Nearest-neighbour baselines for fingerprint prediction from MS/MS spectra under different assumptions
cs.LG, cs.CE, stat.ML
Submitted: 2026-09-30
Updated: 2026-09-30
Comments: 6 pages, 2 figures
License: http://creativecommons.org/licenses/by/4.0/
The gist: 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
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.
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