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.
Keywords
Subject
Publication details
- Journal
- Not available
- Open access
- Green open access
Cite this article
APA 7
Khoo, L. M. S. (2026). Nearest-neighbour baselines for fingerprint prediction from MS/MS spectra under different assumptions. https://omanscience.com/en/articles/nearest-neighbour-baselines-for-fingerprint-prediction-from-ms-ms-spectra-under-different-assumptions
MLA 9
Khoo, Ling Min Serena. "Nearest-neighbour baselines for fingerprint prediction from MS/MS spectra under different assumptions." https://omanscience.com/en/articles/nearest-neighbour-baselines-for-fingerprint-prediction-from-ms-ms-spectra-under-different-assumptions.
Chicago (author–date)
Khoo, Ling Min Serena. 2026. "Nearest-neighbour baselines for fingerprint prediction from MS/MS spectra under different assumptions." https://omanscience.com/en/articles/nearest-neighbour-baselines-for-fingerprint-prediction-from-ms-ms-spectra-under-different-assumptions.
Harvard
Khoo, L. M. S. (2026) 'Nearest-neighbour baselines for fingerprint prediction from MS/MS spectra under different assumptions', Available at: https://omanscience.com/en/articles/nearest-neighbour-baselines-for-fingerprint-prediction-from-ms-ms-spectra-under-different-assumptions.
Vancouver
Khoo LMS. Nearest-neighbour baselines for fingerprint prediction from MS/MS spectra under different assumptions. https://omanscience.com/en/articles/nearest-neighbour-baselines-for-fingerprint-prediction-from-ms-ms-spectra-under-different-assumptions
IEEE
L. M. S. Khoo, "Nearest-neighbour baselines for fingerprint prediction from MS/MS spectra under different assumptions," https://omanscience.com/en/articles/nearest-neighbour-baselines-for-fingerprint-prediction-from-ms-ms-spectra-under-different-assumptions.