We propose a deep generative Markov State Model (DeepGenMSM) learningframework for inference of metastable dynamical systems and prediction of tra-jectories.

Molecular dynamics (MD) is a broadly adopted technique to approximate such quantities.

In real-world applications, data often reside in restricted domains with unknown boundaries, or as high-dimensional point clouds lying on a lower-dimensional, nontrivial, unknown manifold. Traditional Gaussian Processes (GPs) struggle to capture the underlying geometry in such settings. Some existing methods assume a flat space embedded in a point cloud, which can be represented by a single latent chart (latent space), while others exhibit weak performance when the point cloud is sparse or irregularly sampled. The goal of this work is to address these challenges. The main contributions are twofold: (1) We establish the Atlas Brownian Motion (BM) framework for estimating the heat kernel on point clouds with unknown geometries and nontrivial topological structures; (2) Instead of directly using the heat kernel estimates, we construct a Riemannian corrected kernel by combining the global heat kernel with local RBF kernel and leading to the formulation of Riemannian-corrected Atlas Gaussian Processes (RC-AGPs). The resulting RC-AGPs are applied to regression tasks across synthetic and real-world datasets. These examples demonstrate that our method outperforms existing approaches in both heat kernel estimation and regression accuracy. It improves statistical inference by effectively bridging the gap between complex, high-dimensional observations and manifold-based inferences.

We propose a deep generative Markov State Model (DeepGenMSM) learning framework for inference of metastable dynamical systems and prediction of trajectories. After unsupervised training on time series data, the model contains (i) a probabilistic encoder that maps from high-dimensional configuration space to a small-sized vector indicating the membership to metastable (long-lived) states, (ii) a Markov chain that governs the transitions between metastable states and facilitates analysis of the long-time dynamics, and (iii) a generative part that samples the conditional distribution of configurations in the next time step. The model can be operated in a recursive fashion to generate trajectories to predict the system evolution from a defined starting state and propose new configurations. The DeepGenMSM is demonstrated to provide accurate estimates of the long-time kinetics and generate valid distributions for molecular dynamics (MD) benchmark systems. Remarkably, we show that DeepGenMSMs are able to make long time-steps in molecular configuration space and generate physically realistic structures in regions that were not seen in training data.

Molecular dynamics (MD) is a broadly adopted technique to approximate such quantities.

We propose a Likelihood Matching approach for training diffusion models by first establishing an equivalence between the likelihood of the target data distribution and a likelihood along the sample path of the reverse diffusion. To efficiently compute the reverse sample likelihood, a quasi-likelihood is considered to approximate each reverse transition density by a Gaussian distribution with matched conditional mean and covariance, respectively. The score and Hessian functions for the diffusion generation are estimated by maximizing the quasi-likelihood, ensuring a consistent matching of both the first two transitional moments between every two time points. A stochastic sampler is introduced to facilitate computation that leverages on both the estimated score and Hessian information. We establish consistency of the quasi-maximum likelihood estimation, and provide non-asymptotic convergence guarantees for the proposed sampler, quantifying the rates of the approximation errors due to the score and Hessian estimation, dimensionality, and the number of diffusion steps. Empirical and simulation evaluations demonstrate the effectiveness of the proposed Likelihood Matching and validate the theoretical results.

In this paper, we study the Schrödinger Bridge Problem (SBP), which is central to entropic optimal transport. For general reference processes and begin-endpoint distributions, we propose a forward-reverse iterative Monte Carlo procedure to approximate the Schrödinger potentials in a nonparametric way. In particular, we use kernel based Monte Carlo regression in the context of Picard iteration of a corresponding fixed point problem as considered in [5]. By preserving in the iteration positivity and contractivity in a Hilbert metric sense, we develop a provably convergent algorithm. Furthermore, we provide convergence rates for the potential estimates and prove their optimality. Finally, as an application, we propose a non-nested Monte Carlo procedure for the final dimensional distributions of the Schrödinger Bridge process, based on the constructed potentials and the forward-reverse simulation method for conditional diffusions developed in [2].

We propose Riemannian Denoising Diffusion Probabilistic Models (RDDPMs) for learning distributions on submanifolds of Euclidean space that are level sets of functions, including most of the manifolds relevant to applications. Existing methods for generative modeling on manifolds rely on substantial geometric information such as geodesic curves or eigenfunctions of the Laplace-Beltrami operator and, as a result, they are limited to manifolds where such information is available. In contrast, our method, built on a projection scheme, can be applied to more general manifolds, as it only requires being able to evaluate the value and the first order derivatives of the function that defines the submanifold. We provide a theoretical analysis of our method in the continuous-time limit, which elucidates the connection between our RDDPMs and score-based generative models on manifolds. The capability of our method is demonstrated on datasets from previous studies and on new datasets sampled from two high-dimensional manifolds, i.e. $\mathrm{SO}(10)$ and the configuration space of molecular system alanine dipeptide with fixed dihedral angle.

In dynamic decision-making scenarios across business and healthcare, leveraging sample trajectories from diverse populations can significantly enhance reinforcement learning (RL) performance for specific target populations, especially when sample sizes are limited. While existing transfer learning methods primarily focus on linear regression settings, they lack direct applicability to reinforcement learning algorithms. This paper pioneers the study of transfer learning for dynamic decision scenarios modeled by non-stationary finite-horizon Markov decision processes, utilizing neural networks as powerful function approximators and backward inductive learning. We demonstrate that naive sample pooling strategies, effective in regression settings, fail in Markov decision processes.To address this challenge, we introduce a novel ``re-weighted targeting procedure'' to construct ``transferable RL samples'' and propose ``transfer deep $Q^*$-learning'', enabling neural network approximation with theoretical guarantees. We assume that the reward functions are transferable and deal with both situations in which the transition densities are transferable or nontransferable. Our analytical techniques for transfer learning in neural network approximation and transition density transfers have broader implications, extending to supervised transfer learning with neural networks and domain shift scenarios. Empirical experiments on both synthetic and real datasets corroborate the advantages of our method, showcasing its potential for improving decision-making through strategically constructing transferable RL samples in non-stationary reinforcement learning contexts.

We introduce a methodology for performing parameter inference in high-dimensional, non-linear diffusion processes. We illustrate its applicability for obtaining insights into the evolution of and relationships between species, including ancestral state reconstruction. Estimation is performed by utilising score matching to approximate diffusion bridges, which are subsequently used in an importance sampler to estimate log-likelihoods. The entire setup is differentiable, allowing gradient ascent on approximated log-likelihoods. This allows both parameter inference and diffusion mean estimation. This novel, numerically stable, score matching-based parameter inference framework is presented and demonstrated on biological two- and three-dimensional morphometry data.