The paper introduces GenAIMMD, an iterative algorithm that learns the committor function and trains a conditioned Boltzmann Generator to generate uncorrelated transition paths without prior knowledge of the reaction coordinate. This method combines transition path sampling with committor learning, enabling fully parallelizable sampling. Benchmarks on a toy model and a polymer system show a substantial performance improvement over standard TPS.
By Maximilian Negedly, Sebastian Falkner, Alessandro Coretti, Christoph Dellago
The article reviews modern machine learning techniques for estimating the committor and related kinetic statistics from molecular dynamics simulations. It emphasizes self‑supervised methods that solve the underlying dynamical equations instead of relying on labeled data, and unifies various approaches—generator‑based PDEs, variational principles, Markov state models, dynamical Galerkin approximation, and neural networks—under a common operator framework. The review also discusses practical guidance for handling non‑Markovian effects, sampling strategies, and outlines future research directions such as connections to reinforcement learning and generative modeling.
By Jonathan Weare, Aaron R. Dinner
arXiv:2607. 15682v1 Announce Type: new Abstract: Sampling from an unnormalized Boltzmann density requires proposals that move probability mass globally while retaining enough path-probability information for statistical correction.
By Moxian Qian
arXiv:2608. 13800v1 Announce Type: new Abstract: Transition path sampling (TPS) aims to efficiently generate rare molecular transition trajectories between metastable states and is essential for understanding biomolecular mechanisms.
By Jingqian Liu, Yu-Hsiang Wang, Yanru Qu, Ge Liu
Efficient sampling of molecular systems at thermodynamic equilibrium is a hallmark challenge in statistical physics. This challenge has driven the development of Boltzmann Generators (BGs), which allow rapid generation of uncorrelated equilibrium samples by combining a generative model with exact likelihoods and an importance sampling correction.
arXiv:2606. 04100v1 Announce Type: new Abstract: Machine learning interatomic potentials (MLIPs) enable efficient and accurate atomistic simulations but depend critically on the quality and diversity of the training data.
By Joanna Zou, Fraser Birks, Dallas Foster, Youssef Marzouk
arXiv:2606. 27361v1 Announce Type: cross Abstract: Efficient sampling of molecular systems at thermodynamic equilibrium is a hallmark challenge in statistical physics.
By Danyal Rehman, Charlie B. Tan, Yoshua Bengio, Avishek Joey Bose, Alexander Tong
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.
PGFS++ is a synthesis‑aware reinforcement learning framework that improves molecular properties such as drug‑likeness or binding affinity while ensuring the resulting molecules can be synthesized and remain structurally similar to the input. It builds on PGFS+ by using trainable embedding lookup tables for reaction templates and second reactants, a more effective scoring function, and a refined RL algorithm. The method addresses a reward‑hacking failure mode by treating each input molecule as the start of a forward‑synthesis trajectory, applying learned reaction templates with in‑stock building blocks, and producing diverse, high‑quality outputs with explicit synthesis routes.
arXiv:2608. 14076v1 Announce Type: cross Abstract: Transition-state (TS) structures define the energetic barriers and mechanistic pathways of elementary chemical reactions, yet their identification remains computationally demanding because conventional saddle-point searches require expensive quantum-mechanical calculations.
By Kaipeng Zeng, Wenxi Zhai, Shengrui Xu, Jie Zhao, Bowen Li, Shiyue Wang, Junchi Yan, Tong Zhu
PGFS++ is a synthesis‑aware reinforcement learning framework that improves molecular properties while ensuring the resulting molecules can be synthesized and remain structurally similar to the input. It builds on PGFS+ by using trainable embedding lookup tables for reaction templates and second reactants, a more effective scoring function, and a refined RL algorithm. Experiments demonstrate that PGFS++ enhances target properties and preserves high output diversity, overcoming the reward‑hacking failure mode seen in earlier versions.
By Boqiao Zhang, Godbless James, Sai Krishna Gottipati, Andrew Fitzgibbon
The paper introduces a data-driven effective model for stochastic chemical reaction networks that bypasses the high computational cost of the Stochastic Simulation Algorithm (SSA). By approximating the finite-time transition kernel of the SSA-induced continuous-time Markov chain with a generative machine learning model, the method operates on a user-defined coarse time step independent of microscopic reaction events. Using a conditional normalizing flow as the stochastic propagator, the trained model recursively generates statistically consistent trajectories, achieving significant computational savings while maintaining accuracy, as demonstrated through numerous numerical examples.
By Yuan Chen, Weize Mao, Dongbin Xiu