{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/massspecgym-a-benchmark-for-the-discovery-and","title":"MassSpecGym: A benchmark for the discovery and identification of molecules","arxiv_id":"2410.23326","date":"2024-10-30","proceeding":null,"authors":["Roman Bushuiev","Anton Bushuiev","Niek F. de Jonge","Adamo Young","Fleming Kretschmer","Raman Samusevich","Janne Heirman","Fei Wang","Luke Zhang","Kai Dührkop","Marcus Ludwig","Nils A. Haupt","Apurva Kalia","Corinna Brungs","Robin Schmid","Russell Greiner","Bo wang","David S. Wishart","Li-Ping Liu","Juho Rousu","Wout Bittremieux","Hannes Rost","Tytus D. Mak","Soha Hassoun","Florian Huber","Justin J. J. van der Hooft","Michael A. Stravs","Sebastian Böcker","Josef Sivic","Tomáš Pluskal"],"abstract":"The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of molecular structures. However, decoding a molecular structure from its mass spectrum is exceptionally challenging, even when performed by human experts. As a result, the vast majority of acquired MS/MS spectra remain uninterpreted, thereby limiting our understanding of the underlying (bio)chemical processes. Despite decades of progress in machine learning applications for predicting molecular structures from MS/MS spectra, the development of new methods is severely hindered by the lack of standard datasets and evaluation protocols. To address this problem, we propose MassSpecGym -- the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data. Our benchmark comprises the largest publicly available collection of high-quality labeled MS/MS spectra and defines three MS/MS annotation challenges: de novo molecular structure generation, molecule retrieval, and spectrum simulation. It includes new evaluation metrics and a generalization-demanding data split, therefore standardizing the MS/MS annotation tasks and rendering the problem accessible to the broad machine learning community. MassSpecGym is publicly available at https://github.com/pluskal-lab/MassSpecGym.","url_abs":"https://arxiv.org/abs/2410.23326v3","url_pdf":"https://arxiv.org/pdf/2410.23326v3.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"massspecgym-a-benchmark-for-the-discovery-and","repo_url":"https://github.com/pluskal-lab/massspecgym","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"de-novo-molecule-generation-from-ms-ms","task_name":"De novo molecule generation from MS/MS spectrum"},{"task_slug":"de-novo-molecule-generation-from-ms-ms-1","task_name":"De novo molecule generation from MS/MS spectrum (bonus chemical formulae)"},{"task_slug":"ms-ms-spectrum-simulation","task_name":"MS/MS spectrum 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