Explainable Molecular Structure Inference from GC--MS with Diffusion Models and LLM Reranking

arXiv:2610.03066 · physics.chem-ph, cs.LG, physics.comp-ph, physics.data-an · Submitted 2026-10-02 · Read on arXiv

physics.chem-ph, cs.LG, physics.comp-ph, physics.data-an

Submitted: 2026-10-02

Updated: 2026-10-02

Terminology

• Diffusion Model — 1× in this paper · explained in 9 episodes
• Diffusion Models — 1× in this paper · explained in 6 episodes

Sources

• FlowMS: Flow Matching for De Novo Structure Elucidation from Mass Spectra
• Structured Denoising Diffusion Models in Discrete State-Spaces
• DiGress: Discrete Denoising diffusion for graph generation
• Improved Denoising Diffusion Probabilistic Models
• A Generalization of Transformer Networks to Graphs
• Decoupled Weight Decay Regularization
• Super-Convergence: Very Fast Training of Neural Networks Using Large Learning Rates
• MoleCode unlocks structural intelligence in large language models

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