Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Protocol
MassSpecGym · formula (MassSpecGym Molecule retrieval)
MassSpecGym · formula · Table 3. Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split
Sources
MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3: Hit rate @1, formulaOverview
Key specifications have not been extracted for this record. See the linked evaluation and sources for the reported setup.
limited source coverage · Automated source review, 2026-09-17. All specifications and missing details
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
MassSpecGym · formula · Table 3
Hit rate @1 (percent) · Higher values are better.
MassSpecGym · formula (MassSpecGym Molecule retrieval) · MassSpecGym · formula
Evidence origin: Author-reported evaluation.
MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3: Hit rate @1, formula- Source metric equations define hit rates as fractions, while table values use percentage scale; recorded values are not rescaled.
- Zero generation accuracy is a reported result, not missingness.
- No checkpoint revision inferred from method name.
- Bootstrap CIs reflect resampling of this test set; not independently reproduced and not seed standard deviations.
- Full table retained, including weaker/random methods and unavailable formula-simulation similarity cells.
Comparison details and limitations
Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split
Automated source review: 2026-09-17. Numerical source review does not establish independent reproduction.
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.
Showing 5 of 5 matching rows.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Evaluation in this paper
Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split
Sources
MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3: Hit rate @1, formulaEvaluation design
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Benchmarks
Tasks
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Recorded evaluations
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Baseline coverage
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Null control
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This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
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Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-09-29-06401fd5b220. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Strengths and limitations
Limitations and conditions
No source-reviewed explanatory claims are recorded here yet.
Profile review details
Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.
Stable record: paper-protocol-1e7bb17e6ce294d906Specifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | Not extracted or verified for this record. |
| Organisms | Not extracted or verified for this record. |
| Assays | Not extracted or verified for this record. |
| Splits | Not extracted or verified for this record. |
| Allowed inputs | Not extracted or verified for this record. |
| Adaptation | Not extracted or verified for this record. |
| Metrics | Not extracted or verified for this record. |
| Baselines | Not extracted or verified for this record. |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Papers and result coverage
Last literature check: 2026-09-17. Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
| Paper or primary resource | Version | Reference |
|---|---|---|
| MassSpecGym: A benchmark for the discovery and identification of molecules | 2410.23326v1 | Read source |
Historical gaps recorded on 2026-09-17
The catalogue now holds 20 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.
- Independent batch review before import; preserve existing observation identities.
Search and extraction details
complete comparison tables extracted pending publication review
Searches
- MassSpecGym 2410.23326 benchmark results Table 1 Table 2
Evidence locations
- Table 3: Hit rate @1, formula
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
4 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Evaluation in this paper Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Individual claims | MassSpecGym: A benchmark for the discovery and identification of molecules Table 3: Hit rate @1, formula Version: 2410.23326v1 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Introduction MassSpecGym · formula · Table 3. Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Individual claims | MassSpecGym: A benchmark for the discovery and identification of molecules Table 3: Hit rate @1, formula Version: 2410.23326v1 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: evaluates task discovery-benchmark-massspecgym-molecule-retrieval Individual claims | MassSpecGym: A benchmark for the discovery and identification of molecules Table 3: Hit rate @1, formula Version: 2410.23326v1 | source checked automated source review · 2026-09-17 Audit detailsField: Claim: paper-claim-a5d8e86cdbf805cb95 Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: part of discovery-benchmark-massspecgym Individual claims | MassSpecGym: A benchmark for the discovery and identification of molecules Table 3: Hit rate @1, formula Version: 2410.23326v1 | source checked automated source review · 2026-09-17 Audit detailsField: Claim: paper-claim-f62a04f361e74f042e Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
1 source records and release history
- MassSpecGym: A benchmark for the discovery and identification of molecules · Original source · 2410.23326v1
Technical metadata and extraction receipts
Stable ID: paper-protocol-1e7bb17e6ce294d906
- areas
- metabolomics
- entity level
- protocol
- protocol
- Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split
- comparison panels
- id: part2-massspecgym-table3-ac4b0b4611; title: MassSpecGym · formula · Table 3; protocol id: paper-protocol-1e7bb17e6ce294d906; dataset id: paper-dataset-e3dee7ae24615eecfb; metric: Hit rate @1; unit: percent; direction: higher; result ids: paper-result-96eb3d9e4116e85dc3; paper-result-19979776fcf90cd085; paper-result-6d5f81ef670db6f81b; paper-result-7e55a965688b10e2cc; paper-result-761f932c6a35c888bb; source ids: part2-massspecgym-arxiv-v1; source locator: Table 3: Hit rate @1, formula; context: Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split; caveats: Source metric equations define hit rates as fractions, while table values use percentage scale; recorded values are not rescaled.; Zero generation accuracy is a reported result, not missingness.; No checkpoint revision inferred from method name.; Bootstrap CIs reflect resampling of this test set; not independently reproduced and not seed standard deviations.; Full table retained, including weaker/random methods and unavailable formula-simulation similarity cells.; review: method: automated_source_review; date: 2026-09-17; id: part2-massspecgym-table3-a71e8b64c9; title: MassSpecGym · formula · Table 3; protocol id: paper-protocol-1e7bb17e6ce294d906; dataset id: paper-dataset-e3dee7ae24615eecfb; metric: Hit rate @5; unit: percent; direction: higher; result ids: paper-result-6bf388327e502fbdd6; paper-result-1b7eee640fec71e99b; paper-result-773438d255878a0817; paper-result-a2021eb25d2e915417; paper-result-7a7bc4ebdca6051342; source ids: part2-massspecgym-arxiv-v1; source locator: Table 3: Hit rate @5, formula; context: Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split; caveats: Source metric equations define hit rates as fractions, while table values use percentage scale; recorded values are not rescaled.; Zero generation accuracy is a reported result, not missingness.; No checkpoint revision inferred from method name.; Bootstrap CIs reflect resampling of this test set; not independently reproduced and not seed standard deviations.; Full table retained, including weaker/random methods and unavailable formula-simulation similarity cells.; review: method: automated_source_review; date: 2026-09-17; id: part2-massspecgym-table3-8dc4756cf6; title: MassSpecGym · formula · Table 3; protocol id: paper-protocol-1e7bb17e6ce294d906; dataset id: paper-dataset-e3dee7ae24615eecfb; metric: Hit rate @20; unit: percent; direction: higher; result ids: paper-result-1816c840f0de8bc10b; paper-result-c905d384ee9e3b5f91; paper-result-e1302d68232a47d02d; paper-result-46121102e555a35255; paper-result-3b6baab5e2664e30e6; source ids: part2-massspecgym-arxiv-v1; source locator: Table 3: Hit rate @20, formula; context: Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split; caveats: Source metric equations define hit rates as fractions, while table values use percentage scale; recorded values are not rescaled.; Zero generation accuracy is a reported result, not missingness.; No checkpoint revision inferred from method name.; Bootstrap CIs reflect resampling of this test set; not independently reproduced and not seed standard deviations.; Full table retained, including weaker/random methods and unavailable formula-simulation similarity cells.; review: method: automated_source_review; date: 2026-09-17; id: part2-massspecgym-table3-ebdb34929b; title: MassSpecGym · formula · Table 3; protocol id: paper-protocol-1e7bb17e6ce294d906; dataset id: paper-dataset-e3dee7ae24615eecfb; metric: MCES @1; unit: edge-edit distance; direction: lower; result ids: paper-result-8b2608a402d6ab54e6; paper-result-47e90701446fc3f6b0; paper-result-88df2cfb82ff24f522; paper-result-8d04b85ca056e77ff0; paper-result-e5a6f34b3603af99f9; source ids: part2-massspecgym-arxiv-v1; source locator: Table 3: MCES @1, formula; context: Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split; caveats: Source metric equations define hit rates as fractions, while table values use percentage scale; recorded values are not rescaled.; Zero generation accuracy is a reported result, not missingness.; No checkpoint revision inferred from method name.; Bootstrap CIs reflect resampling of this test set; not independently reproduced and not seed standard deviations.; Full table retained, including weaker/random methods and unavailable formula-simulation similarity cells.; review: method: automated_source_review; date: 2026-09-17
- benchmark research
- review date: 2026-09-17; status: complete_comparison_tables_extracted_pending_publication_review; primary sources: part2-massspecgym-arxiv-v1; inspected locators: Table 3: Hit rate @1, formula; searched queries: MassSpecGym 2410.23326 benchmark results Table 1 Table 2; gaps: Independent batch review before import; preserve existing observation identities.; claim scope: Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
- legacy kinds
- benchmark
- entity classification
- review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: part2-massspecgym-arxiv-v1; source locator: Table 3: Hit rate @1, formula; ambiguities: None recorded
Related records
- evaluates task: MassSpecGym Molecule retrieval
- part of: MassSpecGym
- subject: MassSpecGym · formula (MassSpecGym Molecule retrieval): links:evaluates_task:discovery-benchmark-massspecgym-molecule-retrieval
- subject: MassSpecGym · formula (MassSpecGym Molecule retrieval): links:part_of:discovery-benchmark-massspecgym
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