Related papers: Boltzmann Machine Learning with a Parallel, Persis…
At the scale of the individual cell, protein production is a stochastic process with multiple time scales, combining quick and slow random steps with discontinuous and smooth variation. Hybrid stochastic processes, in particular…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
We consider adaptive increasingly rare Markov chain Monte Carlo (MCMC) algorithms, which are adaptive MCMC methods, where the adaptation concerning the "past'' happens less and less frequently over time. Under a contraction assumption with…
Stochastic reaction network models are often used to explain and predict the dynamics of gene regulation in single cells. These models usually involve several parameters, such as the kinetic rates of chemical reactions, that are not…
Spatial Monte Carlo integration (SMCI) is an extension of standard Monte Carlo integration and can approximate expectations on Markov random fields with high accuracy. SMCI was applied to pairwise Boltzmann machine (PBM) learning, with…
Boltzmann machines are physics informed generative models with wide applications in machine learning. They can learn the probability distribution from an input dataset and generate new samples accordingly. Applying them back to physics, the…
In Bayesian phylogenetics, our goal is to estimate the posterior distribution over phylogenetic trees. Markov chain Monte Carlo methods are widely used to approximate the phylogenetic posterior distributions. For large-scale sequence data,…
Modeling the time evolution of discrete sets of items (e.g., genetic mutations) is a fundamental problem in many biomedical applications. We approach this problem through the lens of continuous-time Markov chains, and show that the…
Generative models offer a direct way of modeling complex data. Energy-based models attempt to encode the statistical correlations observed in the data at the level of the Boltzmann weight associated with an energy function in the form of a…
The performance of deep neural networks, such as Deep Belief Networks formed by Restricted Boltzmann Machines (RBMs), strongly depends on their training, which is the process of adjusting their parameters. This process can be posed as an…
Recent work has shown that probabilistic models based on pairwise interactions-in the simplest case, the Ising model-provide surprisingly accurate descriptions of experiments on real biological networks ranging from neurons to genes.…
We propose an expectation-maximization-like(EMlike) method to train Boltzmann machine with unconstrained connectivity. It adopts Monte Carlo approximation in the E-step, and replaces the intractable likelihood objective with efficiently…
The analysis of coevolution of residues in homologous proteins is a powerful tool to predict their native conformation. The standard framework in which coevolutionary analysis is usually worked out is that of equilibrium Potts models,…
Many problems in the physical sciences, machine learning, and statistical inference necessitate sampling from a high-dimensional, multi-modal probability distribution. Markov Chain Monte Carlo (MCMC) algorithms, the ubiquitous tool for this…
The restricted Boltzmann machine is a basic machine learning tool able, in principle, to model the distribution of some arbitrary dataset. Its standard training procedure appears however delicate and obscure in many respects. We bring some…
Machine learning is becoming widely used in analyzing the thermodynamics of many-body condensed matter systems. Restricted Boltzmann Machine (RBM) aided Monte Carlo simulations have sparked interest recently, as they manage to speed up…
We introduce a direct Boltzmann inversion method to infer the interaction potential in particle systems using as input particle configurations generated at an arbitrary state point of the system. Unlike iterative Boltzmann inversion, the…
Most successful applications of deep learning involve similar training and test conditions. However, tasks such as biological sequence design involve searching for sequences that improve desirable properties beyond previously known values,…
Markov chain Monte Carlo (MCMC) is widely used for Bayesian inference in models of complex systems. Performance, however, is often unsatisfactory in models with many latent variables due to so-called poor mixing, necessitating development…
Markov chain Monte Carlo (MCMC) algorithms provide a very general recipe for estimating properties of complicated distributions. While their use has become commonplace and there is a large literature on MCMC theory and practice, MCMC users…