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.

Based on some recent work of the author on stochastic approximation in non-markovian environments, the situation when the driving random process is non-ergodic in addition to being non-markovian is considered. Using this, we propose an analytic framework for understanding transformer based learning, specifically, the `attention' mechanism, and continual learning, both of which depend on the entire past in principle.

We study the following learning problem with dependent data: Given a trajectory of length $n$ from a stationary Markov chain with $k$ states, the goal is to predict the distribution of the next state.

The problem of estimating an unknown discrete distribution from its samples is a fundamental tenet of statistical learning. Over the past decade, it attracted significant research effort and has been solved for a variety of divergence measures. Surprisingly, an equally important problem, estimating an unknown Markov chain from its samples, is still far from understood. We consider two problems related to the min-max risk (expected loss) of estimating an unknown k-state Markov chain from its n sequential samples: predicting the conditional distribution of the next sample with respect to the KL-divergence, and estimating the transition matrix with respect to a natural loss induced by KL or a more general f-divergence measure. For the first measure, we determine the min-max prediction risk to within a linear factor in the alphabet size, showing it is \Omega(k\log\log n/n) and O(k^2\log\log n/n). For the second, if the transition probabilities can be arbitrarily small, then only trivial uniform risk upper bounds can be derived. We therefore consider transition probabilities that are bounded away from zero, and resolve the problem for essentially all sufficiently smooth f-divergences, including KL-, L_2-, Chi-squared, Hellinger, and Alpha-divergences.

A key task in Bayesian machine learning is sampling from distributions that are only specified up to a partition function (i.e., constant of proportionality). One prevalent example of this is sampling posteriors in parametric distributions, such as latent-variable generative models. However sampling (even very approximately) can be #P-hard. Classical results (going back to Bakry and Emery) on sampling focus on log-concave distributions, and show a natural Markov chain called Langevin diffusion mix in polynomial time. However, all log-concave distributions are uni-modal, while in practice it is very common for the distribution of interest to have multiple modes.

We present the first uniform-in-time high-probability bound for SGD under the PL condition, where the gradient noise contains both Markovian and martingale difference components. This significantly broadens the scope of finite-time guarantees, as the PL condition arises in many machine learning and deep learning models while Markovian noise naturally arises in decentralized optimization and online system identification problems. We further allow the magnitude of noise to grow with the function value, enabling the analysis of many practical sampling strategies. In addition to the high-probability guarantee, we establish a matching $1/k$ decay rate for the expected suboptimality. Our proof technique relies on the Poisson equation to handle the Markovian noise and a probabilistic induction argument to address the lack of almost-sure bounds on the objective. Finally, we demonstrate the applicability of our framework by analyzing three practical optimization problems: token-based decentralized linear regression, supervised learning with subsampling for privacy amplification, and online system identification.

Entropy estimation is one of the prototypical problems in distribution property testing. To consistently estimate the Shannon entropy of a distribution on $S$ elements with independent samples, the optimal sample complexity scales sublinearly with $S$ as $\Theta(\frac{S}{\log S})$ as shown by Valiant and Valiant \cite{Valiant--Valiant2011}. Extending the theory and algorithms for entropy estimation to dependent data, this paper considers the problem of estimating the entropy rate of a stationary reversible Markov chain with $S$ states from a sample path of $n$ observations.

Stochastic gradient methods are the workhorse (algorithms) of large-scale optimization problems in machine learning, signal processing, and other computational sciences and engineering. This paper studies Markov chain gradient descent, a variant of stochastic gradient descent where the random samples are taken on the trajectory of a Markov chain. Existing results of this method assume convex objectives and a reversible Markov chain and thus have their limitations. We establish new non-ergodic convergence under wider step sizes, for nonconvex problems, and for non-reversible finite-state Markov chains. Nonconvexity makes our method applicable to broader problem classes. Non-reversible finite-state Markov chains, on the other hand, can mix substatially faster. To obtain these results, we introduce a new technique that varies the mixing levels of the Markov chains. The reported numerical results validate our contributions.

Heavy-tailed distributions are ubiquitous in real-world data, where rare but extreme events dominate risk and variability. However, standard Variational Autoencoders (VAEs) employ simple decoder distributions (e.g., Gaussian) that fail to capture heavy-tailed behavior, while existing heavy-tail-aware extensions remain restricted to predefined parametric families whose tail behavior is fixed a priori. We propose the Phase-Type Variational Autoencoder (PH-VAE), whose decoder distribution is a latent-conditioned Phase-Type (PH) distribution defined as the absorption time of a continuous-time Markov chain (CTMC). This formulation composes multiple exponential time scales, yielding a flexible and analytically tractable decoder that adapts its tail behavior directly from the observed data. Experiments on synthetic and real-world benchmarks demonstrate that PH-VAE accurately recovers diverse heavy-tailed distributions, significantly outperforming Gaussian, Student-t, and extreme-value-based VAE decoders in modeling tail behavior and extreme quantiles. In multivariate settings, PH-VAE captures realistic cross-dimensional tail dependence through its shared latent representation. To our knowledge, this is the first work to integrate Phase-Type distributions into deep generative modeling, bridging applied probability and representation learning.

We study one-sided and $α$-correct sequential hypothesis testing for data generated by an ergodic Markov chain. The null hypothesis is that the unknown transition matrix belongs to a prescribed set $P$ of stochastic matrices, and the alternative corresponds to a disjoint set $Q$. We establish a tight non-asymptotic instance-dependent lower bound on the expected stopping time of any valid sequential test under the alternative. Our novel analysis improves the existing lower bounds, which are either asymptotic or provably sub-optimal in this setting. Our lower bound incorporates both the stationary distribution and the transition structure induced by the unknown Markov chain. We further propose an optimal test whose expected stopping time matches this lower bound asymptotically as $α\to 0$. We illustrate the usefulness of our framework through applications to sequential detection of model misspecification in Markov Chain Monte Carlo and to testing structural properties, such as the linearity of transition dynamics, in Markov decision processes. Our findings yield a sharp and general characterization of optimal sequential testing procedures under Markovian dependence.