Jianan Nie

Jianan Nie, Peng Gao

Mass spectrometry (MS) stands as a cornerstone analytical technique for molecular identification, yet de novo structure elucidation from spectra remains challenging due to the combinatorial complexity of chemical space and the inherent ambiguity of spectral fragmentation patterns. Recent deep learning approaches, including autoregressive sequence models, scaffold-based methods, and graph diffusion models, have made progress. However, diffusion-based generation for this task remains computationally demanding. Meanwhile, discrete flow matching, which has shown strong performance for graph generation, has not yet been explored for spectrum-conditioned structure elucidation. In this work, we introduce FlowMS, the first discrete flow matching framework for spectrum-conditioned de novo molecular generation. FlowMS generates molecular graphs through iterative refinement in probability space, enforcing chemical formula constraints while conditioning on spectral embeddings from a pretrained formula transformer encoder. Notably, it achieves state-of-the-art performance on 5 out of 6 metrics on the NPLIB1 benchmark: 9.15% top-1 accuracy (9.7% relative improvement over DiffMS) and 7.96 top-10 MCES (4.2% improvement over MS-BART). We also visualize the generated molecules, which further demonstrate that FlowMS produces structurally plausible candidates closely resembling ground truth structures. These results establish discrete flow matching as a promising paradigm for mass spectrometry-based structure elucidation in metabolomics and natural product discovery.

Jianan Nie, Peiyao Xiao, Kaiyi Ji et al.

Predicting properties of crystals from their structures is a fundamental yet challenging task in materials science. Unlike molecules, crystal structures exhibit infinite periodic arrangements of atoms, requiring methods capable of capturing both local and global information effectively. However, current works fall short of capturing long-range interactions within periodic structures. To address this limitation, we leverage \emph{reciprocal space}, the natural domain for periodic crystals, and construct a Fourier series representation from fractional coordinates and reciprocal lattice vectors with learnable filters. Building on this principle, we introduce the reciprocal space-based geometry network (\textbf{ReciNet}), a novel architecture that integrates geometric GNNs and reciprocal blocks to model short-range and long-range interactions, respectively. Experimental results on standard benchmarks JARVIS, Materials Project, and MatBench demonstrate that ReciNet achieves state-of-the-art predictive accuracy across a range of crystal property prediction tasks. Additionally, we explore a model extension to multi-property prediction with the mixture-of-experts, which demonstrates high computational efficiency and reveals positive transfer between correlated properties. These findings highlight the potential of our model as a scalable and accurate solution for crystal property prediction.