Computer Science in Neuroscience

I got a job basically through a fellowship which wanted to bring in graduates in Computer Science to look at biological problems. For the past 9 months I have been looking at brain image data especially Diffusion Tensor Data trying to do basic processing and also applying classification methods and developing segmentation methods with several collaborators. Because of the channel I was hired through and because of the circle I am spending my working (and social) hours I can clearly see how Neuroscience (and biology in general) can drastically benefit from CS wisdom. It's an intriguing thing that our quest for machines laid the foundation to understand their language which in turn gave a fresh perspective for the foundation of modern science that in turn can help define our understanding of life.

CS wisdom can affect research pace in neuroscience on many many different levels. Just by applying software engineering skills you can grease a lot of processing. Machine learning/data mining/Artificial Intelligence methods can obviously help making sense of the biological sensor data. CS wisdom can help apply blackbox type research style to start making progress. This wisdom is almost always the fundamental tool in complexity theory: we need to start somewhere for the general problem setting and then dig deeper to exploit specific instances of problems as needed. One thing I noticed is that lack of such perspective can hold back lot of progress. Also another wisdom you can get from CS scientists like Umesh Vazirani is to focus on higher order bits. Well as I mentioned in my previous post building bridges for wisdom between CS and Neuroscience is allowing me some good times.

Building bridges

We all want to work in a way we like and these likes evolve over time based on amount of success (positive feedback) one has in it. Typically in an academic career path one has to build either a combination of consulting + research or teaching + research. Teaching + research is a bit harder path and typically requires shiny background like top schools top thesis etc. Consulting + research is more viable for average PhDs (like mine) and not so ivory background. Good thing is transitioning between the two is possible thanks to interdisciplinary and more importantly applied research. It's always nicer to be able to communicate between seemingly unrelated groups of research as it can save lots of redundant efforts. Having strong bridges between spheres of our knowledge makes the knowledge base only stronger. There is lot of opportunity currently in building bridges in research which in my opinion is another crowning impact of Computer Science in terms of actual machines, software and most importantly complexity theory.

Streaks of thought: Streak 26

A while ago I had a post on human rights and money. The point kind of was that our progress can be measured by our affordability of human rights. Well why do we call that progress? It's because it gives more chances to people to spring back from honest mistakes. There might be some abusers of the progress but usually those can be caught. This is because giving second chances to people is inherently rooted in wanting second chances for oneself! It all has to do with estimating empathy in lives. I have been procrastinating to write a post about it. Hopefully I will finish it sometime this year!

Animal analysis

For past two nights I was watching Animal Planet before going to bed (to avoid repeats on CNN). One night I saw "Monsters Inside Me" which showed the dangers of parasites lurking around us. The wilder the environment gets the more danger we run into. The show reminded how our "civilization (= rights + responsibilities)" process was not just for sympathy, empathy in the high-functioning sense but essentially a Darwinian process. We had to cluster around to separate other killers and the purpose of clustering is defeated without civilization because we would kill among ourselves. We still do but we came a long way.

Yesterday I watched "Killing for Living" which showed how in many species many babies are born-murderers and kill their siblings and in some cases parents kill their children etc. for food. Males kill each other and get killed by females for mating etc. The show said "Just because you are their kind doesn't mean they won't kill you!" One particular instance was striking: Typically stags fight almost to death for mating with female deers but one specific sub-species just have an "abstract fight" where they decide who the winner is without touching each other just by making abstract fight moves!! That is an instance of using brain more than bran! We probably evolved from such sub-species of apes who loved being alive more than sex and reproduction! This probably was the first instance of questioning the instincts! Of course now questioning is one of the seed pillars of our civilization!

Sometimes when things in our high-functioning world relationships (both professional and personal) are frustrating such animal knowledge can give good perspectives on how better off we are in the race of evolution. Killings in today's societies are still very marginal (except for extreme cases like Darfur etc. where the population is still behind in civilization) and most of us get food and get to mate without getting killed!!

Streaks of thought: Streak 25

CNN is a great way to get political news! Being liberal I tried MSNBC and did not like the certainty pitch. I didn't even bother to try Fox not for their rightwingness but because I assumed their certainty! I like CNN's certainty in uncertainty. Watching news gives me some nice streaks for my blog: American democracy is strong because it has strong middle class. But what does it take for a society to have a strong middle class. As a gross oversimplification I had a streak saying that we need people with balls. Then a strong sense of entitlement and a pinch of empathy (added with lot of perspiration to enforce, of course) can produce both world class rich people and constantly strong middle class!

Vacation by choice

August 2009 has been a great month in many aspects which kind of means lesser posts on my blog as well. More or less after graduating it's been harder to wander in meta space of analyzing life since I am actually living the life!

For the first time in my life every I had a vacation by choice/ Although I managed to sneak in a few hours of meetings this has been a great vacation with my friend Amy! I have taken time off from work a few times before but it's mostly been very situational and for others and not really by choice for the vacation sake! After a wonderful weekend trip to Niagara falls (trying hard not to get trapped on the Canadian side) we spent the week just in the wonder of taking a vacation!

In creating value I realized the concept of affording (not just financially) vacation is a good indicator of measuring the success! Even religions also encourage this idea by concepts like keeping sabbath etc. It's just probably trivial to acknowledge that relaxing for relaxing sake is a good idea to being balanced ensuring long-term productivity. But actually experiencing that is not so trivial experience especially for someone growing up in a lower middle class in a third world country. The fact that such experiences are possible is a good way to keep human efforts for progress stimulated!

Affording half-knowledge

I wanted to write this post in late September 2007 when I was still figuring out how to create enough value for my work in computer vision and robotics that would be worth an average PhD from CIS department at Temple University. Growing up in a country not only with low resource/population ratio and system's quite immature (relative to US standards: look we need some standards and I prefer US standards!) it was a common thing to hear "Half-knowledge is dangerous". Such perspectives are so deeply rooted in the culture that risk taking is almost impossible (probabilistically people who take risk is roughly 0.000001=1/Million).

Risk for potential embarrassment and failure is a necessity for growth! This assumption was revived after watch season 1.4 of The Universe which inspired me to finish this post. One episode on "Beyond Big Bang" was really appealing as it showed the journey of humans' theorizing about the universe. History channel put together these events nicely in perspective of how the current established theory (still of course incomplete) about universe is an outcome of so many attempts which were either only partially correct or wrong. So essentially we all survived through "half-knowledge" phases and still do not have complete knowledge about anything. There are dangers in having half-knowledge but this is a necessary transitional stage to attaining full-knowledge as it is continuous process. So it always essential to be able to afford half-knowledge.

To afford half-knowledge we need to create value which is a very important part of the survival business. Creating value obviously needs forward filtering and backward smoothing by developing models, gathering observations and evaluating them by communicating with the rest of the human community. The key point I want to make though is that we need to start with some model, some proposal distribution, some importance weighting scheme so that we can eventually get it right. The point is there's is no point in waiting for ever to get it all right since that would mean not being able to afford half-knowledge. Scientists or systems that can afford half-knowledge are analogous "bullet-swallowers" unlike "bullet-dodgers". So questions like: When are you ready to graduate? When is a romantic relationship good enough for marriage? How much money do I need to open a company? When do you sell a product? etc. all can be answered only if we can "swallow" and create value to be able to afford half-knowledge.