The inverse Potts problem for estimating evolutionary single-site fields and pairwise couplings in homologous protein sequences from their single-site and pairwise amino acid frequencies observed in their multiple sequence alignment would be still one of useful methods in the studies of protein structure and evolution. Since the reproducibility of fields and couplings are the most important, the Boltzmann machine method is employed here, although it is computationally intensive. In order to reduce computational time required for the Boltzmann machine, parallel, persistent Markov chain Monte Carlo method is employed to estimate the single-site and pairwise marginal distributions in each learning step. Also, stochastic gradient descent methods are used to reduce computational time for each learning. Another problem is how to adjust the values of hyperparameters; there are two regularization parameters for evolutionary fields and couplings. The precision of contact residue pair prediction is often used to adjust the hyperparameters. However, it is not sensitive to these regularization parameters. Here, they are adjusted for the fields and couplings to satisfy a specific condition that is appropriate for protein conformations. This method has been applied to eight protein families.

Boltzmann machines are able to learn highly complex, multimodal, structured and multiscale real-world data distributions. Parameters of the model are usually learned by minimizing the Kullback-Leibler (KL) divergence from training samples to the learned model. We propose in this work a novel approach for Boltzmann machine training which assumes that a meaningful metric between observations is known. This metric between observations can then be used to define the Wasserstein distance between the distribution induced by the Boltzmann machine on the one hand, and that given by the training sample on the other hand. We derive a gradient of that distance with respect to the model parameters. Minimization of this new objective leads to generative models with different statistical properties. We demonstrate their practical potential on data completion and denoising, for which the metric between observations plays a crucial role.

Boltzmann machines are powerful distributions that have been shown to be an effective prior over binary latent variables in variational autoencoders (VAEs). However, previous methods for training discrete VAEs have used the evidence lower bound and not the tighter importance-weighted bound. We propose two approaches for relaxing Boltzmann machines to continuous distributions that permit training with importance-weighted bounds. These relaxations are based on generalized overlapping transformations and the Gaussian integral trick. Experiments on the MNIST and OMNIGLOT datasets show that these relaxations outperform previous discrete VAEs with Boltzmann priors. An implementation which reproduces these results is available.

Boltzmann machines are powerful distributions that have been shown to be an effective prior over binary latent variables in variational autoencoders (VAEs).

CP decomposition compresses an input tensor into a sum of rank-one components, and Tucker decomposition approximates an input tensor by a core tensor multiplied by matrices. To date, matrix and tensor decomposition has been extensively analyzed, and there are a number of variations of such decomposition (Kolda and Bader, 2009), where the common goal is to approximate a given tensor by a smaller number of components, or parameters,inanefficientmanner. However, despite the recent advances of decomposition techniques, a learning theory that can systematically define decomposition for any order tensors including vectors and matrices is still under development. Moreover, it is well known that CP and Tucker tensor decomposition include non-convex optimization and that the global convergence is not guaranteed.

Weconsider the task of learning an RBM given samples generated according to it.

Inparticular,weshowthat using the popular k (persistent) contrastive divergence approaches, with k small, the dynamics of the learned model are extremely slow and often dominated by strong out-of-equilibrium effects.

Graphical models are powerful tools for modeling high-dimensional data, but learning graphical models in the presence of latent variables is well-known to be difficult. In this work we give new results for learning Restricted Boltzmann Machines, probably the most well-studied class of latent variable models. Our results are based on new connections to learning two-layer neural networks under $\ell_{\infty}$ bounded input; for both problems, we give nearly optimal results under the conjectured hardness of sparse parity with noise. Using the connection between RBMs and feedforward networks, we also initiate the theoretical study of {\em supervised RBMs} \citep{hinton2012practical}, a version of neural-network learning that couples distributional assumptions induced from the underlying graphical model with the architecture of the unknown function class. We then give an algorithm for learning a natural class of supervised RBMs with better runtime than what is possible for its related class of networks without distributional assumptions.