Non-Gaussian Discriminative Factor Models via the Max-Margin Rank-Likelihood

We consider the problem of discriminative factor analysis for data that are in general non-Gaussian. A Bayesian model based on the ranks of the data is proposed. We first introduce a new {\em max-margin} version of the rank-likelihood. A discriminative factor model is then developed, integrating the max-margin rank-likelihood and (linear) Bayesian support vector machines, which are also built on the max-margin principle. The discriminative factor model is further extended to the {\em nonlinear} case through mixtures of local linear classifiers, via Dirichlet processes. Fully local conjugacy of the model yields efficient inference with both Markov Chain Monte Carlo and variational Bayes approaches. Extensive experiments on benchmark and real data demonstrate superior performance of the proposed model and its potential for applications in computational biology.Comment: 14 pages, 7 figures, ICML 201

Identification of functionally related enzymes by learning-to-rank methods

Enzyme sequences and structures are routinely used in the biological sciences as queries to search for functionally related enzymes in online databases. To this end, one usually departs from some notion of similarity, comparing two enzymes by looking for correspondences in their sequences, structures or surfaces. For a given query, the search operation results in a ranking of the enzymes in the database, from very similar to dissimilar enzymes, while information about the biological function of annotated database enzymes is ignored. In this work we show that rankings of that kind can be substantially improved by applying kernel-based learning algorithms. This approach enables the detection of statistical dependencies between similarities of the active cleft and the biological function of annotated enzymes. This is in contrast to search-based approaches, which do not take annotated training data into account. Similarity measures based on the active cleft are known to outperform sequence-based or structure-based measures under certain conditions. We consider the Enzyme Commission (EC) classification hierarchy for obtaining annotated enzymes during the training phase. The results of a set of sizeable experiments indicate a consistent and significant improvement for a set of similarity measures that exploit information about small cavities in the surface of enzymes

Statistical Physics and Representations in Real and Artificial Neural Networks

This document presents the material of two lectures on statistical physics and neural representations, delivered by one of us (R.M.) at the Fundamental Problems in Statistical Physics XIV summer school in July 2017. In a first part, we consider the neural representations of space (maps) in the hippocampus. We introduce an extension of the Hopfield model, able to store multiple spatial maps as continuous, finite-dimensional attractors. The phase diagram and dynamical properties of the model are analyzed. We then show how spatial representations can be dynamically decoded using an effective Ising model capturing the correlation structure in the neural data, and compare applications to data obtained from hippocampal multi-electrode recordings and by (sub)sampling our attractor model. In a second part, we focus on the problem of learning data representations in machine learning, in particular with artificial neural networks. We start by introducing data representations through some illustrations. We then analyze two important algorithms, Principal Component Analysis and Restricted Boltzmann Machines, with tools from statistical physics