arXiv Machine Learning July 28, 2026 By Montgomery Bohde, Hongxuan Liu, Mrunali Manjrekar, Magdalena Lederbauer, Shuiwang Ji, Runzhong Wang, Connor W. Coley

FRIGID: Scaling Diffusion-Based Molecular Generation from Mass Spectra at Training and Inference Time

Read the original on arXiv Machine Learning →

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.

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arXiv Machine Learning

Jul 7

MARLIN: De Novo Molecular Structure Elucidation from Tandem Mass Spectra without a Ground-Truth Formula

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.

By Xujun Che, Xiuxia Du, Depeng Xu

llms diffusion benchmarks

arXiv Machine Learning

Jul 28

MS-GPT: Rethinking MS/MS De Novo Structure Elucidation as Spectrum-Induced Posterior Querying of a Molecule-Language Model

arXiv:2607. 23607v1 Announce Type: new Abstract: Molecular structure elucidation from tandem mass spectra (MS/MS) is a central inverse problem in analytical chemistry.

By Xin Zhao, Yumin Liu, Zhuo Li, Weichu Zheng, Feng Zhu, Xiaokang Yang, Yaohui Jin, Yanyan Xu

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arXiv Machine Learning

5d ago

MSAlign: Aligning Molecule and Mass Spectra representations for Metabolite Identification

The paper introduces MSAlign, a lightweight model that aligns frozen foundation models for mass spectra (DreaMS) and molecules (MolDeBERTa) to improve metabolite identification from MS/MS spectra. It presents a unified framework for representation alignment and contrastive learning, demonstrates that a score fusion strategy further boosts performance at minimal cost, and addresses evaluation challenges by quantifying distribution shift in data splitting strategies. All resources, including datasets, splits, and code, are publicly released to promote reproducible research.

By Paul Krzakala, Gabriel Melo, Camille Lan\c{c}on, Charlotte Laclau, R\'emi Flamary, Etienne Th\'evenot, Florence d'Alch\'e-Buc

benchmarks safety

arXiv Machine Learning

Jun 30

GLACIER: Rethinking Mass Spectrum Prediction as an Object Detection Problem

arXiv:2606. 29161v1 Announce Type: new Abstract: Predicting tandem mass spectra (MS/MS) from molecular structures represents a central task in analytical chemistry with direct relevance to clinical metabolomics, systems biology, and adjacent disciplines.

By Rui-Xi Wang, Runzhong Wang, Connor W. Coley

llms computer-vision fine-tuning benchmarks

arXiv AI

Jun 15

FlexMS: A Unified Public Benchmark for Molecule Tandem Mass Spectrum Prediction

arXiv:2602. 22822v3 Announce Type: replace Abstract: Tandem mass spectrometry (MS/MS) is central to small molecule identification, but current deep learning systems for spectrum prediction still remain difficult to evaluate and deploy in practice.

By Yunhua Zhong, Yixuan Tang, Yifan Li, Pan Liu, Zhiwen Yang, Jie Yang, Jun Xia

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arXiv Machine Learning

Jun 2

Data-Driven Spectral Prediction for Accelerating Large-Scale Electronic Structure Calculations

arXiv:2606. 00401v1 Announce Type: cross Abstract: Simulating large molecular systems comprising thousands of atoms requires highly scalable methodologies.

By Abhiram Badrinarayanan, Davor Davidovic, Edoardo Di Napoli, Jurica Novak, Luigi Genovese, Gustavo Ramirez-Hidalgo, Xinzhe Wu

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Related stories

MARLIN: De Novo Molecular Structure Elucidation from Tandem Mass Spectra without a Ground-Truth Formula

MS-GPT: Rethinking MS/MS De Novo Structure Elucidation as Spectrum-Induced Posterior Querying of a Molecule-Language Model

MSAlign: Aligning Molecule and Mass Spectra representations for Metabolite Identification

GLACIER: Rethinking Mass Spectrum Prediction as an Object Detection Problem

FlexMS: A Unified Public Benchmark for Molecule Tandem Mass Spectrum Prediction

Data-Driven Spectral Prediction for Accelerating Large-Scale Electronic Structure Calculations