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Benchmark

MSAlign molecular retrieval evaluations

Spectrum-to-molecule retrieval comparisons on NPLIB1, Spectraverse and two MassSpecGym splits, reported in MSAlign Table 3. Formula availability and candidate pools remain separate.

36 evaluations · 108 metric rows

Overview

Spectrum-to-molecule retrieval comparisons on NPLIB1, Spectraverse and two MassSpecGym splits, reported in MSAlign Table 3. Formula availability and candidate pools remain separate.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Results

Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.

MSAlign molecular retrieval MassSpecGym formula split: formula supplied, R@1: MassSpecGym formula split retrieval with formula supplied

recall_at_1 (percent) · Higher values are better.

Every method MSAlign molecular retrieval reports on MassSpecGym formula split retrieval with formula supplied, scored with Recall@1 on MassSpecGym formula split, formula supplied candidate pool.

MSAlign molecular retrieval MassSpecGym formula split: formula supplied, R@1: MassSpecGym formula split retrieval with formula supplied · MassSpecGym formula split, formula supplied candidate pool (MSAlign molecular retrieval split)

Evidence origin: Independent external evaluation, Author-reported evaluation. Numerical source review does not establish independent reproduction.

msalign: Primary paper PDF · Table 3, MassSpecGym formula split, R@1; Section 5.1

Molecular formula is additional information. Formula-conditioned and formula-free methods are kept in separate panels.

All comparison limitations (4)
  • Molecular formula is additional information. Formula-conditioned and formula-free methods are kept in separate panels.
  • NPLIB1 uses 256 candidates here; do not compare it with scores from different candidate pools.
  • Table 3 prints percentages, including 09.5 and 20.00. Source precision is preserved.
  • Exact test denominators, checkpoint hashes and evaluator revision have not been established for these cells.

Automated source review: 2026-09-23.

No unavailable values; missing scores remain labelled and are never plotted as zero.

Showing 3 of 3 matching rows.

Tested configuration
0255075100
Reported score
  1. MSAlign (+Filter)61.3
  2. MIST46.8
  3. FLARE31.8

Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Evaluation design

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Protocols

These source-backed links do not make different protocols or scores interchangeable.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 48 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

Baseline status by linked protocol

Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums

Coverage is derived from release 2026-09-23-2b89723c6dd9. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run this benchmark

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Run this benchmark

The paper describes its common evaluation implementation and candidate pools. Rewire has not executed this benchmark and has no verified pinned runner recipe; original split and evaluator revisions remain unextracted.

A maintained rewire runner has not been verified for this benchmark. Check data access, weights, licences, dependencies and hardware in the linked official documentation; requirements have not been fully extracted.

msalign: Primary paper PDF · Section 5.1; Table 3
Strengths, limitations and unresolved questions

Evidence

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Evidence table

Inspect claims, sources and review details

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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-23-2b89723c6dd9
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Sources and history

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Release 2026-09-23-2b89723c6dd9 · Record review: source checked

1 source records and release historyDownload this release
Technical metadata and extraction receipts

Stable ID: msalign-2026-molecular-retrieval

areas
metabolomics
run documentation
record id: msalign-2026-molecular-retrieval; status: source_reviewed_not_executed; source ids: evidence-official-760ab2fa8c396aeb796c; source locator: Section 5.1; Table 3; summary: The paper describes its common evaluation implementation and candidate pools. Rewire has not executed this benchmark and has no verified pinned runner recipe; original split and evaluator revisions remain unextracted.
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