The rare-event sampling problem has long been the central limiting factor in molecular dynamics (MD), especially in biomolecular simulation. Recently, diffusion models such as BioEmu have emerged as powerful equilibrium samplers that generate independent samples from complex molecular distributions, eliminating the cost of sampling rare transition events. However, a sampling problem remains when computing observables that rely on states which are rare in equilibrium, for example folding free energies. Here, we introduce enhanced diffusion sampling, enabling efficient exploration of rare-event regions while preserving unbiased thermodynamic estimators. The key idea is to perform quantitatively accurate steering protocols to generate biased ensembles and subsequently recover equilibrium statistics via exact reweighting. We instantiate our framework in three algorithms: UmbrellaDiff (umbrella sampling with diffusion models), $Δ$G-Diff (free-energy differences via tilted ensembles), and MetaDiff (a batchwise analogue for metadynamics). Across toy systems, protein folding landscapes and folding free energies, our methods achieve fast, accurate, and scalable estimation of equilibrium properties within GPU-minutes to hours per system -- closing the rare-event sampling gap that remained after the advent of diffusion-model equilibrium samplers.

An important aspect of studying these systems is predicting the equilibrium behavior of the system upon an intervention, and selecting high-value interventions.

This amount depends on the previously estimated difference in skills between i and j .

An important aspect of studying these systems is predicting the equilibrium behavior of the system upon an intervention, and selecting high-value interventions.

Accurate characterization of the equilibrium distributions of complex molecular systems and their dependence on environmental factors such as temperature is essential for understanding thermodynamic properties and transition mechanisms. Projecting these distributions onto meaningful low-dimensional representations enables interpretability and downstream analysis. Recent advances in generative AI, particularly flow models such as Normalizing Flows (NFs), have shown promise in modeling such distributions, but their scope is limited without tailored representation learning. In this work, we introduce Latent Thermodynamic Flows (LaTF), an end-to-end framework that tightly integrates representation learning and generative modeling. LaTF unifies the State Predictive Information Bottleneck (SPIB) with NFs to simultaneously learn low-dimensional latent representations, referred to as Collective Variables (CVs), classify metastable states, and generate equilibrium distributions across temperatures beyond the training data. The two components of representation learning and generative modeling are optimized jointly, ensuring that the learned latent features capture the system's slow, important degrees of freedom while the generative model accurately reproduces the system's equilibrium behavior. We demonstrate LaTF's effectiveness across diverse systems, including a model potential, the Chignolin protein, and cluster of Lennard Jones particles, with thorough evaluations and benchmarking using multiple metrics and extensive simulations. Finally, we apply LaTF to a RNA tetraloop system, where despite using simulation data from only two temperatures, LaTF reconstructs the temperature-dependent structural ensemble and melting behavior, consistent with experimental and prior extensive computational results.

We study zero-sum games in the space of probability distributions over the Euclidean space $\mathbb{R}^d$ with entropy regularization, in the setting when the interaction function between the players is smooth and strongly convex-concave. We prove an exponential convergence guarantee for the mean-field min-max Langevin dynamics to compute the equilibrium distribution of the zero-sum game. We also study the finite-particle approximation of the mean-field min-max Langevin dynamics, both in continuous and discrete times. We prove biased convergence guarantees for the continuous-time finite-particle min-max Langevin dynamics to the stationary mean-field equilibrium distribution with an explicit bias estimate which does not scale with the number of particles. We also prove biased convergence guarantees for the discrete-time finite-particle min-max Langevin algorithm to the stationary mean-field equilibrium distribution with an additional bias term which scales with the step size and the number of particles. This provides an explicit iteration complexity for the average particle along the finite-particle algorithm to approximately compute the equilibrium distribution of the zero-sum game.

We present a theoretical analysis of the Elo rating system, a popular method for ranking skills of players in an online setting. In particular, we study Elo under the Bradley--Terry--Luce model and, using techniques from Markov chain theory, show that Elo learns the model parameters at a rate competitive with the state of the art. We apply our results to the problem of efficient tournament design and discuss a connection with the fastest-mixing Markov chain problem.

The committor function is a central object for quantifying the transitions between metastable states of dynamical systems. Recently, a number of computational methods based on deep neural networks have been developed for computing the high-dimensional committor function. The success of the methods relies on sampling adequate data for the transition, which still is a challenging task for complex systems at low temperatures. In this work, we propose a deep learning method with two novel adaptive sampling schemes (I and II). In the two schemes, the data are generated actively with a modified potential where the bias potential is constructed from the learned committor function. We theoretically demonstrate the advantages of the sampling schemes and show that the data in sampling scheme II are uniformly distributed along the transition tube. This makes a promising method for studying the transition of complex systems. The efficiency of the method is illustrated in high-dimensional systems including the alanine dipeptide and a solvated dimer system.

We study a particular class of cyclic causal models, where each variable is a (possibly nonlinear) function of its parents and additive noise. We prove that the causal graph of such models is generically identifiable in the bivariate, Gaussian-noise case. We also propose a method to learn such models from observational data. In the acyclic case, the method reduces to ordinary regression, but in the more challenging cyclic case, an additional term arises in the loss function, which makes it a special case of nonlinear independent component analysis. We illustrate the proposed method on synthetic data.