Flow matching for reaction pathway generation

📄 Abstract

Abstract: Elucidating reaction mechanisms hinges on efficiently generating transition states (TSs), products, and complete reaction networks. Recent generative models, such as diffusion models for TS sampling and sequence-based architectures for product generation, offer faster alternatives to quantum-chemistry searches. But diffusion models remain constrained by their stochastic differential equation (SDE) dynamics, which suffer from inefficiency and limited controllability. We show that flow matching, a deterministic ordinary differential (ODE) formulation, can replace SDE-based diffusion for molecular and reaction generation. We introduce MolGEN, a conditional flow-matching framework that learns an optimal transport path to transport Gaussian priors to target chemical distributions. On benchmarks used by TSDiff and OA-ReactDiff, MolGEN surpasses TS geometry accuracy and barrier-height prediction while reducing sampling to sub-second inference. MolGEN also supports open-ended product generation with competitive top-k accuracy and avoids mass/electron-balance violations common to sequence models. In a realistic test on the $\gamma$-ketohydroperoxide decomposition network, MolGEN yields higher fractions of valid and intended TSs with markedly fewer quantum-chemistry evaluations than string-based baselines. These results demonstrate that deterministic flow matching provides a unified, accurate, and computationally efficient foundation for molecular generative modeling, signaling that flow matching is the future for molecular generation across chemistry.