One big recent piece of news from across the Atlantic is that the European Commission is funding a brain simulation project to the tune of a billion Euros. Roughly, the objective is to simulate the entire human brain using a supercomputer. Needless to say, many people are skeptical and there are lots of reasons that one might think this project is unlikely to yield useful results. One criticism centers on whether even a supercomputer can simulate the complexity of the brain. A first step towards simulating a brain is thinking about how many FLOP/s (floating point operations per second) would be necessary to implement similar functionality in conventional computer hardware. Here I will discuss two back-of-the-envelope estimates of this computational capacity. (Don’t take these too seriously, they’re a little crazy and just shooting for orders of magnitude.)
Continue reading “What is the Computational Capacity of the Brain?”
There are several topics I would like to talk about in the future posts, and they generally fall under the category of theoretical (or systems) neuroscience, and sometimes more broadly biological physics. The topics to be discussed include: the problem of invariance in theoretical neuroscience, Schrodinger’s take on physics of living matter and other modern thoughts on fundamental principles underlying biology (optimality principle, role of noise, etc), dynamics and computation: are they mutually exclusive concepts?, correlations (correlations in statistical physics, and the role of correlation in an ensemble of neurons), reinforcement learning, and more. I will start with the post on invariance.
Continue reading “Introductory post, and the invariance problem”
In my previous post I suggested that models of neural computation can be expressed as prior distributions over functional and effective connectivity, and with this common specification we can compare models by their posterior probability given neural recordings. I would like to explore this idea in more detail by first describing functional and effective connectivity and then considering how various models could be expressed in this framework.
Functional and effective connectivity are concepts originating in neuroimaging and spike train analysis. Functional connectivity measures the correlation between neurophysiological events (e.g. spikes on neurons or BOLD signal in fMRI voxels), whereas effective connectivity is a statement about the causal nature of a system. Effective connectivity captures the influence one neurophysiological event has upon another, either directly via a synapse, or indirectly via a polysynaptic pathway or a parallel connection. In my usage, effective connectivity may include deterministic as well as stochastic relationships. Both concepts are in contrast to structural connectivity which captures the physical synapses or fiber tracts within the brain. Of course these concepts are interrelated: functional and effective connectivity are ultimately mediated by structural connectivity, and causal effective connections imply correlational functional connections.
Continue reading “Priors for Functional and Effective Connectivity”
One basic aim of cognitive neuroscience is to answer questions like 1) what does a neuron or a group of neurons represent, and 2) how is cognitive computation implemented in neuronal hardware? A common critique is that the field has simply failed to shed light on either of these questions. Our experimental techniques are perhaps too crude: fMRI’s temporal resolution is way too slow, EEG and MEG’s spatial resolution is far too coarse, electrode recordings miss the forest for the trees. But underlying these criticisms is the assumption that there is some implementation-level description of neural activity that is interpretable at the level of cognition: if only we recorded from a sufficient number of neurons and actually knew what the underlying connectivity looked like, then we could finally figure out what neurons are doing, and what they represent — whether it’s features, or population codes, or prediction error, or whatever.
Is this a reasonable thing to hope for? Should neurons be interpretable at all? Clearly, no, Marr Level-1-ophiles will argue. After all, you wouldn’t hope to learn how a computer works by watching its bits flip, right?
Continue reading “Should neurons be interpretable?”
My aim in this introductory post is to provide context for future contributions by sharing my thoughts on the role of computer scientists in the study of brain, particularly in the field of computational neuroscience. For a field with “computation” in the name, it seems that computer scientists are underrepresented. I believe there are significant open questions in neuroscience which are best addressed by those who study the theory of computation, learning, and algorithms, and the systems upon which they are premised.
In my opinion “computational neuroscience” has two definitions: the first, from Marr, is the study of the computational capabilities of the brain, their algorithmic details, and their implementation in neural circuits; the second, stemming from machine learning, is the design and application of computational algorithms, either to solve problems in a biologically-inspired manner, or to aid in the processing and interpretation of neural data. Though quite different, I believe these are complementary and arguably co-dependent endeavors. The forward hypothesis generation advocated by the former seems unlikely to get the details right without the aid of computational and statistical tools for extracting patterns from neural recordings, guiding hypothesis generation, and comparing the evidence for competing models. Likewise, attempts to infer the fundamentals of neural computation from the bottom-up without strong inductive biases appear doomed to wander the vastness of the hypothesis space. How then, can computer scientists contribute to both aspects of computational neuroscience? Continue reading “The “Computation” in Computational Neuroscience”
Last week I attended the NIPS 2012 workshop on Connectomics: Opportunities and Challenges for Machine Learning, organized by Viren Jain and Moritz Helmstaedter. Connectomics is an emerging field that aims to map the neural wiring diagram of the brain. The current bottleneck to progress is analyzing the incredibly large (terabyte-petabyte range) data sets of 3d images obtained via electron microscopy. The analysis of the images entails tracing the neurons across images and eventually inferring synaptic connections based on physical proximity and other visual cues. One approach is manual tracing: at the workshop I learned that well over one million dollars has already been spent hiring manual tracers, resulting in data that is useful but many orders of magnitude short of even a very small brain.
The NIPS workshop was about using machine learning to speed up the process, and it consisted of talks, posters, and discussion. A previous workshop on this subject had a different flavor: it was a challenge workshop at ISBI 2012 (a similar idea to the Netflix challenge). To enter the challenge, anyone could download the training set and upload their results on the test data, which were then evaluated before the workshop (results here). At the NIPS workshop, the ISBI challenge was mentioned frequently, and scoring well on it seemed to be an important source credibility. Such a challenge can have a profound impact on the field, but is it a positive impact? Continue reading “Healthy Competition?”