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.

Behavioral goals are achieved reliably and repeatedly with movements rarely reproducible in their detail. Here we offer an explanation: we show that not only are variability and goal achievement compatible, but indeed that allowing variability in redundant dimensions is the optimal control strategy in the face of uncertainty. The optimal feedback control laws for typical motor tasks obey a "minimal intervention" principle: deviations from the average trajectory are only corrected when they interfere with the task goals. The resulting behavior exhibits task-constrained variability, as well as synergetic coupling among actuators--which is another unexplained empirical phenomenon.

The focus of the paper is the problem of learning kernel operators from empirical data. We cast the kernel design problem as the construction of an accurate kernel from simple (and less accurate) base kernels. We use the boosting paradigm to perform the kernel construction process. To do so, we modify the booster so as to accommodate kernel operators. We also devise an efficient weak-learner for simple kernels that is based on generalized eigen vector decomposition. We demonstrate the effectiveness of our approach on synthetic data and on the USPS dataset. On the USPS dataset, the performance of the Perceptron algorithm with learned kernels is systematically better than a fixed RBF kernel.

We introduce the notion of Morton-style factorial coding and illustrate how it may help understand information integration and perceptual coding in the brain. We show that by focusing on average responses one may miss the existence of factorial coding mechanisms that become only apparent when analyzing spike count histograms. We show evidence suggesting that the classical/nonclassical receptive field organization in the cortex effectively enforces the development of Morton-style factorial codes. This may provide some cues to help understand perceptual coding in the brain and to develop new unsupervised learning algorithms. While methods like ICA (Bell & Sejnowski, 1997) develop independent codes, in Morton-style coding the goal is to make two or more external aspects of the world become independent when conditioning on internal representations.

We propose analysis of information in speech using three sources - language (phone), speaker and channeL Information in speech is measured as mutual information between the source and the set of features extracted from speech signaL We assume that distribution of features can be modeled using Gaussian distribution. The mutual information is computed using the results of analysis of variability in speech. We observe similarity in the results of phone variability and phone information, and show that the results of the proposed analysis have more meaningful interpretations than the analysis of variability. 1 Introduction Speech signal carries information about the linguistic message, the speaker, the communication channeL In the previous work [1, 2], we proposed analysis of information in speech as analysis of variability in a set of features extracted from the speech signal. The variability was measured as covariance of the features, and analysis was performed using using multivariate analysis of variance (MANOVA). Total variability was divided into three types of variabilities, namely, intra-phone (or phone) variability, speaker variability, and channel variability.

In these types of synapses, the short-term dynamics of the synaptic efficacies are governed by the relative timing of the pre-and post-synaptic spikes, while on long time scales the efficacies tend asymptotically to either a potentiated state or to a depressed one. We fabricated a prototype VLSI chip containing a network of integrate and fire neurons interconnected via bistable STDP synapses. Test results from this chip demonstrate the synapse's STDP learning properties, and its long-term bistable characteristics.

We consider loopy belief propagation for approximate inference in probabilistic graphical models. A limitation of the standard algorithm is that clique marginals are computed as if there were no loops in the graph. To overcome this limitation, we introduce fractional belief propagation. Fractional belief propagation is formulated in terms of a family of approximate free energies, which includes the Bethe free energy and the naive mean-field free as special cases. Using the linear response correction of the clique marginals, the scale parameters can be tuned. Simulation results illustrate the potential merits of the approach.

Monaural speech separation has been studied in previous systems that incorporate auditory scene analysis principles. A major problem for these systems is their inability to deal with speech in the highfrequency range. Psychoacoustic evidence suggests that different perceptual mechanisms are involved in handling resolved and unresolved harmonics. Motivated by this, we propose a model for monaural separation that deals with low-frequency and highfrequency signals differently. For resolved harmonics, our model generates segments based on temporal continuity and cross-channel correlation, and groups them according to periodicity. For unresolved harmonics, the model generates segments based on amplitude modulation (AM) in addition to temporal continuity and groups them according to AM repetition rates derived from sinusoidal modeling. Underlying the separation process is a pitch contour obtained according to psychoacoustic constraints. Our model is systematically evaluated, and it yields substantially better performance than previous systems, especially in the high-frequency range.

We present the bump mixture model, a statistical model for analog data where the probabilistic semantics, inference, and learning rules derive from low-level transistor behavior. The bump mixture model relies on translinear circuits to perform probabilistic inference, and floating-gate devices to perform adaptation. This system is low power, asynchronous, and fully parallel, and supports various on-chip learning algorithms. In addition, the mixture model can perform several tasks such as probability estimation, vector quantization, classification, and clustering. We tested a fabricated system on clustering, quantization, and classification of handwritten digits and show performance comparable to the EM algorithm on mixtures of Gaussians.

Using a Markov chain perspective of spectral clustering we present an algorithm to automatically find the number of stable clusters in a dataset. The Markov chain's behaviour is characterized by the spectral properties of the matrix of transition probabilities, from which we derive eigenflows along with their halflives. An eigenflow describes the flow of probability mass due to the Markov chain, and it is characterized by its eigenvalue, or equivalently, by the halflife of its decay as the Markov chain is iterated. A ideal stable cluster is one with zero eigenflow and infinite half-life. The key insight in this paper is that bottlenecks between weakly coupled clusters can be identified by computing the sensitivity of the eigenflow's halflife to variations in the edge weights.