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.
arXiv:2604. 13213v2 Announce Type: replace-cross Abstract: Rare events such as conformational changes in biomolecules, phase transitions, and chemical reactions are central to the behavior of many physical systems, yet they are extremely difficult to study computationally because unbiased simulations seldom produce them.
By Yuanqi Du, Jiajun He, Dinghuai Zhang, Eric Vanden-Eijnden, Carles Domingo-Enrich
arXiv:2608. 07648v1 Announce Type: cross Abstract: Sampling high-dimensional probability distributions is a central task in scientific computing, with applications ranging from Bayesian inference to statistical physics and molecular simulation.
By Marylou Gabri\'e
arXiv:2605. 00337v2 Announce Type: replace Abstract: Sampling the distribution of collective variables (CVs) and estimating the associated free energy surface are crucial problems in statistical physics, as they underpin a better understanding of chemical reactions and conformational transitions.
By Zichen Liu, Tiejun Li
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
arXiv:2607. 05252v1 Announce Type: new Abstract: Simulation-Based Inference (SBI) is critical for scientific discovery, with generative models offering a promising path toward efficient inference.
By Weichen Qin, Yufan Xie, Peihao Wang, Chia-Jui Chou, Minghui Du, Peng Xu, Ziren Luo, Yi Yang, Jingyi Yu, Bo Liang, Jiakai Zhang
arXiv:2606. 11138v1 Announce Type: new Abstract: We introduce First-Order Trajectory Matching (FTM), a surrogate-modeling method that learns the first-order local transport of probability mass from trajectories of stochastic systems.
By Shreya Jha, Timo Schorlepp, Nicholas Geissler, Jules Berman, Benjamin Peherstorfer
arXiv:2601. 22123v4 Announce Type: replace Abstract: Simulating the long-time evolution of Hamiltonian systems is limited by the small timesteps required for stable numerical integration.
By Winfried Ripken, Michael Plainer, Gregor Lied, Thorben Frank, Oliver T. Unke, Stefan Chmiela, Frank No\'e, Klaus-Robert M\"uller
arXiv:2602. 24007v3 Announce Type: replace-cross Abstract: Protein function relies on dynamic conformational ensembles, yet current generative models like AlphaFold3 often fail to produce ensembles that match experimental data.
By Advaith Maddipatla, Anar Rzayev, Marco Pegoraro, Martin Pacesa, Paul Schanda, Ailie Marx, Sanketh Vedula, Alex M. Bronstein
arXiv:2602. 13136v2 Announce Type: replace Abstract: Template-free retrosynthesis methods treat the task as black-box sequence generation, limiting learning efficiency, while semi-template approaches rely on rigid reaction libraries that constrain generalization.
By Chenguang Wang, Zihan Zhou, Lei Bai, Tianshu Yu
arXiv:2606. 09949v1 Announce Type: cross Abstract: Data-driven PDE surrogates are trained with data produced by numerical PDE solvers.
By Pierre Cesar (DATAMOVE), Sofya Dymchenko (DATAMOVE), Abhishek Purandare (DATAMOVE), Bruno Raffin (DATAMOVE)
arXiv:2608. 12438v1 Announce Type: new Abstract: We formulate generative modeling as a path integral in which flow-based, diffusion-based, variational, and adversarial models arise as different evaluation principles for a single master action.
By Ramon Winterhalder