Nearest-neighbour baselines for fingerprint prediction from MS/MS spectra under different assumptions
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.
| Authors | Ling Min Serena Khoo |
|---|---|
| Primary category | cs.LG |
| Published | 30 September 2026 |
| Last updated at source | 30 September 2026 |
Popularity, last 2 days
0 now. Counts as reported by the source, snapshotted daily by Silytics.
Silytics shows public metadata from arXiv and links to the original. Information may be incomplete or out of date. Last refreshed 18 October 2026. Licenses and terms of the original apply to the work itself. Not financial, legal or professional advice.