Reverse Engineering Brain Networks: Testing the Brain like One would Test a Neural Network

Typical steps in a neural network modeling study are the definition of a particular cognitive phenomenon, the creation and definition of the network model by specifying the neural architecture, activation functions and the learning rules. One then sets out to test
how well the network model matches up with the phenomenon, and to the extent that it does and is parsimonious, and has neural plausibility, it is a good model.

It is then not difficult to imagine how we can do the same thing with the brain by treating it as a neural model that's already built, and we're just trying to discover its architecture, its activation functions and its learning rules. Thus, we run the brain through simulations, observe the input and resulting output, and hypothesize the parameters that led to the observation.

We can then reverse engineer these parameters into the model (which is what we do anyway), and again, test how good the model is.

Neurotree

This is a cool website that tracks who was taught by who, and through it, you could trace how ideas get formulated and how they evolve...or not!!!

My Neurotree

HBM Conference 2007 Chicago

Went to Human Brain Mapping Conference last week. Stayed at Sheraton Hotel. We ate at several places during that time, so hungry...because always using brain, so all the sugar used up. But it was fun. First night we arrived, there were fireworks and the Blues Fest was on in Grant Park. Anyway, no photos because too busy working. Check out what was cool at the conference [click here].

Here are the eatery reviews:
Happy Chef Chinatown
Always my standard place to eat...we had dim sum there, although usually for dinner, you can do a set meal for very cheap (works out usually to be ~$8), and it comes with free lobster or crab.

Oysy
Japanese sushi place. Not bad...but probably Sai Cafe is better but more expensive. Anyway, its one of those modern sushi places. There's two outlets, one on Grand, and one one Michigan. Average cost ~$20-$30, depending on what you order.

Dao Thai Restaurant
Good food and cheap prices (~$6). Has some pretty authentic Thai dishes, and the restaurant has nice Thai looking decor where you sit on floors with wells in them so that you are the same height as the table...get it?

Gino's East
Took a while to get our pizzas, but that's because they were making it fresh, as any good pizza should be. The pizza is pretty good. Nice and thick. We had a mix of supremo and vege. The sauce was not too sweet or rich, so its good. ~$15. Giordano's near the Water Tower still has my vote.

John Hancock, the Signature Room on 95th Floor
What would a trip to downtown Chicago be without a brunch at the Signature Room? $20. Best view with food combination. Menu changes. Brunch is from 11.30am to 2.30pm. This is the same view you get as when you go to the observatory, for which you must pay ~$15. So go do the math...

Andy's Jazz Pub
In my opinion, this is the heart of Chicago, and the most worthwhile place to hang out for good music. Don't come here to have deep conversation. Come here to listen to the depths of music. Cover $5-$20. Drinks are decent, not too wide ranged, but enough, serves dinner too. Historically, several notable musicians have jammed here. I like the way you can sit right in front of the band, and also the jam nights...informal, naughty, crazy, eclectic, and it all gets into your ears. Trumpets, guitars, drums, piano, bass, the whole shebang.

House of Blues
Significant venue where many musicians have performed including Louis Armstrong. Its a theatre set up inside. Cover is more expensive, concert based. You'll have to check online to get tickets in advance. Serves food. I think its worthwhile to visit once.

Red Fish
Cajun style. Food is pretty good. ~$20. They have a live band. Plays rock.

Some Tapas bar somewhere...

Cool Studies at HBM 2007 Chicago

Day 1
Cultural Neuroscience
Thinking of culture using a top-down versus bottom-up framework. Trey Hedden (MIT) and Angela Gutchess (Harvard University)...notable speaker presentations.

Visual Field Maps, Plasticity, Reading
Discovery of retinotopic visual representation in visual cortical areas other than V1. Apparently, V2, V3, even V4 and MT have some retinotopy. Speaker session by Brian Wandell (Stanford University).

Day 2
Brain Noise
Didn't attend this one, but it seems that people are looking into neural noise as a predictor of subsequent brain activity and behavior. McIntosh was one of the speakers.

Manipulative Neuroscience
Awesome talk by Mitsuo Kawato (ATR, Kyoto). He is the brainchild of DB, humanoid robot that is able to mimic human movements by visual observation, eg drumming, juggling, dancing. The talk covered latest research about controlling robot movements through brain-computer interface as well as visual and tactile feedback.

Perceptual Decision Making
Great talks relevant to the visual discrimination project. Generally, I got ideas about how to proceed with the project in terms of possible analyses, and also the fact that others have done this before. The main question is, how does the brain make perceptual discriminations of visual information? What are the mechanisms and neural correlates? Most notable speaker for me here was Paul Sajda.

Day 3
Dual Brain Systems
Control vs Representation systems in the brain. Typically showing that the control network resides in frontal, parietal regions, and representations in the primary and secondary unimodal areas. Check out www.walterschneider.net.

Repetition and the Brain
Another notable symposium of talks. Kalanit Grill-Spector hosted this one. The topic is self-explanatory, but there were some main novel directions. There is distinction between repetition suppression for immediately repeated stimuli vs stimuli repeated over interspersed trials (Grill-Spector). There is an interesting finding that for interspersed trial repetition of object naming tasks, pre-op patients for removal of lateral anterior temporal poles showed normal repetition suppression of repeated objects was observed in the ventral visual areas. But after operation with temporal poles removed, suppression disappeared even in lower perceptual areas suggesting that suppression has a top-down source in this case (Rik Henson). Another contention was Grill-Spector's testing of the fatigue vs facilitation models of adaptation effects. She found evidence for fatigue rather than facilitation, but note that her design involved immediate repetition.

Day 4
Representation and Processes
Didn't attend all, but most notable for me was John-Dylan Haynes' talk on reading hidden intentions in the human brain. They used classifier algorithms on clusters of voxels in the whole brain to identify brain areas that would reliably discriminate between stimuli. This could be applied to the visual discrimination project.

HBM: Ideas: Visual Discrimination Project: General Questions

1. Is there poorer behavioral perceptual discrimination with age?
2. If so, what are the neural correlates? Is it a perceptual representation problem (ventral visual dedifferentiation)? Or is it a selection/decision-making/control process problem (noise, non-selectivity in frontal cortex)?
3. Is this the same across all types of stimuli (eg faces, patterns, random shapes)?
4. Is there a constant in terms of brain activation pattern across all individuals which is necessary for discrimination?
5. Which parts of the brain are predictive of whether the individual is able to discriminate visual stimuli (classifier algorithms on whole brain)?
6. What leads to individual differences in performance? And if all individuals are equated at some level of performance, do the individual differences disappear?

John 3:22-26

"After these things..." refer to the Passover and Nicodemus's visit. It is important to note that Jesus was gathering quite a crowd here, and that there was quite a religious sentiment going on in the Judean region, especially in Jerusalem. Also note that Jesus' disciples were baptizing. Referring back to the section in the John posts on baptizing we see that it was quite a common practice, however, its origins are not clear, and what Jesus' disciples were baptizing the people for is also not mentioned. It might be that while they were baptizing, Jesus was also teaching, since it is mentioned that He Himself did not baptize. This also tells us that Jesus' disciples at this time might have some religious status and recognition, being associated with a popular teacher, Jesus.

In any case, there arose a debate. How often, when there is a large crowd of believers, even religious leaders, there will also be a debate. And note that it was a purification, a debate about rituals probably between John's disciples and the Jews (probably the Pharisees), a dispute about who is doing what and who is right about it. Perhaps we can get the sense here that while the Pharisees were in legal religious authority, there were bands of teachers who might have disagreed with them, and there was constant voicing of religious ideas. Can we map this on to the way churches and religious organizations behave now?

But note even more surprising is that while the dispute was about purification, what John's disciples asked John about was nothing about purification but they were concerned about Jesus having more followers than John! Perhaps they were not really concerned about purification after all, perhaps it was bothering them that this thing was happening, and the unrest made them choose a topic just to vent? Again, do we do that ourselves? This is a call to re-examine our motives, no matter how admirable, we may have the best of intentions to dispute about religious motives and practices, but is that really our concern, and even more important, is that really what matters? Did we miss the point about what Jesus is doing?

Examine John's response deeply, because it seems in contrast to his disciples' and perhaps may be what John the author is putting as an example for us to follow in response to the Christ.

"He must increase, but I must decrease".

We are but witnesses to a more glorious Light. Always remember that. Be humble. Especially in the presence of One who comes from above and testifies to that which He has seen and heard. This statement constitute another testimony from John the Baptist as quoted by John the author, another testimony about the Christ. And Christ's testimony, through His actions, about Himself.

CNS 2007: New York City

New York, New York. The greatest city on earth...lah. We walk here walk there, walk everywhere. This photo show the city from the New Jersey side. A dense fog is covering the midtown area. Very thick, very mystery one.

Anyway, someone may is being asking me, why you go there ah? So I have to tell you, is not for fun one ok! Is for work. We is actuallying doing work lah. Conference. CNS Conference. Stand for Cognitive Neuroscience Society lah. Is for people who do my kind of work one, neuroscience. About the brain lah. Anyway, as you can see, we are very busy. So cannot talk very long. We are constantly finding out new, and interesting and important things, so also have to keep ourselves fit in order to maximize productivity. This next photo is showing Wenjing eating the duck bones, then Blair is eating the fish bone. See we very poor, eat only bones.

The the city also very one kind, the sell us jiu. Then got so many kinds. We dunno what to get, so we see this one, must be super good lah. Because the name is SIMI. So we think this one is asking us "Kua Si Mi?" That's means is got very stylo right? Because got attitude. Then you know this one is for when you dunno what jiu this is, you ask the store owner, he will recommend and say "Simi jiu you want?" Then of course you say "yes!"

Then not say I say what lah, but there is a very good sushi place called Yuka in the Upper East Side, this is in the upper side, in the east. That side. Is eat all you can one, anytime. Most New York eat all you can is only on certain days only and at some times only. This one is everyday, anytime also can. Only about $20. Is cheap already lah for New York. Only thing is you must not over order. So if you order, then never eat, then must pay the full price for ala carte. Remember ah, don't order too much, then no more siao mei mei price.














The next time is we go to the statue lah. Here is the poem they write about it. Acherly, not they lah, is one xiao jie write one. Is talking about the liberty, the freedom, is so good. Everyone also is like.













Then hor, lastly but not least lah, is the brunch in the West Village in place call Manteno, or Man something lah....and dinner in Le Petite Bistro.













This one is the You've Got Mail restaurant where the guy pretend to dunno the girl like that, then sian her from there lor.













So you can see we is very busy lah. I also recommend you see this movie lah. Is very good, but because take on phone may give you headache. [movie] And no say I never tell you ah, this movie is quite long one...about 20min long!

Why did Jesus Christ have to die?

There are many aspects to this question, but I would first deal with the most direct one and leave the rest for later comments and feedback.

Christ died because of our sin. Therefore, first we have to know what sin is. Sin is not just doing "bad" things like stealing, lying, or even killing. The core of sin is not knowing God as God. We all have sinned in that we all are born into this world not immediately knowing who God is, and not immediately acknowledging Him. All of us, at one point in our lives, were separate from God. This is a result of the original sin from Adam. But the sin also lies on us as well.

The result of our sin, is our death. Not just physical death, but death as separation. That is, once we are separated from God, we remain always separated. The problem is that God does not have sin, and therefore there is separation. On the other hand, God does not think that this separation is totally good. It is better for us to be with Him. So He worked out a way for us to be with Him again, even though we have sinned. The answer is Jesus.

Jesus Christ is God. Although He is God, He took on our sin, and died. This at once forms a bridge. It is both shocking as well as beautiful all at once, because God who cannot even have a hint of sin, took on our sin. And God, in whom is life itself, died. This might sound impossible, or ridiculous, or contradictory at first. But consider that there is a lot about God we don't fully understand. Furthermore, what is impossible to man, is possible to God. To live and die at the same time, to be pure but tainted at the same time. This is a radical concept, that perhaps we can slightly identify with in the form of our own emotions. How we can feel so completely elated but hollow, sad and happy, worried but at peace, angry yet in love, hate but respectful. How we can be many persons yet the same person at one time. Is it any more impossible for God to have this characteristic too but in infinite terms?

In any case, once Christ died, we see that the separation is made null, because God crossed over to our side, and in doing so, brought us back to Him. There is identification and acknowledgment. There is also a form of payment, as it were. A ransom for the price of sin. Sin meant death for us, but in our stead, Christ died. Ironically, it is Christ/God that defined that sin means death. So in essence, He was both fulfilling His own law as well as abolishing Himself and His law.

The story doesn't end there of course, because Christ also rose again from the dead.

Parko Cho-O

No, this isn't a tribal dance. No, this isn't us burning the house. It is us saying goodbye to a dear friend. Parting is never easy. Which is why we do it with some partying. Parko Cho-O was held at Hessel Park, 6pm. BBQ, good food, good company. At first, the weather forecast threatened to thunderstorm, but, I quote someone, "60% chance for thunderstorm means, 40% chance". It all turned out well. People gathering wood, people burning marshmellows. Everyone just being plain crazy. We wish you all safe journey, and a better road ahead.

Check out the awesome pyro fest [movie].

Galactica Finale

There's a reason for him grabbing you...its because it is the end. The final five...the return of Starbuck...the silly music...Earth!

Ending episode of Galactica 3rd season finale.

Goose on Roof

Walking along the Beckman Quad, it was a breezy Spring evening. When something caught my eye on the right. Two geese. Flying in tandem, barking! They swooped past behind and landed on the roof of the computer science building. Tension ruffled in the air. What would they do next?

Click [here] to find out!

Press Release: Culture and Aging fMRI Study

Culture, Aging fMR-Adaptation press release in UIUC News Bureau.

http://www.news.uiuc.edu/news/07/0501culture.html

Culture, Age and Eye-Movements

We repeated the same experiment as in the culture and aging adaptation fMRI study. Only this time, we were recording subject eye-movements. We know that there were already cultural differences in old adults in terms of brain activity. Specifically, old East Asian adults did not engage the object processing regions to the same degree as Old Westerners. But how do we really know for sure that this was related to visual processing and not some other form of cognitive operations at work. A way to understand this better was to use eye-tracking. Which is what mainly motivated this study. In parallel, this eye-tracking version of the paradigm allowed to examine three main questions:

1. Cultural experience with age predicts that individuals become more different as they become more developed in their culture (assuming that the cultures are different on some dimensions and levels). However, aging also leads to a phenomena called de-differentiation, which refers to the fact that cognitive processing in older adults becomes less individually distinct due to general decline and increased variability in performance. So it would seem these two forces are in opposition. Thus, one question was whether cultural difference diverge or converge with age.

2. Another question was whether these cultural differences are robust to environmental biases. Cultural biases are such that East Asians are context-oriented and Westerners are object-oriented. These are sweeping statements of course, and should in no way be understood as stereotypical. However, there is evidence that suggests that, for whatever reason, there are visual processing differences that are related to the cultural background of individuals, including this current study. The question though is if we were exposed to visual environments that biased us to attend to objects or backgrounds, how would we behave given our own cultural biases to one component over the other?

3. Finally, the last question is whether these cultural biases in visual processing is just an inconsequential behavior, or if it does indeed have impact on other cognitive processes, perhaps an obviously important process such as memory.

In sum, we found that cultural differences diverge with age, these cultural biases remain despite environmental biases, at least in a passive viewing case, and these biases also impact on memory such that the item we attend to less is subsequently less well remembered.

[CNS Poster 2007.pdf]

Sonic Route 44 Lemon Berry Slush

It is 77 Fahrenheit. It is hot. It is sunny. It is Spring. You haven't seen the sun in months at this intensity. Your tongue is dry. Your throat is dry. You are driving. Where do you go? What do you do about your life problems?

YOU GO GET A ROUTE 44 LEMON BERRY SLUSH FROM THE SONIC ON NEIL ST, THAT'S WHAT YOU DO!!!!! DO IT!!!

Courier Breakfast

Ahhh, the smell of pancakes, coffee, omelettes, and bacon in the morning. And to have it in an old fashion place that seems to have some sense of history soaked into its seats. This is a winner here in terms of identity and character. Home-grown, no franchise, Champaign-Urbana place to eat. Breakfasts are great. I had the steak and omelette, there's other great stuff of course!

Check out the movie here [movie].

Check their website out too:
http://www.couriersilvercreek.com/couriercafe/

Texas Roadhouse, Champaign, IL

Standard Texas steak dinner here. They throw their peanut shells on the floor. Quite a busy place, very popular. Food is not bad. Not gourmet, but think of it as upper-class comfort meat food place. What was fun though, was the peanut shells and the noisy crowd. And they celebrate birthdays there by making the birthday person sit on a horse saddle, and yell out their name, and shout "Yee Ha!" They also do this quirky looking dance. Oh, and although they are Texas Roadhouse, they originated in Indiana. Check out the movie here [movie].

Crash!

It happened again! This is the second time I have witness a truck crashing into the train bridge across Springfield Ave. The first time was when we were walking along Springfield on the way home. And then, BAM! This truck's container hits the bridge because it was to low. That truck ended up stuck underneath because it was going fast enough so that the momentum got it through a little under the bridge. But then it was unable to move forward or backward anymore.

This one happened before we got there. But again, we were walking to work when we say this truck there. When will they ever learn? Is the signage of the bridge height inaccurate? Do truck drivers not know the height of their trucks? Do truck drivers not believe in the laws of physics? Are train bridges invisible to truck drivers? Is there a gravitational singularity in the Springfield train bridge that draws large bodies such as trucks to itself uncontrollably?

Stay tuned next time, when we find out the answers to...The Mystery of the Crashing Trucks

SPRING 2007!

It took a while lah. At first the weather turn hot, then it suddenly snow again. But now it look like it is here to stay lor. The flower all come out again. This shot is of a tree outside my apartment. The flower bloom white one. Quite the very impressive lah. More thing happening now.

Feedback about recent heated Intelligent Design debate

Here are some recent articles in CNN about the science and intelligent design debate. The first article [download] considers a scientists reasons for why he believes in God as a scientist. The second article [download] talks about the possibility that religion is simply a matter of evolutionary necessity.

Recently, this author has heard about some incidences which reflected a bias of non-religious scientists who think that religious people do not consider what the evidence is suggesting. This comment arose out of a scientific discussion on how our personal beliefs do affect the way we interpret objective data.

I think I will have to comment on this as I feel that the discussion has a very crucial point, and the remark made by non-religious scientists may not be a fair one. Firstly, I do not think that the discussion point was wrong. In fact, I agree with it. Beliefs most certainly bias our interpretation of the world, and of reality. In fact, that is fundamentally what belief is. It is attributing meaning and cause to what we see around us. In this sense, the idea that belief is a psychological state innate in human beings (since we do not seem to see animals that have beliefs) out of evolutionary necessity. One theory is that if we do not have something to believe in, human beings would not function, we would in fact go crazy. Thus, to resolve this state, we developed religion.

This might be true, it might not. Scientifically, we cannot prove that it does not exist. No science can prove that anything does not exist. I think scientists have to conceed to this. This author is a scientist too, and I think there is no reasonable argument to suggest that science can ever get past this problem of proving non-existence, at least with current empirical methods. Similarly, science cannot prove the non-existence of God.

But back to religion as an evolutionary outcome. If in fact this is true, it says nothing about whether God is real. Just because we think our ideas of God are a result of our neurons firing, which are a result of our DNA "directing" our neurons to wire in a certain way, that results in this "feeling" or state of thinking there is a God, these do not have bearing on whether God exists or not. If God exists, he exists whether I think he does or not, he exists whether my thoughts about his existence arise out of a reflection of truth or if they arise due to pure chance.

That being said, religious people, specifically Christians, do not necessarily disagree with the existence of evolution. In theory, God could implement evolution as his way things should work? Is it not also a theory that he did not? What I mean is, these are theories, not facts. And science has yet to show that it can prove that evolution = no God.

So, in sum, we all belief something. For the non-religious scientist, it is simply that they believe that all they can observe has no intelligent cause. For the religious scientist, we also need to look at the objective evidence that there is intelligent cause for everything we see. No one is spared this burden. And surely, which side we are on, will bias the way we see thing. The point is not to say the other side believes what they do because they are not objective. The point is to recognize how we ourselves are biased, and how others might have different biases, and consider the data together.

If God exists, then the data will show it, if indeed this method can show it. If he does not, then the data will show it too, if this method permits, however, we know that this method cannot show that something does not exist. So perhaps we should be thinking if there is ever any way to show that something does not exist?

Binding and Bandwidth

This is an idea about what might happen if different types of information were attended to. Consider this thought experiment:

There is an item A, and another item B. A and B both contain sub-features A1...An, B1...Bn. When we attend to A or B, we are in fact binding A1...An, and/or B1...Bn, to represent A, B.

Now, we have limited bandwidth. Which means, we can only process a limited amount of information at any one time. Consider for the moment that we can only process 4 bits of information. So, if we attend to A, we only process A1-A4, and if we process B, we process B1-B4. We could, by way of divided attention, process A1,A2,B1,B4. Assuming that there is minimal cost in having to dissociate between two different groupings of features (which is rarely the case, but lets just assume that this is possible for argument's sake). This also means, we do not process the other information about the other features that are present.

Now, consider another type of processing, or rather, another level. If in fact we process something called A-B. That is, we bring the binding function up from the item level of A and B, to a higher representation that binds both A-B. What would this result in terms of the amount of information we can process at a time?

This is now only 1 bit of information. We would have more capacity left over (3 bits) from our initial 4 bits. Furthermore, within the 1 bit, we might be able to reinstate the original A1-A4, and B1-B4 via past experience. However, we will suffer from interference in this case, since we did not explicitly process A1-A4 or B1-B4, but rather A-B. Thus, there should be a cost of attending to this higher level at the expense of the lower levels. Likewise, there is a cost of attending to the lower levels at the expense of the higher levels. This is also known in the literature as chunking.

Thus, in summary is that the level of binding should be inversely related to the bandwidth, or the amount of information we can process at any one time.