Hanyu Gao
Publications
Towards Generalizable and Evidential Nuclear Magnetic Resonance-Based Molecular Structure Elucidation via Large Language Model Agent
Nuclear Magnetic Resonance (NMR) spectroscopy is the gold standard for molecular structure elucidation, yet interpreting complex spectra for unknown molecules remains a bottleneck reliant on human expertise. While artificial intelligence has advanced this field, current methods face a critical trade-off: database retrieval cannot identify novel scaffolds, while de novo molecular structure elucidation models operate as black boxes, lacking the atom-level interpretability required for rigorous scientific validation. Here, we present NMRAgent, an evidential reasoning agent powered by large language models (LLMs) that bridges this gap by integrating specialized spectral analysis tools with chemical knowledge graphs. Unlike previous approaches, NMRAgent mimics the deductive reasoning of human experts: it takes experimental NMR spectra and molecular formula as input, plans the elucidation process, proposes candidate structures, verifies peak-atom consistency, and refines misaligned substructure through formula-aware fragment optimization. Enabled by its evidential reasoning, NMRAgent outperforms state-of-the-art methods, improving top-1 accuracy by 46.5% and Tanimoto similarity by 0.502 on a scaffold-split benchmark with novel scaffolds in the test set. Besides, we demonstrate the agent's practical utility by elucidating the structures of two previously unknown natural products isolated from Hydrangea davidii and Vitex trifolia, and by correcting structural misassignments in established literature. By combining high-accuracy prediction with transparent and evidence-based reasoning, NMRAgent establishes a new paradigm for interpretable AI in analytical chemistry.
XDecomposer: Learning Prior-Free Set Decomposition for Multiphase X-ray Diffraction
Multiphase powder X-ray diffraction (PXRD) analysis remains a fundamental bottleneck in structure identification, as real-world synthesis often produces complex mixtures whose constituent phases (components) cannot be reliably disentangled. While recent advances in representation-based crystal retrieval and generation suggest the possibility of inferring structures directly from PXRD, existing approaches largely assume single-phase inputs and break down in multiphase settings. Here, we present XDecomposer, a prior-free framework for joint decomposition and identification of multiphase XRD patterns without requiring candidate phase lists, structural templates, or prior knowledge of phase number. We formulate multiphase diffraction analysis as a set prediction problem, where the model infers an unordered set of phase-resolved components, their mixture proportions, and corresponding structural representations within a unified architecture. A phase-query-driven decomposition mechanism, together with diffraction-consistent physical reconstruction, enables accurate source separation while preserving crystallographic fidelity. Extensive experiments on both simulated and experimental datasets show that XDecomposer substantially improves reconstruction accuracy and phase identification across diverse chemical systems, while maintaining strong generalization to unseen mixtures. These results provide a practical route toward data-driven, source-resolved multiphase XRD analysis and reduce long-standing dependence on prior-guided iteratively phase matching. The code is openly available at https://github.com/Licht0812/XDecomposer