Correlation-Free Transition Path Sampling through Shooting Point Generation Guided by Committor Learning
Authors: Maximilian Negedly, Sebastian Falkner, Alessandro Coretti, Christoph Dellago
Organizations: Faculty of Physics, University of Vienna, 1090 Vienna, Austria · Vienna Doctoral School in Physics, University of Vienna, 1090 Vienna, Austria · Institute of Physics, University of Augsburg, 86159 Augsburg, Germany
Studying the dynamical behavior of a system often depends on characterizing how it transitions between long-lived states. Because such transitions are rare, observing them usually requires specialized enhanced sampling techniques. Transition Path Sampling (TPS) is a well-established method for generating reactive trajectories, which is simple to implement and does not require the definition of a preconceived reaction coordinate. However, its efficiency is limited by its sequential nature and the resulting correlations between sampled paths. Previous work addressed this limitation by combining TPS with a sampling scheme based on conditioned Boltzmann Generators, a generative machine learning model capable of sampling a given target probability distribution. This approach produces uncorrelated transition paths but relies on an accurate reaction coordinate, which is rarely known in advance. Building on recent advances in committor learning, specifically on the Artificial Intelligence for Molecular Mechanism Discovery (AIMMD) method, in this work we introduce GenAIMMD, an iterative algorithm that actively and self-consistently learns the ideal reaction coordinate (the committor) and trains a conditioned Boltzmann Generator to sample from arbitrary bias windows along it. GenAIMMD thereby provides a correlation-free and fully parallelizable path sampling scheme that does not require prior knowledge of the system's transition mechanism. We apply GenAIMMD to a two-dimensional toy model and a higher-dimensional polymer system. In both cases, GenAIMMD succeeds in training the Boltzmann Generator and learning the committor. Benchmark results show a substantial increase in performance compared to standard TPS.
Most molecular transitions occur on timescales far beyond direct molecular dynamics simulations. The committor, the probability that a configuration reaches a product state before a reactant state, is a central kinetic statistic, providing a mechanism-independent reaction coordinate and a foundation for transition path theory and the calculation of rates. This review surveys modern approaches for estimating the committor and related kinetic statistics from molecular simulations, with an emphasis on self-supervised methods that learn solutions of their defining dynamical equations rather than relying on labeled shooting data. We develop a common operator viewpoint connecting generator-based partial differential equations, variational principles, Markov state models, dynamical Galerkin approximation, and neural networks. Empirical and theoretical evidence points to the efficiency of these methods. We provide theoretical and practical guidance for realizing their full potential in applications, including strategies for treating non-Markovian effects and for sampling. We conclude by identifying opportunities for further research, including connections to reinforcement learning and generative modeling.
Path sampling methods generate ensembles of reactive trajectories connecting metastable states, but extracting mechanistic insight from these data remains nontrivial. We introduce Flux Matching, a framework that learns two complementary objects directly from reactive trajectory data: a current velocity u(z), whose streamlines trace the dominant reaction pathways, and a scalar potential h(z), obtained from a weighted Helmholtz-Hodge decomposition of the reactive current, that serves as a data-driven reaction coordinate. Both minimize quadratic functionals over the reactive path ensemble, analogous to the flow matching loss in generative modeling, and require no knowledge of the underlying dynamics or stationary distribution. Unlike committor-based methods, u and h remain well-defined under projection onto non-Markovian collective variables, and their level sets in turn provide adaptive interfaces for improved sampling with enhanced sampling methods. Flux Matching is validated through the generation of current velocity trajectories and rate constant calculations on molecular systems.
Rishal Aggarwal, David Ryan Koes, Nicholas M. Boffi +1
Inference-time reward alignment steers pretrained diffusion and flow-based generative models to satisfy user-specified rewards without retraining. Recently, Sequential Monte Carlo (SMC) has emerged as a powerful framework for this task by iteratively filtering and propagating multiple particles. However, we show that standard SMC-based methods often suffer from poor performance because they initialize particles from a standard prior, whereas high-reward regions in complex reward landscapes are extremely rare. Further, we show that even recent reward-aware initial sampling approaches remain vulnerable to getting trapped in local modes, as complex reward landscapes are often multi-modal. To overcome these limitations, we propose PATHS (PArallel Tempering for High-complexity reward Sampling), a novel initialization method that couples multiple sampling chains through parallel tempering. PATHS maintains a ladder of reward-tempered chains and periodically performs Metropolis swaps, enabling efficient exploration across flattened reward landscapes, thereby mitigating the mode-trapping issues. Our analysis reveals that this mechanism substantially enhances the finite-budget exploration of rare, high-reward regions that are typically challenging to sample. Experiments on layout-to-image and quantity-aware generation show that PATHS achieves consistent gains in alignment quality, particularly on complex prompts.