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[Submitted on 30 Sep 2026] Title:Nearest-neighbour baselines for fingerprint prediction from MS/MS spectra under different assumptions View a PDF of the paper titled Nearest-neighbour baselines for fingerprint prediction from MS/MS spectra under different assumptions, by Ling Min Serena Khoo View PDF HTML (experimental) Abstract:It has recently been shown that nearest-neighbour retrieval provides a strong baseline for molecular fingerprint prediction from MS/MS spectra, with several variants matching or outperforming current deep learning models (Khoo and Barzilay, 2026; Liu et al., 2026; Gupta et al., 2026). Importantly, "nearest neighbour" encompasses a family of retrieval methods that differ in the information assumed to be available at inference. In this report, we systematically compare several nearest-neighbour variants and show how these differing assumptions affect performance. Our goal is to establish stricter baselines that enable more rigorous benchmarking and better measure progress in this area. Comments: 6 pages, 2 figures Subjects: Machine Learning (cs.LG); Computational Engineering, Finance, and Science (cs.CE); Machine Learning (stat.ML) Cite as: arXiv:2610.02249 [cs.LG] (or arXiv:2610.02249v1 [cs.LG] for this version) https://doi.org/10.48550/arXiv.2610.02249 arXiv-issued DOI via DataCite Submission history From: Ling Min Serena Khoo [view email] [v1] Wed, 30 Sep 2026 18:41:00 UTC (12 KB) Full-text links: Access Paper: View a PDF of the paper titled Nearest-neighbour baselines for fingerprint prediction from MS/MS spectra under different assumptions, by Ling Min Serena Khoo View PDF HTML (experimental) TeX Source view license Current browse context: cs.LG new | recent | 2026-10 Change to browse by: cs cs.CE stat stat.ML References & Citations NASA ADS Google Scholar Semantic Scholar Loading... Data provided by: Bibliographic Tools Bibliographic and Citation Tools Bibliographic Explorer Toggle Bibliographic Explorer (What is the Explorer?) Connected Papers Toggle Connected Papers (What is Connected Papers?) Litmaps Toggle Litmaps (What is Litmaps?) scite.ai Toggle scite Smart Citations (What are Smart Citations?) Code, Data, Media Code, Data and Media Associated with this Article alphaXiv Toggle alphaXiv (What is alphaXiv?) Links to Code Toggle CatalyzeX Code Finder for Papers (What is CatalyzeX?) DagsHub Toggle DagsHub (What is DagsHub?) GotitPub Toggle Gotit.pub (What is GotitPub?) Huggingface Toggle Hugging Face (What is Huggingface?) ScienceCast Toggle ScienceCast (What is ScienceCast?) Demos Demos Replicate Toggle Replicate (What is Replicate?) Spaces Toggle Hugging Face Spaces (What is Spaces?) Spaces Toggle TXYZ.AI (What is TXYZ.AI?) Related Papers Recommenders and Search Tools Link to Influence Flower Influence Flower (What are Influence Flowers?) Core recommender toggle CORE Recommender (What is CORE?) IArxiv recommender toggle IArxiv Recommender (What is IArxiv?) Author Venue Institution Topic About arXivLabs arXivLabs: experimental projects with community collaborators arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs. Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)