Side-chain prediction is an important subtask in the protein-folding problem. We show that finding a minimal energy side-chain configuration is equivalent to performing inference in an undirected graphical model. The graphical model is relatively sparse yet has many cycles. We used this equivalence to assess the performance of approximate inference algorithms in a real-world setting. Specifically we compared belief propagation (BP), generalized BP (GBP) and naive mean field (MF).

How do cortical neurons represent the acoustic environment? This question is often addressed by probing with simple stimuli such as clicks or tone pips. Such stimuli have the advantage of yielding easily interpreted answers, but have the disadvantage that they may fail to uncover complex or higher-order neuronal response properties. Here we adopt an alternative approach, probing neuronal responses with complex acoustic stimuli, including animal vocalizations and music. We have used in vivo whole cell methods in the rat auditory cortex to record subthreshold membrane potential fluctuations elicited by these stimuli.

A key challenge for neural modeling is to explain how a continuous stream of multi-modal input from a rapidly changing environment can be processed by stereotypical recurrent circuits of integrate-and-fire neurons in real-time. We propose a new computational model that is based on principles of high dimensional dynamical systems in combination with statistical learning theory. It can be implemented on generic evolved or found recurrent circuitry.

We develop and test new machine learning methods for the prediction of topological representations of protein structures in the form of coarse-or fine-grained contact or distance maps that are translation and rotation invariant. The methods are based on generalized input-output hidden Markov models (GIOHMMs) and generalized recursive neural networks (GRNNs). The methods are used to predict topology directly in the fine-grained case and, in the coarsegrained case, indirectly by first learning how to score candidate graphs and then using the scoring function to search the space of possible configurations. Computer simulations show that the predictors achieve state-of-the-art performance.

Side-chain prediction is an important subtask in the protein-folding problem. We show that finding a minimal energy side-chain configuration is equivalent to performing inference in an undirected graphical model. The graphical model is relatively sparse yet has many cycles. We used this equivalence to assess the performance of approximate inference algorithms in a real-world setting. Specifically we compared belief propagation (BP), generalized BP (GBP) and naive mean field (MF).

We consider the hypothesis that systems learning aspects of visual perception may benefit from the use of suitably designed developmental progressions during training. Four models were trained to estimate motion velocities in sequences of visual images. Three of the models were "developmental models" in the sense that the nature of their input changed during the course of training. They received a relatively impoverished visual input early in training, and the quality of this input improved as training progressed. One model used a coarse-to-multiscale developmental progression (i.e. it received coarse-scale motion features early in training and finer-scale features were added to its input as training progressed), another model used a fine-to-multiscale progression, and the third model used a random progression.

We present a method to distinguish direct connections between two neurons from common input originating from other, unmeasured neurons. The distinction is computed from the spike times of the two neurons in response to a white noise stimulus. Although the method is based on a highly idealized linear-nonlinear approximation of neural response, we demonstrate via simulation that the approach can work with a more realistic, integrate-and-fire neuron model. We propose that the approach exemplified by this analysis may yield viable tools for reconstructing stimulus-driven neural networks from data gathered in neurophysiology experiments.

Well-known applications include part-of-speech (POS) tagging, named entity classification, information extraction, text segmentation and phoneme classification in text and speech processing [7] as well as problems like protein homology detection, secondary structure prediction or gene classification in computational biology [3]. Up to now, the predominant formalism for modeling and predicting label sequences has been based on Hidden Markov Models (HMMs) and variations thereof. Yet, despite its success, generative probabilistic models - of which HMMs are a special case - have two major shortcomings, which this paper is not the first one to point out. First, generative probabilistic models are typically trained using maximum likelihood estimation (MLE) for a joint sampling model of observation and label sequences. As has been emphasized frequently, MLE based on the joint probability model is inherently non-discriminative and thus may lead to suboptimal prediction accuracy. Secondly, efficient inference and learning in this setting often requires to make questionable conditional independence assumptions.

We present a new method for learning good strategies in zero-sum Markov games in which each side is composed of multiple agents collaborating against an opposing team of agents. Our method requires full observability and communication during learning, but the learned policies can be executed in a distributed manner. The value function is represented as a factored linear architecture and its structure determines the necessary computational resources and communication bandwidth. This approach permits a tradeoff between simple representations with little or no communication between agents and complex, computationally intensive representations with extensive coordination between agents. Thus, we provide a principled means of using approximation to combat the exponential blowup in the joint action space of the participants. The approach is demonstrated with an example that shows the efficiency gains over naive enumeration.

A neurotrophic model for the co-development of topography and ocular dominance columns in the primary visual cortex has recently been proposed. In the present work, we test this model by driving it with the output of a pair of neuronal vision sensors stimulated by disparate moving patterns. We show that the temporal correlations in the spike trains generated by the two sensors elicit the development of refined topography and ocular dominance columns, even in the presence of significant amounts of spontaneous activity and fixed-pattern noise in the sensors.