MassSpecGym MCES split, formula supplied candidate pool (MSAlign molecular retrieval split)

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3 evaluations · 9 metric rows. Different protocols are not a single leaderboard.

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: FLARE	Protocol: MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@1: MassSpecGym MCES split retrieval with formula supplied Dataset subset: MassSpecGym MCES split, formula supplied candidate pool (MSAlign molecular retrieval split)	27.2% recall_at_1 percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · source checked Methods, coverage and source FLARE on MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@1: MassSpecGym MCES split retrieval with formula supplied 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. Aggregation: Not reported msalign: Primary paper PDF · Table 3, MassSpecGym MCES split, row R@1, column 10 (FLARE)
Configuration: FLARE	Protocol: MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@20: MassSpecGym MCES split retrieval with formula supplied Dataset subset: MassSpecGym MCES split, formula supplied candidate pool (MSAlign molecular retrieval split)	80.2% recall_at_20 percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · source checked Methods, coverage and source FLARE on MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@20: MassSpecGym MCES split retrieval with formula supplied 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. Aggregation: Not reported msalign: Primary paper PDF · Table 3, MassSpecGym MCES split, row R@20, column 10 (FLARE)
Configuration: FLARE	Protocol: MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@5: MassSpecGym MCES split retrieval with formula supplied Dataset subset: MassSpecGym MCES split, formula supplied candidate pool (MSAlign molecular retrieval split)	53.8% recall_at_5 percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · source checked Methods, coverage and source FLARE on MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@5: MassSpecGym MCES split retrieval with formula supplied 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. Aggregation: Not reported msalign: Primary paper PDF · Table 3, MassSpecGym MCES split, row R@5, column 10 (FLARE)
Configuration: MIST	Protocol: MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@1: MassSpecGym MCES split retrieval with formula supplied Dataset subset: MassSpecGym MCES split, formula supplied candidate pool (MSAlign molecular retrieval split)	14.6% recall_at_1 percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · source checked Methods, coverage and source MIST on MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@1: MassSpecGym MCES split retrieval with formula supplied 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. Aggregation: Not reported msalign: Primary paper PDF · Table 3, MassSpecGym MCES split, row R@1, column 9 (MIST)
Configuration: MIST	Protocol: MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@20: MassSpecGym MCES split retrieval with formula supplied Dataset subset: MassSpecGym MCES split, formula supplied candidate pool (MSAlign molecular retrieval split)	59.1% recall_at_20 percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · source checked Methods, coverage and source MIST on MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@20: MassSpecGym MCES split retrieval with formula supplied 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. Aggregation: Not reported msalign: Primary paper PDF · Table 3, MassSpecGym MCES split, row R@20, column 9 (MIST)
Configuration: MIST	Protocol: MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@5: MassSpecGym MCES split retrieval with formula supplied Dataset subset: MassSpecGym MCES split, formula supplied candidate pool (MSAlign molecular retrieval split)	34.9% recall_at_5 percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · source checked Methods, coverage and source MIST on MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@5: MassSpecGym MCES split retrieval with formula supplied 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. Aggregation: Not reported msalign: Primary paper PDF · Table 3, MassSpecGym MCES split, row R@5, column 9 (MIST)
Configuration: MSAlign (+Filter)	Protocol: MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@1: MassSpecGym MCES split retrieval with formula supplied Dataset subset: MassSpecGym MCES split, formula supplied candidate pool (MSAlign molecular retrieval split)	32.3% recall_at_1 percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source MSAlign (+Filter) on MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@1: MassSpecGym MCES split retrieval with formula supplied 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. Aggregation: Not reported msalign: Primary paper PDF · Table 3, MassSpecGym MCES split, row R@1, column 11 (MSAlign (+Filter))
Configuration: MSAlign (+Filter)	Protocol: MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@20: MassSpecGym MCES split retrieval with formula supplied Dataset subset: MassSpecGym MCES split, formula supplied candidate pool (MSAlign molecular retrieval split)	85.5% recall_at_20 percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source MSAlign (+Filter) on MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@20: MassSpecGym MCES split retrieval with formula supplied 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. Aggregation: Not reported msalign: Primary paper PDF · Table 3, MassSpecGym MCES split, row R@20, column 11 (MSAlign (+Filter))
Configuration: MSAlign (+Filter)	Protocol: MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@5: MassSpecGym MCES split retrieval with formula supplied Dataset subset: MassSpecGym MCES split, formula supplied candidate pool (MSAlign molecular retrieval split)	61.8% recall_at_5 percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source MSAlign (+Filter) on MSAlign molecular retrieval MassSpecGym MCES split: formula supplied, R@5: MassSpecGym MCES split retrieval with formula supplied 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. Aggregation: Not reported msalign: Primary paper PDF · Table 3, MassSpecGym MCES split, row R@5, column 11 (MSAlign (+Filter))

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Claims, original sources and review scope · Release 2026-09-23-2b89723c6dd9
Property and statement	Original source and location	Review and provenance
description Dataset subset reported in MSAlign v1: Table 3. Exact split manifest remains unextracted; source-table identity is retained. Context-only references	msalign: Primary paper PDF Original source ↗ No field-specific location recorded Version: 2605.19752v1 Retrieved: 2026-09-16T20:04:04.777728+00:00	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `7395a55141ee7916741b7d9e6d4f42a1d3a03217a36ce6824ac3ff48afd4f26f` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
name MassSpecGym MCES split, formula supplied candidate pool (MSAlign molecular retrieval split) Context-only references	msalign: Primary paper PDF Original source ↗ No field-specific location recorded Version: 2605.19752v1 Retrieved: 2026-09-16T20:04:04.777728+00:00	not individually reviewed No individual claim review recorded Audit details Field: `name` 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-dataset-massspecgym-mces-split-formula-supplied-candidate-pool

areas: molecular-omics
missing metadata: version: unreported; url: unextracted

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