MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3)
MassSpecGym formula-known retrieval (bonus) on the test fold, scored by MCES@1; mean over test spectra.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
18 recorded evaluations, 18 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
18 evaluations · 18 results. Different protocols are not a single leaderboard.
Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) · Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)
Sorted by Top-1 MCES (retrieval) (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
All 18 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: ChemBERTa SMILES classifier (spectrum-free), corrected candidate canonicalization (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 13.8 (13.64-13.96) Top-1 MCES (retrieval) unitless · lower Uncertainty: 99.9% CI 13.64 to 13.96. Range printed in parentheses after the mean. Appendix 'Confidence Intervals': 99.9% bootstrap interval over 20,000 resamples of the test set. Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcelit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Exploiting Canonicalization Artifacts (Not Valid Under Corrected Candidate Canonicalization)', row '(3) ChemBERTa SMILES classifier (corrected)', column 'MCES@1' |
| Configuration: ChemBERTa SMILES classifier (spectrum-free), original candidate canonicalization (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 0.05 (0.03-0.07) Top-1 MCES (retrieval) unitless · lower Uncertainty: 99.9% CI 0.03 to 0.07. Range printed in parentheses after the mean. Appendix 'Confidence Intervals': 99.9% bootstrap interval over 20,000 resamples of the test set. Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcelit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Exploiting Canonicalization Artifacts (Not Valid Under Corrected Candidate Canonicalization)', row '(3) ChemBERTa SMILES classifier (inflated)', column 'MCES@1' |
| Configuration: ChemFormer two-stage retrieval, corrected candidate canonicalization (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 13.23 (13.06-13.39) Top-1 MCES (retrieval) unitless · lower Uncertainty: 99.9% CI 13.06 to 13.39. Range printed in parentheses after the mean. Appendix 'Confidence Intervals': 99.9% bootstrap interval over 20,000 resamples of the test set. Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcelit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Exploiting Canonicalization Artifacts (Not Valid Under Corrected Candidate Canonicalization)', row '(2) ChemFormer Two-Stage Retrieval (corrected)', column 'MCES@1' |
| Configuration: ChemFormer two-stage retrieval, original candidate canonicalization (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 5.39 (5.20-5.60) Top-1 MCES (retrieval) unitless · lower Uncertainty: 99.9% CI 5.20 to 5.60. Range printed in parentheses after the mean. Appendix 'Confidence Intervals': 99.9% bootstrap interval over 20,000 resamples of the test set. Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcelit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Exploiting Canonicalization Artifacts (Not Valid Under Corrected Candidate Canonicalization)', row '(2) ChemFormer Two-Stage Retrieval (inflated)', column 'MCES@1' |
| Configuration: DiffMS generative retrieval (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 6.67 (6.50-6.84) Top-1 MCES (retrieval) unitless · lower Uncertainty: 99.9% CI 6.50 to 6.84. Range printed in parentheses after the mean. Table 3 caption: 99.9% BCa bootstrap intervals over 20,000 resamples, stated for all bracketed values. Value repeated from the cited work; that work's own interval settings were not checked. Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceDiffMS generative retrieval on MassSpecGym formula-retrieval (MCES@1) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Reported Performance in Retrieval Task w/ Bonus (i.e., Formula Known)', row 'DiffMS (generative retrieval)', column 'MCES@1' |
| Configuration: DreaMS spectral encoder aligned to frozen ChemBERTa, corrected candidate canonicalization (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 13.13 (12.97-13.28) Top-1 MCES (retrieval) unitless · lower Uncertainty: 99.9% CI 12.97 to 13.28. Range printed in parentheses after the mean. Appendix 'Confidence Intervals': 99.9% bootstrap interval over 20,000 resamples of the test set. Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcelit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Exploiting Canonicalization Artifacts (Not Valid Under Corrected Candidate Canonicalization)', row '(1) DreaMS + ChemBERTa Alignment (corrected)', column 'MCES@1' |
| Configuration: DreaMS spectral encoder aligned to frozen ChemBERTa, original candidate canonicalization (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 2.86 (2.70-3.03) Top-1 MCES (retrieval) unitless · lower Uncertainty: 99.9% CI 2.70 to 3.03. Range printed in parentheses after the mean. Appendix 'Confidence Intervals': 99.9% bootstrap interval over 20,000 resamples of the test set. Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcelit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Exploiting Canonicalization Artifacts (Not Valid Under Corrected Candidate Canonicalization)', row '(1) DreaMS + ChemBERTa Alignment (inflated)', column 'MCES@1' |
| Configuration: FLARE (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 9.00 (8.82–9.18) Top-1 MCES (retrieval) unitless · lower Uncertainty: 99.9% CI 8.82 to 9.18. Range printed in parentheses after the mean. Table 3 caption: 99.9% BCa bootstrap intervals over 20,000 resamples, stated for all bracketed values. Value repeated from the cited work; that work's own interval settings were not checked. Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceFLARE on MassSpecGym formula-retrieval (MCES@1) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Reported Performance in Retrieval Task w/ Bonus (i.e., Formula Known)', row 'FLARE', column 'MCES@1' |
| Configuration: FRIGID generative retrieval (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 6.28 (6.09-6.47) Top-1 MCES (retrieval) unitless · lower Uncertainty: 99.9% CI 6.09 to 6.47. Range printed in parentheses after the mean. Table 3 caption: 99.9% BCa bootstrap intervals over 20,000 resamples, stated for all bracketed values. Value repeated from the cited work; that work's own interval settings were not checked. Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceFRIGID generative retrieval on MassSpecGym formula-retrieval (MCES@1) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Reported Performance in Retrieval Task w/ Bonus (i.e., Formula Known)', row 'FRIGID (generative retrieval)', column 'MCES@1' |
| Configuration: ICEBERG forward-model retrieval with imputed collision energies (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 6.61 (6.43–6.79) Top-1 MCES (retrieval) unitless · lower Uncertainty: 99.9% CI 6.43 to 6.79. Range printed in parentheses after the mean. Appendix 'Confidence Intervals': 99.9% bootstrap interval over 20,000 resamples of the test set. Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcelit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Reported Performance in Retrieval Task w/ Bonus (i.e., Formula Known)', row 'ICEBERG (forward model retrieval)', column 'MCES@1' |
| Configuration: JESTR (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 11.71 (11.54-11.87) Top-1 MCES (retrieval) unitless · lower Uncertainty: 99.9% CI 11.54 to 11.87. Range printed in parentheses after the mean. Table 3 caption: 99.9% BCa bootstrap intervals over 20,000 resamples, stated for all bracketed values. Value repeated from the cited work; that work's own interval settings were not checked. Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceJESTR on MassSpecGym formula-retrieval (MCES@1) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Reported Performance in Retrieval Task w/ Bonus (i.e., Formula Known)', row 'JESTR', column 'MCES@1' |
| Configuration: MIST, DiffMS checkpoint (vDiffMS) (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 7.72 (7.51-7.95) Top-1 MCES (retrieval) unitless · lower Uncertainty: 99.9% CI 7.51 to 7.95. Range printed in parentheses after the mean. Table 3 caption: 99.9% BCa bootstrap intervals over 20,000 resamples, stated for all bracketed values. Value repeated from the cited work; that work's own interval settings were not checked. Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceMIST, DiffMS checkpoint (vDiffMS) on MassSpecGym formula-retrieval (MCES@1) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Reported Performance in Retrieval Task w/ Bonus (i.e., Formula Known)', row 'MIST vDiffMS', column 'MCES@1' |
| Configuration: MIST, FRIGID checkpoint (vFRIGID) (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 5.16 (4.99-5.33) Top-1 MCES (retrieval) unitless · lower Uncertainty: 99.9% CI 4.99 to 5.33. Range printed in parentheses after the mean. Table 3 caption: 99.9% BCa bootstrap intervals over 20,000 resamples, stated for all bracketed values. Value repeated from the cited work; that work's own interval settings were not checked. Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceMIST, FRIGID checkpoint (vFRIGID) on MassSpecGym formula-retrieval (MCES@1) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Reported Performance in Retrieval Task w/ Bonus (i.e., Formula Known)', row 'MIST vFRIGID', column 'MCES@1' |
| Configuration: MIST + MolForge generative retrieval, reimplemented by the authors (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 8.73 (8.53-8.96) Top-1 MCES (retrieval) unitless · lower Uncertainty: 99.9% CI 8.53 to 8.96. Range printed in parentheses after the mean. Appendix 'Confidence Intervals': 99.9% bootstrap interval over 20,000 resamples of the test set. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcelit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Reported Performance in Retrieval Task w/ Bonus (i.e., Formula Known)', row 'MIST+MolForge (generative retrieval)†', column 'MCES@1' |
| Configuration: MVP (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 10.36 (10.19-10.53) Top-1 MCES (retrieval) unitless · lower Uncertainty: 99.9% CI 10.19 to 10.53. Range printed in parentheses after the mean. Table 3 caption: 99.9% BCa bootstrap intervals over 20,000 resamples, stated for all bracketed values. Value repeated from the cited work; that work's own interval settings were not checked. Coverage: Not reported scored / Not reported eligible | Result quoted from another source · Source checkedMethods, coverage and sourceMVP on MassSpecGym formula-retrieval (MCES@1) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Reported Performance in Retrieval Task w/ Bonus (i.e., Formula Known)', row 'MVP', column 'MCES@1' |
| Configuration: Nearest neighbour, reimplemented by the authors (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 13.82 (13.64-13.99) Top-1 MCES (retrieval) unitless · lower Uncertainty: 99.9% CI 13.64 to 13.99. Range printed in parentheses after the mean. Appendix 'Confidence Intervals': 99.9% bootstrap interval over 20,000 resamples of the test set. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNearest neighbour, reimplemented by the authors on MassSpecGym formula-retrieval (MCES@1) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Reported Performance in Retrieval Task w/ Bonus (i.e., Formula Known)', row 'Nearest Neighbor†', column 'MCES@1' |
| Configuration: PubChem default ranking (spectrum-blind) (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 7.43 (7.22-7.64) Top-1 MCES (retrieval) unitless · lower Uncertainty: 99.9% CI 7.22 to 7.64. Range printed in parentheses after the mean. Appendix 'Confidence Intervals': 99.9% bootstrap interval over 20,000 resamples of the test set. Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePubChem default ranking (spectrum-blind) on MassSpecGym formula-retrieval (MCES@1) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Exploiting Other Structure Biases (Spectrum-Blind Stress Test)', row '(4) PubChem default ranking', column 'MCES@1' |
| Configuration: Ranking by number of chiral atoms (spectrum-blind) (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), MCES@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 14.4 (14.23-14.56) Top-1 MCES (retrieval) unitless · lower Uncertainty: 99.9% CI 14.23 to 14.56. Range printed in parentheses after the mean. Appendix 'Confidence Intervals': 99.9% bootstrap interval over 20,000 resamples of the test set. Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRanking by number of chiral atoms (spectrum-blind) on MassSpecGym formula-retrieval (MCES@1) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Exploiting Other Structure Biases (Spectrum-Blind Stress Test)', row '(5) Ranking by num. of chiral atoms', column 'MCES@1' |
Source checking is not independent reproduction. Release 2026-10-23-5347695500ed.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- ChemBERTa SMILES classifier (spectrum-free), corrected candidate canonicalization on MassSpecGym formula-retrieval (MCES@1)
- ChemBERTa SMILES classifier (spectrum-free), original candidate canonicalization on MassSpecGym formula-retrieval (MCES@1)
- ChemFormer two-stage retrieval, corrected candidate canonicalization on MassSpecGym formula-retrieval (MCES@1)
- ChemFormer two-stage retrieval, original candidate canonicalization on MassSpecGym formula-retrieval (MCES@1)
- DiffMS generative retrieval on MassSpecGym formula-retrieval (MCES@1)
- DreaMS spectral encoder aligned to frozen ChemBERTa, corrected candidate canonicalization on MassSpecGym formula-retrieval (MCES@1)
- DreaMS spectral encoder aligned to frozen ChemBERTa, original candidate canonicalization on MassSpecGym formula-retrieval (MCES@1)
- FLARE on MassSpecGym formula-retrieval (MCES@1)
- FRIGID generative retrieval on MassSpecGym formula-retrieval (MCES@1)
- ICEBERG forward-model retrieval with imputed collision energies on MassSpecGym formula-retrieval (MCES@1)
- JESTR on MassSpecGym formula-retrieval (MCES@1)
- MIST, DiffMS checkpoint (vDiffMS) on MassSpecGym formula-retrieval (MCES@1)
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 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- Author-reported evaluations
- 9
- External evaluations
- 2
- paper compilation
- 7
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Select a task-valid null control after reviewing inputs and metric
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Select an upstream conventional reference after reviewing the full protocol
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-23-5347695500ed. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
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Evidence
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Evidence table
Inspect claims, sources and review details
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Sources and history
Release 2026-10-23-5347695500ed · Record review: source checked
1 source record and release history
- MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Original source · arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering
Technical metadata and extraction receipts
Stable ID: lit-otheromics-20261011-msgwild-protocol-formula-retrieval-mces-1
- areas
- metabolomics
- contexts
- research
- protocol
- MassSpecGym formula-known retrieval (bonus); MCES@1
- version
- MassSpecGym as audited in arXiv:2606.19624v1
- metric
- top-1-mces
- metric direction
- lower
- unit
- unitless
- metric qualifier
- retrieval
- source locator
- Table 3 column 'MCES@1'; Appendix 'Confidence Intervals'
- limitations
- Rows mix values copied from the literature with the authors' own runs; see each evaluation's origin.; Grey rows are results the authors consider leaking or inflated.
Related records
- part of: MassSpecGym
- evaluates task: MassSpecGym Molecule retrieval
- uses data: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)
- assessment: ChemBERTa SMILES classifier (spectrum-free), corrected candidate canonicalization on MassSpecGym formula-retrieval (MCES@1)
- assessment: ChemBERTa SMILES classifier (spectrum-free), original candidate canonicalization on MassSpecGym formula-retrieval (MCES@1)
- assessment: ChemFormer two-stage retrieval, corrected candidate canonicalization on MassSpecGym formula-retrieval (MCES@1)
- assessment: ChemFormer two-stage retrieval, original candidate canonicalization on MassSpecGym formula-retrieval (MCES@1)
- assessment: DiffMS generative retrieval on MassSpecGym formula-retrieval (MCES@1)
- assessment: DreaMS spectral encoder aligned to frozen ChemBERTa, corrected candidate canonicalization on MassSpecGym formula-retrieval (MCES@1)
- assessment: DreaMS spectral encoder aligned to frozen ChemBERTa, original candidate canonicalization on MassSpecGym formula-retrieval (MCES@1)
- assessment: FLARE on MassSpecGym formula-retrieval (MCES@1)
- assessment: FRIGID generative retrieval on MassSpecGym formula-retrieval (MCES@1)
- assessment: ICEBERG forward-model retrieval with imputed collision energies on MassSpecGym formula-retrieval (MCES@1)
- assessment: JESTR on MassSpecGym formula-retrieval (MCES@1)
- assessment: MIST, DiffMS checkpoint (vDiffMS) on MassSpecGym formula-retrieval (MCES@1)
- assessment: MIST, FRIGID checkpoint (vFRIGID) on MassSpecGym formula-retrieval (MCES@1)
- assessment: MIST + MolForge generative retrieval, reimplemented by the authors on MassSpecGym formula-retrieval (MCES@1)
- assessment: MVP on MassSpecGym formula-retrieval (MCES@1)
- assessment: Nearest neighbour, reimplemented by the authors on MassSpecGym formula-retrieval (MCES@1)
- assessment: PubChem default ranking (spectrum-blind) on MassSpecGym formula-retrieval (MCES@1)
- assessment: Ranking by number of chiral atoms (spectrum-blind) on MassSpecGym formula-retrieval (MCES@1)