# Nearest-neighbour baselines for fingerprint prediction from MS/MS spectra under different assumptions

> Source: <https://arxiv.org/abs/2610.02249>
> Published: 2026-10-05 04:00:00+00:00

# Computer Science > Machine Learning

  [Submitted on 30 Sep 2026]

# Title:Nearest-neighbour baselines for fingerprint prediction from MS/MS spectra under different assumptions

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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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