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Remi Monasson

Publications and source records attributed to Remi Monasson.

At least 19 recordsLinked to original sources

Disentangling representations in Restricted Boltzmann Machines without adversaries

A goal of unsupervised machine learning is to build representations of complex high-dimensional data, with simple relations to their properties. Such disentangled representations make easier to interpret the significant latent factors of variation in the data, as well as to generate new data with desirable features. Methods for disentangling representations often rely on an adversarial scheme, in which representations are tuned to avoid discriminators from being able to reconstruct information about the data properties (labels). Unfortunately adversarial training is generally difficult to implement in practice. Here we propose a simple, effective way of disentangling representations without any need to train adversarial discriminators, and apply our approach to Restricted Boltzmann Machines (RBM), one of the simplest representation-based generative models. Our approach relies on the introduction of adequate constraints on the weights during training, which allows us to concentrate information about labels on a small subset of latent variables. The effectiveness of the approach is illustrated with four examples: the CelebA dataset of facial images, the two-dimensional Ising model, the MNIST dataset of handwritten digits, and the taxonomy of protein families. In addition, we show how our framework allows for analytically computing the cost, in terms of log-likelihood of the data, associated to the disentanglement of their representations.

cs.LG

Inferring epistasis from genomic data with comparable mutation and outcrossing rate

We consider a population evolving due to mutation, selection and recombination, where selection includes single-locus terms (additive fitness) and two-loci terms (pairwise epistatic fitness). We further consider the problem of inferring fitness in the evolutionary dynamics from one or several snap-shots of the distribution of genotypes in the population. In the recent literature this has been done by applying the Quasi-Linkage Equilibrium (QLE) regime first obtained by Kimura in the limit of high recombination. Here we show that the approach also works in the interesting regime where the effects of mutations are comparable to or larger than recombination. This leads to a modified main epistatic fitness inference formula where the rates of mutation and recombination occur together. We also derive this formula using by a previously developed Gaussian closure that formally remains valid when recombination is absent. The findings are validated through numerical simulations.

q-bio.PE

On the Spectrum of Multi-Space Euclidean Random Matrices

We consider the additive superimposition of an extensive number of independent Euclidean Random Matrices in the high-density regime. The resolvent is computed with techniques from free probability theory, as well as with the replica method of statistical physics of disordered systems. Results for the spectrum and eigenmodes are shown for a few applications relevant to computational neuroscience, and are corroborated by numerical simulations.

cond-mat.dis-nn

Inference of compressed Potts graphical models

We consider the problem of inferring a graphical Potts model on a population of variables, with a non-uniform number of Potts colors (symbols) across variables. This inverse Potts problem generally involves the inference of a large number of parameters, often larger than the number of available data, and, hence, requires the introduction of regularization. We study here a double regularization scheme, in which the number of colors available to each variable is reduced, and interaction networks are made sparse. To achieve this color compression scheme, only Potts states with large empirical frequency (exceeding some threshold) are explicitly modeled on each site, while the others are grouped into a single state. We benchmark the performances of this mixed regularization approach, with two inference algorithms, the Adaptive Cluster Expansion (ACE) and the PseudoLikelihood Maximization (PLM) on synthetic data obtained by sampling disordered Potts models on an Erdos-Renyi random graphs. We show in particular that color compression does not affect the quality of reconstruction of the parameters corresponding to high-frequency symbols, while drastically reducing the number of the other parameters and thus the computational time. Our procedure is also applied to multi-sequence alignments of protein families, with similar results.

cond-mat.stat-mech

'Place-cell' emergence and learning of invariant data with restricted Boltzmann machines: breaking and dynamical restoration of continuous symmetries in the weight space

Distributions of data or sensory stimuli often enjoy underlying invariances. How and to what extent those symmetries are captured by unsupervised learning methods is a relevant question in machine learning and in computational neuroscience. We study here, through a combination of numerical and analytical tools, the learning dynamics of Restricted Boltzmann Machines (RBM), a neural network paradigm for representation learning. As learning proceeds from a random configuration of the network weights, we show the existence of, and characterize a symmetry-breaking phenomenon, in which the latent variables acquire receptive fields focusing on limited parts of the invariant manifold supporting the data. The symmetry is restored at large learning times through the diffusion of the receptive field over the invariant manifold; hence, the RBM effectively spans a continuous attractor in the space of network weights. This symmetry-breaking phenomenon takes place only if the amount of data available for training exceeds some critical value, depending on the network size and the intensity of symmetry-induced correlations in the data; below this 'retarded-learning' threshold, the network weights are essentially noisy and overfit the data.

cond-mat.dis-nn

Adaptation of olfactory receptor abundances for efficient coding

Olfactory receptor usage is highly heterogeneous, with some receptor types being orders of magnitude more abundant than others. We propose an explanation for this striking fact: the receptor distribution is tuned to maximally represent information about the olfactory environment in a regime of efficient coding that is sensitive to the global context of correlated sensor responses. This model predicts that in mammals, where olfactory sensory neurons are replaced regularly, receptor abundances should continuously adapt to odor statistics. Experimentally, increased exposure to odorants leads variously, but reproducibly, to increased, decreased, or unchanged abundances of different activated receptors. We demonstrate that this diversity of effects is required for efficient coding when sensors are broadly correlated, and provide an algorithm for predicting which olfactory receptors should increase or decrease in abundance following specific environmental changes. Finally, we give simple dynamical rules for neural birth and death processes that might underlie this adaptation.

q-bio.NC

Innovation rather than improvement: a solvable high-dimensional model highlights the limitations of scalar fitness

Much of our understanding of ecological and evolutionary mechanisms derives from analysis of low-dimensional models: with few interacting species, or few axes defining "fitness". It is not always clear to what extent the intuition derived from low-dimensional models applies to the complex, high-dimensional reality. For instance, most naturally occurring microbial communities are strikingly diverse, harboring a large number of coexisting species, each of which contributes to shaping the environment of others. Understanding the eco-evolutionary interplay in these systems is an important challenge, and an exciting new domain for statistical physics. Recent work identified a promising new platform for investigating highly diverse ecosystems, based on the classic resource competition model of MacArthur. Here, we describe how the same analytical framework can be used to study evolutionary questions. Our analysis illustrates how, at high dimension, the intuition promoted by a one-dimensional (scalar) notion of fitness can become misleading. Specifically, while the low-dimensional picture emphasizes organism cost or efficiency, we exhibit a regime where cost becomes irrelevant for survival, and link this observation to generic properties of high-dimensional geometry.

q-bio.PE

Inverse Statistical Physics of Protein Sequences: A Key Issues Review

In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques, sequence data accumulate at unprecedented pace. This provides large sets of so-called homologous, i.e.~evolutionarily related protein sequences, to which methods of inverse statistical physics can be applied. Using sequence data as the basis for the inference of Boltzmann distributions from samples of microscopic configurations or observables, it is possible to extract information about evolutionary constraints and thus protein function and structure. Here we give an overview over some biologically important questions, and how statistical-mechanics inspired modeling approaches can help to answer them. Finally, we discuss some open questions, which we expect to be addressed over the next years.

q-bio.BM

A collective phase in resource competition in a highly diverse ecosystem

Organisms shape their own environment, which in turn affects their survival. This feedback becomes especially important for communities containing a large number of species; however, few existing approaches allow studying this regime, except in simulations. Here, we use methods of statistical physics to analytically solve a classic ecological model of resource competition introduced by MacArthur in 1969. We show that the non-intuitive phenomenology of highly diverse ecosystems includes a phase where the environment constructed by the community becomes fully decoupled from the outside world.

q-bio.PE

Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction

Despite the biological importance of non-coding RNA, their structural characterization remains challenging. Making use of the rapidly growing sequence databases, we analyze nucleotide coevolution across homologous sequences via Direct-Coupling Analysis to detect nucleotide-nucleotide contacts. For a representative set of riboswitches, we show that the results of Direct-Coupling Analysis in combination with a generalized Nussinov algorithm systematically improve the results of RNA secondary structure prediction beyond traditional covariance approaches based on mutual information. Even more importantly, we show that the results of Direct-Coupling Analysis are enriched in tertiary structure contacts. By integrating these predictions into molecular modeling tools, systematically improved tertiary structure predictions can be obtained, as compared to using secondary structure information alone.

q-bio.BM

Stochastic Ratchet Mechanisms for Replacement of Proteins Bound to DNA

Experiments indicate that unbinding rates of proteins from DNA can depend on the concentration of proteins in nearby solution. Here we present a theory of multi-step replacement of DNA-bound proteins by solution-phase proteins. For four different kinetic scenarios we calculate the depen- dence of protein unbinding and replacement rates on solution protein concentration. We find (1) strong effects of progressive 'rezipping' of the solution-phase protein onto DNA sites liberated by 'unzipping' of the originally bound protein; (2) that a model in which solution-phase proteins bind non-specifically to DNA can describe experiments on exchanges between the non specific DNA- binding proteins Fis-Fis and Fis-HU; (3) that a binding specific model describes experiments on the exchange of CueR proteins on specific binding sites.

q-bio.BM

From principal component to direct coupling analysis of coevolution in proteins: Low-eigenvalue modes are needed for structure prediction

Various approaches have explored the covariation of residues in multiple-sequence alignments of homologous proteins to extract functional and structural information. Among those are principal component analysis (PCA), which identifies the most correlated groups of residues, and direct coupling analysis (DCA), a global inference method based on the maximum entropy principle, which aims at predicting residue-residue contacts. In this paper, inspired by the statistical physics of disordered systems, we introduce the Hopfield-Potts model to naturally interpolate between these two approaches. The Hopfield-Potts model allows us to identify relevant 'patterns' of residues from the knowledge of the eigenmodes and eigenvalues of the residue-residue correlation matrix. We show how the computation of such statistical patterns makes it possible to accurately predict residue-residue contacts with a much smaller number of parameters than DCA. This dimensional reduction allows us to avoid overfitting and to extract contact information from multiple-sequence alignments of reduced size. In addition, we show that low-eigenvalue correlation modes, discarded by PCA, are important to recover structural information: the corresponding patterns are highly localized, that is, they are concentrated in few sites, which we find to be in close contact in the three-dimensional protein fold.

q-bio.BM

High-Dimensional Inference with the generalized Hopfield Model: Principal Component Analysis and Corrections

We consider the problem of inferring the interactions between a set of N binary variables from the knowledge of their frequencies and pairwise correlations. The inference framework is based on the Hopfield model, a special case of the Ising model where the interaction matrix is defined through a set of patterns in the variable space, and is of rank much smaller than N. We show that Maximum Lik elihood inference is deeply related to Principal Component Analysis when the amp litude of the pattern components, xi, is negligible compared to N^1/2. Using techniques from statistical mechanics, we calculate the corrections to the patterns to the first order in xi/N^1/2. We stress that it is important to generalize the Hopfield model and include both attractive and repulsive patterns, to correctly infer networks with sparse and strong interactions. We present a simple geometrical criterion to decide how many attractive and repulsive patterns should be considered as a function of the sampling noise. We moreover discuss how many sampled configurations are required for a good inference, as a function of the system size, N and of the amplitude, xi. The inference approach is illustrated on synthetic and biological data.

cond-mat.stat-mech

Fast Inference of Interactions in Assemblies of Stochastic Integrate-and-Fire Neurons from Spike Recordings

We present two Bayesian procedures to infer the interactions and external currents in an assembly of stochastic integrate-and-fire neurons from the recording of their spiking activity. The first procedure is based on the exact calculation of the most likely time courses of the neuron membrane potentials conditioned by the recorded spikes, and is exact for a vanishing noise variance and for an instantaneous synaptic integration. The second procedure takes into account the presence of fluctuations around the most likely time courses of the potentials, and can deal with moderate noise levels. The running time of both procedures is proportional to the number S of spikes multiplied by the squared number N of neurons. The algorithms are validated on synthetic data generated by networks with known couplings and currents. We also reanalyze previously published recordings of the activity of the salamander retina (including from 32 to 40 neurons, and from 65,000 to 170,000 spikes). We study the dependence of the inferred interactions on the membrane leaking time; the differences and similarities with the classical cross-correlation analysis are discussed.

stat.ML

Theory of spike timing based neural classifiers

We study the computational capacity of a model neuron, the Tempotron, which classifies sequences of spikes by linear-threshold operations. We use statistical mechanics and extreme value theory to derive the capacity of the system in random classification tasks. In contrast to its static analog, the Perceptron, the Tempotron's solutions space consists of a large number of small clusters of weight vectors. The capacity of the system per synapse is finite in the large size limit and weakly diverges with the stimulus duration relative to the membrane and synaptic time constants.

q-bio.NC

Dynamical modelling of molecular constructions and setups for DNA unzipping

We present a dynamical model of DNA mechanical unzipping under the action of a force. The model includes the motion of the fork in the sequence-dependent landscape, the trap(s) acting on the bead(s), and the polymeric components of the molecular construction (unzipped single strands of DNA, and linkers). Different setups are considered to test the model, and the outcome of the simulations is compared to simpler dynamical models existing in the literature where polymers are assumed to be at equilibrium.

q-bio.BM

A review of the Statistical Mechanics approach to Random Optimization Problems

We review the connection between statistical mechanics and the analysis of random optimization problems, with particular emphasis on the random k-SAT problem. We discuss and characterize the different phase transitions that are met in these problems, starting from basic concepts. We also discuss how statistical mechanics methods can be used to investigate the behavior of local search and decimation based algorithms.

cs.CC

Relationship between clustering and algorithmic phase transitions in the random k-XORSAT model and its NP-complete extensions

We study the performances of stochastic heuristic search algorithms on Uniquely Extendible Constraint Satisfaction Problems with random inputs. We show that, for any heuristic preserving the Poissonian nature of the underlying instance, the (heuristic-dependent) largest ratio $α_a$ of constraints per variables for which a search algorithm is likely to find solutions is smaller than the critical ratio $α_d$ above which solutions are clustered and highly correlated. In addition we show that the clustering ratio can be reached when the number k of variables per constraints goes to infinity by the so-called Generalized Unit Clause heuristic.

cs.CC