arXiv:2607. 19816v1 Announce Type: cross Abstract: Determining molecular structures from spectroscopic data remains fundamentally challenging because the inverse problem is intrinsically underdetermined: individual spectra are sparse, low-dimensional, and encode only partial structural evidence relative to the vast space of possible molecules.
arXiv:2604. 16648v2 Announce Type: replace Abstract: Tandem mass spectrometry is prominent in scientific discovery workflows for identifying unknown small molecules, yet high-throughput structural elucidation remains challenging.
arXiv:2512. 19733v3 Announce Type: replace-cross Abstract: Molecular structure elucidation from spectroscopic data is a long-standing challenge in Chemistry, traditionally requiring expert interpretation.
arXiv:2607. 26164v1 Announce Type: new Abstract: Automated molecular structure elucidation from infrared (IR) spectroscopy data has seen significant advancements in recent years, but its broad applicability is limited by a reliance on pre-determined chemical formulas provided as auxiliary model inputs.
arXiv:2607. 04774v1 Announce Type: new Abstract: Untargeted tandem mass spectrometry (MS/MS) detects thousands of small molecules per biological sample, yet most go unidentified because they are absent from spectral libraries.
The paper introduces DiffGCMS, a discrete graph diffusion model that generates molecular structures directly from GC–EI–MS spectra, and couples it with a large language model for post‑processing. In the first stage, DiffGCMS produces candidate structures; the LLM then validates, repairs, and reranks these candidates while offering interpretable explanations of fragment‑ion peaks. On a large NIST 20 test set, the combined approach improves accuracy and ensures 100% candidate validity for small molecules, demonstrating the value of spectrum‑aware post‑processing.
arXiv:2608. 14720v1 Announce Type: cross Abstract: Following the molecular discovery and synthesis revolutions, scalable automated structure elucidation from routine spectroscopic data remains an outstanding challenge.
arXiv:2608.30910v1 Announce Type: new Abstract: Spectroscopic structure elucidation is central to molecular analysis, but recent Large Language Model (LLM)-based methods mostly formulate it as direct...
GC--EI--MS is an important technique for analyzing volatile and semivolatile compounds in complex samples. However, conventional methods rely heavily on reference spectral library matching, limiting t...
arXiv:2607. 23607v1 Announce Type: new Abstract: Molecular structure elucidation from tandem mass spectra (MS/MS) is a central inverse problem in analytical chemistry.
The paper introduces two closed‑form projection operators that enforce physical validity in biomolecular diffusion models during inference. One operator resolves inter‑chain van der Waals clashes, while the other restores ligand geometry, including bond lengths, angles, planarity, and chirality. These lightweight, model‑agnostic corrections preserve structural accuracy and ligand placement across multiple benchmarks without adding runtime or memory overhead.
Exploring the chemical space of flexible molecules remains challenging because the vast number of possible compounds and conformations, together with the increasing cost and limited generalization of...