(ECoG) and electroencephalogram (EEG). Oscillations have proved to be </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">a fundamental component of neural communication and network coordination, </span></span></div>
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<span style="font-size: xx-small;"><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">putatively through their interactions with local population spiking </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">activity via spike/fi</span><span style="background-color: yellow; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">eld or phase/amplitude coupling (PAC). Importantly, </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">population spiking and the oscillatory frequency of a neuronal population </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">can be different from the spiking frequency of individual neurons in the </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">neural region generating the oscillation, however the interrelationship </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">between oscillatory coupling and PAC remains unclear. Across several </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">datasets, collected from multiple investigators—ranging from whole-cell </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">patch clamp with concurrent LFP to human subdural ECoG—we fi nd that </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">temporally de-correlated spiking activity: 1) Is associated with a “fl</span><span style="background-color: yellow; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">attening” </span></span></div>
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<span style="font-size: xx-small;"><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(whitening) of the LFP and ECoG power spectral density; 2) Reduces </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">phase amplitude coupling; and, 3) Biases perceptual behaviors such that </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">ongoing shifts in the spectral shape predict trial-by-trial response times. </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">These results are supported by computational modeling and single-unit </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">in vivo patch-clamp and LFP data. Thus, we have outlined a pathway by </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">which spiking connects the biology of oscillatory mechanics to complex </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">behaviors in humans.</span></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Whatever. Good enough.</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><b>Now it was time for some simple analyses:</b></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">What words were most used to describe the posters? </span><br />
<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Well most words don’t mean much like “the” and “of” so I decided that I would limit my text analysis to more neuroscience-y words that might better characterize the interesting aspects of the abstracts. Luckily the group at NeuroSynth compiled a list of 3407 useful neuroscience words like 'attention' and 'dopamine'. I took each abstract and counted each time a word from this bank was used and put it into dictionaries. Now all of the posters looked like this:</span><span style="color: black; font-family: "arial"; line-height: 1.38; vertical-align: baseline; white-space: pre-wrap;"> (Thanks </span><a href="http://neurosynth.org/" style="line-height: 1.38; text-decoration: none;"><span style="font-family: "arial"; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">http://neurosynth.org/</span></a><span style="font-family: "arial"; line-height: 1.38; vertical-align: baseline; white-space: pre-wrap;">) </span></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 14px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">{'SUPPORTED': 1, 'FUNCTIONS': 1, 'PERCEPTION': 1, 'MULTIPLE': 1, 'NETWORK': 1, 'INDIVIDUAL': 1, 'INTERACTIONS': 1, 'HUMANS': 2, 'GENERATING': 1, 'COLLECTED': 1, 'SCALE': 1, 'ONGOING': 1, 'FUNDAMENTAL': 1, 'OSCILLATIONS': 3, 'EEG': 1, 'DYNAMICS': 1, 'POPULATION': 4, 'SPECTRAL': 3, 'UNCLEAR': 1, 'COMPLEX': 1, 'COUPLING': 3, 'POWER': 1, 'PATHWAY': 1, 'EXECUTIVE': 1, 'COORDINATION': 1, 'SHAPE': 1, 'CRITICAL': 1, 'BEHAVIOR': 1, 'PHASE': 1, 'IMPORTANTLY': 1, 'FUNCTIONING': 1, 'BEHAVIORS': 2, 'PLAY': 1, 'NEURONAL': 2, 'DENSITY': 1, 'REDUCES': 1, 'HUMAN': 1, 'TIMES': 1, 'POTENTIAL': 1, 'NEURONS': 1, 'MODELING': 1, 'LOCAL': 3, 'RESPONSE': 1, 'EMOTION': 1, 'AMPLITUDE': 1, 'COMPUTATIONAL': 1, 'CONCURRENT': 1, 'PREDICT': 1, 'COMMUNICATION': 1, 'COMPONENT': 1, 'TEMPORALLY': 1, 'VIVO': 1, 'SHIFTS': 1, 'FREQUENCY': 2, 'ROLE': 1, 'INFLUENCES': 1, 'MEMORY': 1, 'PERCEPTUAL': 1, 'BIASES': 1}</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.6667px; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><b style="font-weight: normal;"><br /></b></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(This is what that transformation did to the same poster as above)</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Using this format let me sum all of the mentions of certain words together across all 902 posters, I found that these were the most commonly used words:</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
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<a href="http://4.bp.blogspot.com/-s5ZYJP3TVk8/Vfpiv-9WU5I/AAAAAAAAAWo/1dZfBFr9y0g/s1600/Screen%2BShot%2B2015-09-16%2Bat%2B4.41.31%2BPM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="color: black;"><img border="0" height="396" src="https://4.bp.blogspot.com/-s5ZYJP3TVk8/Vfpiv-9WU5I/AAAAAAAAAWo/1dZfBFr9y0g/s640/Screen%2BShot%2B2015-09-16%2Bat%2B4.41.31%2BPM.png" width="640" /></span></a></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Again, I analyzed 902 abstracts. Memory is mentioned 1189 times. On average, that’s more than once per abstract!</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /><br /><span style="vertical-align: baseline;">To prove to myself that this wasn't a bogus finding caused by some outlier or problem with my cleaning process, I plotted how often each abstract used the word "memory". </span></span></div>
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<a href="http://1.bp.blogspot.com/-Vz3B911f_-M/Vfpi8mzZjRI/AAAAAAAAAWw/iJa0J219VBQ/s1600/Screen%2BShot%2B2015-09-16%2Bat%2B4.48.09%2BPM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="color: black;"><img border="0" height="440" src="https://1.bp.blogspot.com/-Vz3B911f_-M/Vfpi8mzZjRI/AAAAAAAAAWw/iJa0J219VBQ/s640/Screen%2BShot%2B2015-09-16%2Bat%2B4.48.09%2BPM.png" width="640" /></span></a></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 14.6667px; vertical-align: baseline;"><br /></span></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="line-height: 20.24px;">It looks pretty reasonable. Some abstracts mention memory a whole lot and some don’t mention it at all. Also, the posters here are in plotted in order of poster session. And the poster sessions each have a topic. Its cool that you can easily guess which sessions were about memory and which weren't.</span></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span>
<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">This abstract used the word “memory” 16 times!</span><br />
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<span style="font-size: xx-small;"><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">TRANSCRANIAL DIRECT CURRENT STIMULATION IMPROVES </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">ASSOCIATIVE </span><span style="background-color: orange; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">MEMORY</span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> IN INDIVIDUALS WITH DEPRESSION. </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Cheryl Abellanoza1, James Schaeffer1, Heekyeong Park1; 1University of Texas </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">- Arlington — The dorsolateral prefrontal cortex (DLPFC) is important for </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">both working </span><span style="background-color: orange; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">memory</span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> and long-term </span><span style="background-color: orange; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">memory</span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">, such that DLPFC activity </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">promotes associative </span><span style="background-color: orange; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">memory</span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> by forming relational processing between </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">items during on-line processing. fMRI studies have shown that increased </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">DLPFC activity during encoding relates to successful associative </span><span style="background-color: orange; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">memory</span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">in normal controls. Neuropsychological patients, including depression </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">patients, show disorders in DLPFC activity, along with impairments in </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">associative </span><span style="background-color: orange; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">memory</span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. Transcranial direct current stimulation (tDCS) is </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">a noninvasive, safe, and cost-effective form of brain stimulation that is a </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">useful tool for examining the causal relationship between brain areas and </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">cognitive functions. The present study investigated whether tDCS of the </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">left DLPFC would enhance associative </span><span style="background-color: orange; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">memory</span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> in individuals with depressive </span></span></div>
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<span style="font-size: xx-small;"><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">symptoms. Subjects (depression, control) engaged in a double-blind, </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">two-session (anodal, sham) study where they studied items and </span></span></div>
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<span style="font-size: xx-small;"><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">completed item and associative </span><span style="background-color: orange; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">memory</span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> tests. tDCS was administered prior </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">to </span><span style="background-color: orange; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">memory</span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> tasks. For item </span><span style="background-color: orange; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">memory</span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> test, subjects studied a list of items </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">and made “old/new” recognition judgments with confi dence ratings. For </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">associative </span><span style="background-color: orange; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">memory</span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> test, subjects studied word pairs and indicated if test </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">pairs were studied in the same pairing at study (“intact”), studied but with </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">different pairings (“rearranged”), or not studied (“new”). Results showed </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">that only the depression group showed enhanced associative </span><span style="background-color: orange; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">memory</span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> after </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">anodal tDCS administration. However, such </span><span style="background-color: orange; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">memory</span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> enhancement effects </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">due to tDCS were not found in item </span><span style="background-color: orange; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">memory</span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. Control subjects did not show </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">any difference due to tDCS. These fi ndings demonstrate the role of DLPFC </span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">in associative </span><span style="background-color: orange; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">memory</span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> and the nature of </span><span style="background-color: orange; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">memory</span><span style="background-color: white; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> defi cits in depression.</span></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 14.6667px; vertical-align: baseline;"><b style="font-weight: normal;"><br /></b></span></span><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 14.6667px; vertical-align: baseline;"><b style="font-weight: normal;">Ugh. Ok. We get it. This is about memory.</b></span></span>
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 14.6667px; vertical-align: baseline;"><b style="font-weight: normal;"><br /></b></span></span><br />
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><b>Anyways, let's move on. Here's another interesting thing that I found:</b></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 14.6667px; vertical-align: baseline;"><br /></span></span>
<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="vertical-align: baseline;"><span style="vertical-align: baseline;">I used a quick clustering algorithm to group abstracts by the words that were used. I found some categories that resemble the fields of neuroscience...kind of. The algorithm I used doesn't name the clusters so I just made those up myself.</span></span></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 14.6667px; vertical-align: baseline;"><span style="font-size: 14.6667px; vertical-align: baseline;"><br /></span></span></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-size: 14.6667px; vertical-align: baseline;"><span style="font-size: 14.6667px; vertical-align: baseline;"><span id="docs-internal-guid-e767b164-da14-4da7-9801-a31c03e7d9f5"><br /></span></span></span></span></div>
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<table style="border-collapse: collapse; border: none; width: 624px;"><colgroup><col width="*"></col><col width="*"></col></colgroup><tbody>
<tr style="height: 0px;"><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Topic</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Key terms:</span></div>
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<tr style="height: 0px;"><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Topic 1: Oscillation things</span></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 14px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">STIMULATION MOTOR ALPHA THETA EEG POWER PHASE ACTION OSCILLATIONS HZ</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 14px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span></div>
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<tr style="height: 0px;"><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Topic 2: Language and Speaking</span></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 14px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">LANGUAGE SENTENCES ENGLISH SENTENCE COMPREHENSION READING BILINGUALS HEMISPHERE NATIVE SPEAKERS</span><span style="background-color: white; color: black; font-family: "arial"; font-size: 14px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Topic 3: ERPology</span></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 14px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">ERP ERPS EFFECT EFFECTS RESPONSE AMPLITUDE POTENTIALS CONDITION LARGER EARLY</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Topic 4: Memory and Hippocampus</span></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 14px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">MEMORY RETRIEVAL ENCODING WORKING EPISODIC RECOGNITION HIPPOCAMPUS HIPPOCAMPAL INFORMATION WM</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Topic 5: Actual Cognitive Neuroscience</span></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 14px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">COGNITIVE TASK ET AL USING TASKS NEUROSCIENCE PERFORMANCE RESEARCH INDIVIDUAL</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Topic 6: Reward or something?</span></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 14px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">TASK INFORMATION REWARD CONTROL RESPONSE COGNITIVE CUES TRIALS MODEL PREDICTION</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Topic 7: Learning (and sleep?)</span></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 14px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">LEARNING TRAINING SLEEP LEARNED GROUP NOVEL SESSION PERFORMANCE TEST NEW</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Topic 8: Old People and Young People</span></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 14px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">ADULTS AGE OLDER CHILDREN PERFORMANCE YOUNG FUNCTION YEARS DEVELOPMENT ABILITY</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Topic 9: Vision and Attention</span></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 14px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">VISUAL ATTENTION STIMULI LOCATION OBJECTS SPATIAL OBJECT PRESENTED TARGET REPRESENTATIONS</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Topic 10: Emotional Emotions</span></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 14px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">EMOTIONAL EMOTION STRESS NEUTRAL NEGATIVE STIMULI ANXIETY AFFECTIVE COGNITIVE POSITIVE</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Topic 11: Cortical Networks</span></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 14px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">NETWORK CONNECTIVITY FRONTAL NETWORKS GYRUS PREFRONTAL INFERIOR ANTERIOR TEMPORAL PARIETAL</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Topic 12: Words</span></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 14px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">WORDS WORD SEMANTIC EFFECT EFFECTS PRESENTED INCONGRUENT RECOGNITION PRIMING LEXICAL</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Topic 13: Faces</span></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 14px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">FACES SOCIAL FACE ASD PERCEPTION FACIAL INDIVIDUALS STIMULI PRESENTED AUTISM</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Topic 14: Brain Structure</span></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 14px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">CONTROLS MATTER COGNITIVE VOLUME HEALTHY WHITE CORTICAL INDIVIDUALS DISEASE STRUCTURAL</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Topic 15: Hearing</span></div>
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<span style="background-color: white; color: black; font-family: "arial"; font-size: 14px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">AUDITORY SPEECH FEEDBACK MUSIC PERCEPTION PITCH TEMPORAL SOUNDS PERCEPTUAL FREQUENCY</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="line-height: 20.24px;">Torben. What the hell am I looking at?</span></span></div>
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<span id="docs-internal-guid-e767b164-da14-8b11-221d-d63f9d5274ad"><span style="background-color: transparent; color: black; font-family: "arial"; vertical-align: baseline; white-space: pre-wrap;">Good question, dear reader. I used Latent </span><span style="background-color: transparent; color: black; font-family: "arial"; vertical-align: baseline; white-space: pre-wrap;">Dirichlet Allocation (LDA) </span><a href="https://en.wikipedia.org/wiki/Latent_Dirichlet_allocation" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: "arial"; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">https://en.wikipedia.org/wiki/Latent_Dirichlet_allocation</span></a><span style="background-color: transparent; color: black; font-family: "arial"; vertical-align: baseline; white-space: pre-wrap;"> to cluster all of the abstracts into categories based on their content. Basically, I told this algorithm to split the abstracts into 15 groups. Fifteen being a completely arbitrary number. The groups were decided based on how specific certain words are to certain categories. I displayed the 10 words that most characterized each group, the first word being the most characteristic.</span></span></div>
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<span id="docs-internal-guid-e767b164-da14-8b11-221d-d63f9d5274ad"><span style="background-color: transparent; color: black; font-family: "arial"; line-height: 1.45715; text-indent: 48px; vertical-align: baseline; white-space: pre-wrap;">It is important to point out that LDA is sensitive to the parameters that I used behind the scenes. </span><span style="background-color: transparent; color: black; font-family: "arial"; line-height: 1.45715; text-indent: 48px; white-space: pre-wrap;">For example, I ran the same analysis with different numbers of categories to see how that would affect the output. It shuffled and mixed these categories around a little bit but the gist was the same. </span><span style="background-color: transparent; color: black; font-family: "arial"; line-height: 1.45715; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span></span></div>
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<span id="docs-internal-guid-e767b164-da14-8b11-221d-d63f9d5274ad"><span style="background-color: transparent; color: black; font-family: "arial"; vertical-align: baseline; white-space: pre-wrap;">Using LDA, we can also plug an abstract back into the model and see which categories it fits. Here’s how mine did:</span></span></div>
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<a href="http://1.bp.blogspot.com/-x4M8K2bDxc4/VfpjnF4DADI/AAAAAAAAAW4/GmNmaUilFqw/s1600/Screen%2BShot%2B2015-09-16%2Bat%2B5.50.48%2BPM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="color: black;"><img border="0" height="452" src="https://1.bp.blogspot.com/-x4M8K2bDxc4/VfpjnF4DADI/AAAAAAAAAW4/GmNmaUilFqw/s640/Screen%2BShot%2B2015-09-16%2Bat%2B5.50.48%2BPM.png" width="640" /></span></a></div>
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<span id="docs-internal-guid-e767b164-da15-5db0-60c9-a30d88b8362d"><span style="background-color: transparent; color: black; font-family: "arial"; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">Looks like my paper fits into the cognitive neuroscience, hearing(?) and oscillation categories. I thought my paper would be more in the Oscillation category but I used a lot of 'Cognitive' words and words like 'perception' and 'auditory' from the Hearing category so it makes sense that my paper would fall into a couple categories.</span></span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; line-height: 1.45715; text-indent: 36pt; white-space: pre-wrap;">Well first of all it is pretty cool that the categories that I found mostly reflect the submission categories for CNS. You can clearly see the canonical fields of study like memory and vision reflected by these clusters. But there's more here. I think it's a funny easter egg that ET and AL showed up in the Cognitive category. For those of you who don't know, you put "et al." in your byline if you have many authors. This suggests that much larger research groups are working on these kinds of problems. Hmm. Weird.</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; line-height: 1.45715; text-indent: 36pt; white-space: pre-wrap;">One idea from this analysis is that maybe conferences should use LDA from the previous year to decide what categories they should use for poster sessions. For example, there are people really interested in the structure of the brain but there wasn’t a specific session for only that. It would be cool if the structure of science could update itself in real time. </span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; line-height: 1.45715; text-indent: 36pt; white-space: pre-wrap;">But what is super, super interesting is that the people studying oscillations are the first group. This means that the vocabulary they use is the most specific. (The distribution of topics has a Dirichlet prior meaning it tends to have a log-normal-ly looking distribution). It’s literally like they are speaking in a different language than everybody else! This means that very few people in other fields are talking about things like oscillations and the power spectrum, at least in their abstracts, with regard to their more specific field of study. My work was one of the few posters that partly fell into the oscillation category and in my anecdotal experience, I only connected with a few other people interested in these kinds of things at this conference.</span></div>
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<span style="background-color: transparent; color: black; font-family: "arial"; text-indent: 36pt;"><span style="font-size: 14.6667px; line-height: 1.45715; white-space: pre-wrap;">The lesson here is that it’s often helpful to take a step back and look at the big picture. Science happens in a social and linguistic context and not enough scientists who participate in this system recognize this fact. Doing meta-analyses of our process can show us things that aren't evident at smaller scales. In this case, scientists seemed more interested in memory than </span><span style="font-size: 14.6667px; line-height: 21.3716px; white-space: pre-wrap;">cognition</span><span style="font-size: 14.6667px; line-height: 1.45715; white-space: pre-wrap;"> at this 'cognitive neuroscience' conference and the few people were using an 'oscillation' vocabulary in their work. It would behoove us all to be mindful of how we structure our science, communicate our ideas, and listen to other perspectives.</span></span><br />
<span style="background-color: transparent; color: black; font-family: "arial"; text-indent: 36pt;"><span style="font-size: 14.6667px; line-height: 1.45715; white-space: pre-wrap;"><br /></span></span><span style="font-family: "arial"; line-height: 23.3144px; text-indent: 48px; white-space: pre-wrap;">If you're interested, t</span><span style="background-color: transparent; color: black; font-family: "arial"; text-indent: 36pt;"><span style="line-height: 1.45715; white-space: pre-wrap;">he cleaned abstract metadata and some the interesting parts of the code can be found here: </span></span><span style="font-family: "arial";"><span style="line-height: 21.3716px; white-space: pre-wrap;"><a href="https://github.com/torbenator/cns_analysis">https://github.com/torbenator/cns_analysis</a></span></span></div>
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Torbenhttp://www.blogger.com/profile/03586733786614548430noreply@blogger.com0