[Submitted on 30 Sep 2026]
[View PDF](https://arxiv.org/pdf/2610.02249)
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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.
Submission history #
From: Ling Min Serena Khoo [
[view email](https://arxiv.org/show-email/01818007/2610.02249)]
**[v1]** Wed, 30 Sep 2026 18:41:00 UTC (12 KB)
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