FragFM: Efficient Fragment-Based Molecular Generation via Discrete Flow Matching

Abstract

We introduce FragFM, a novel fragment-based discrete flow matching framework for molecular graph generation. FragFM generates molecules at the fragment level, leveraging a coarse-to-fine autoencoding mechanism to reconstruct atom-level details. This approach reduces computational complexity while maintaining high chemical validity, enabling more efficient and scalable molecular generation. We benchmark FragFM against state-of-the-art diffusion- and flow-based models on standard molecular generation benchmarks and natural product datasets, demonstrating superior performance in validity, property control, and sampling efficiency. Notably, FragFM achieves over 99\% validity with significantly fewer sampling steps, improving scalability while preserving molecular diversity. These results highlight the potential of fragment-based generative modeling for large-scale, property-aware molecular design, paving the way for more efficient exploration of chemical space.