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A new approach to maximum likelihood learning of discrete graphical models and RBM in particular is introduced. Our method, Perturb and Descend (PD) is inspired by two ideas (I) perturb and MAP method for sampling (II) learning by…
Restricted Boltzmann machines (RBMs) and their variants are usually trained by contrastive divergence (CD) learning, but the training procedure is an unsupervised learning approach, without any guidances of the background knowledge. To…
In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under physiological conditions. Since then the biophysics community…
Proteins are dynamic, adopting ensembles of conformations. The nature of this conformational heterogenity is imprinted in the raw electron density measurements obtained from X-ray crystallography experiments. Fitting an ensemble of protein…
Since learning is typically very slow in Boltzmann machines, there is a need to restrict connections within hidden layers. However, the resulting states of hidden units exhibit statistical dependencies. Based on this observation, we propose…
Generative models coupled with reinforcement learning (RL), such as REINVENT and PepINVENT, have emerged as a powerful framework for de novo molecular design. During the ideation process these generative frameworks utilize various…
Deep learning methods relying on multi-layered networks have been actively studied in a wide range of fields in recent years, and deep Boltzmann machines(DBMs) is one of them. In this study, a model of DBMs with some properites of weight…
The inverse Potts problem to infer a Boltzmann distribution for homologous protein sequences from their single-site and pairwise amino acid frequencies recently attracts a great deal of attention in the studies of protein structure and…
We investigate how machine learning models acquire the ability to compose music and how musical information is internally represented within such models. We develop a composition algorithm based on a restricted Boltzmann machine (RBM), a…
Domain motions involved in the function of proteins can often be well described as a combination of motions along a handfull of low-frequency modes, that is, with the values of a few normal coordinates. This means that, when the functional…
Sampling molecular conformations from the Boltzmann distribution is essential for computational chemistry, but iterative diffusion methods are prohibitively slow. Drifting Models offer one-step generation, yet their equilibrium matches the…
Protein conformational transitions, which are essential for function, may be driven either by entropy or enthalpy when molecular systems comprising solute and solvent molecules are the focus. Revealing thermodynamic origin of a given…
Energy-based generative models, such as restricted Boltzmann machines (RBMs), require unbiased Boltzmann samples for effective training. Classical Markov chain Monte Carlo methods, however, converge slowly and yield correlated samples,…
Restricted Boltzmann machines are undirected neural networks which have been shown to be effective in many applications, including serving as initializations for training deep multi-layer neural networks. One of the main reasons for their…
Nanomolecular assemblies of C$_{60}$ can be synthesized to enclose dipolar molecules. The low-temperature states of such endofullerenes are described by quantum mechanical rotors, which are candidates for quantum information devices with…
Restricted Boltzmann Machines and Deep Belief Networks have been successfully used in probabilistic generative model applications such as image occlusion removal, pattern completion and motion synthesis. Generative inference in such…
In recent years, researchers have been exploring ways to generalize Boltzmann machines (BMs) to quantum systems, leading to the development of variations such as fully-visible and restricted quantum Boltzmann machines (QBMs). Due to the…
Coarse-grained (CG) models provide an effective route to reducing the complexity of molecular simulations (MD), but conventional approaches depend heavily on long all-atom MD trajectories to adequately sample configurational space. This…
Training generative adversarial networks is unstable in high-dimensions as the true data distribution tends to be concentrated in a small fraction of the ambient space. The discriminator is then quickly able to classify nearly all generated…
We consider the problem of generating valid and small prediction sets by sampling outputs (e.g., software code and natural language text) from a black-box deep generative model for a given input (e.g., textual prompt). The validity of a…