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

Overview

MassSpecGym formula split retrieval with formula supplied. Scored with Recall@1 on MassSpecGym formula split, formula supplied candidate pool. Section 5.1 candidate retrieval: 256 mass-matched PubChem candidates per spectrum without formula; formula-conditioned methods can exploit true formula and MSAlign+Filter reduces the pool to about 100. Preserve the named source split; exact original split hashes remain unextracted.

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Results

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Evaluation scope and datasetMetric and reported setup

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.

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Reported score

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Methods and evaluation design

Procedure, tasks and evaluated configurations

Evaluation design

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Benchmarks

MSAlign molecular retrieval evaluations

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Baseline coverage

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Author-reported evaluations: 1
External evaluations: 2

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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.

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Evidence

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Evidence table

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1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-09-23-2b89723c6dd9
Property and statement	Original source and location	Review and provenance
Relationship: part of msalign-2026-molecular-retrieval Individual claims	msalign: Primary paper PDF Original source ↗ Table 3, MassSpecGym formula split, R@1; Section 5.1 Version: 2605.19752v1 Retrieved: 2026-09-16T20:04:04.777728+00:00	source checked automated source review · 2026-09-23 Audit details Primary-source transcription with no human sign-off and no independent reproduction. Field: `links:part_of:msalign-2026-molecular-retrieval` Claim: msalign-2026-table3-association-massspecgym-formula-split-formula-supplied-r-1 Source artifact SHA-256: `7395a55141ee7916741b7d9e6d4f42a1d3a03217a36ce6824ac3ff48afd4f26f` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

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

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msalign: Primary paper PDF · Original source · 2605.19752v1

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Technical metadata and extraction receipts

Stable ID: msalign-2026-table3-task-massspecgym-formula-split-formula-supplied-r-1

areas: molecular-omics
tasks: MassSpecGym formula split retrieval with formula supplied
metric: Recall@1
metric direction: higher
dataset: MassSpecGym formula split, formula supplied candidate pool
protocol: Section 5.1 candidate retrieval: 256 mass-matched PubChem candidates per spectrum without formula; formula-conditioned methods can exploit true formula and MSAlign+Filter reduces the pool to about 100. Preserve the named source split; exact original split hashes remain unextracted.
source locator: Table 3, MassSpecGym formula split, R@1; Section 5.1
comparison panels: id: msalign-2026-table3-panel-massspecgym-formula-split-formula-supplied-r-1; title: MSAlign molecular retrieval MassSpecGym formula split: formula supplied, R@1: MassSpecGym formula split retrieval with formula supplied; protocol id: msalign-2026-table3-task-massspecgym-formula-split-formula-supplied-r-1; dataset id: msalign-2026-table3-dataset-massspecgym-formula-split-formula-supplied-candidate-pool; metric: recall_at_1; unit: percent; direction: higher; result ids: msalign-2026-table3-result-mist-massspecgym-formula-split-formula-supplied-r-1-recall-at-1; msalign-2026-table3-result-flare-massspecgym-formula-split-formula-supplied-r-1-recall-at-1; msalign-2026-table3-result-msalign-plus-filter-massspecgym-formula-split-formula-supplied-r-1-recall-at-1; source ids: evidence-official-760ab2fa8c396aeb796c; source locator: Table 3, MassSpecGym formula split, R@1; Section 5.1; context: 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.; caveats: 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.; review: method: automated_source_review; date: 2026-09-23
entity level: protocol

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