MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3); MassSpecGym as audited in arXiv:2606.19624v1

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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.

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Results

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All evaluations

18 evaluations · 18 results. Different protocols are not a single leaderboard.

Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3) · Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)

Sorted by Top-5 accuracy (retrieval) (higher 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.

Tested configuration	Top-5 accuracy (retrieval)
ChemBERTa SMILES classifier (spectrum-free), original candidate canonicalization (MassSpecGym in the Wild)Evaluation	99.84 (99.72-99.92)% (best in column)
DreaMS spectral encoder aligned to frozen ChemBERTa, original candidate canonicalization (MassSpecGym in the Wild)Evaluation	92.57 (91.91-93.21)%
ChemFormer two-stage retrieval, original candidate canonicalization (MassSpecGym in the Wild)Evaluation	70.52 (69.37-71.70)%
MIST, FRIGID checkpoint (vFRIGID) (MassSpecGym in the Wild)Evaluation	65.32 (64.09-66.45)%
ICEBERG forward-model retrieval with imputed collision energies (MassSpecGym in the Wild)Evaluation	60.70 (59.58–61.86)%
FRIGID generative retrieval (MassSpecGym in the Wild)Evaluation	58.30 (57.02-59.48)%
MIST, DiffMS checkpoint (vDiffMS) (MassSpecGym in the Wild)Evaluation	54.74 (53.43-55.96)%
DiffMS generative retrieval (MassSpecGym in the Wild)Evaluation	54.36 (53.11-55.58)%
PubChem default ranking (spectrum-blind) (MassSpecGym in the Wild)Evaluation	54.13 (52.93-55.28)%
FLARE (MassSpecGym in the Wild)Evaluation	50.00 (48.78–51.22)%
MIST + MolForge generative retrieval, reimplemented by the authors (MassSpecGym in the Wild)Evaluation	49.25 (47.98-50.48)%
MVP (MassSpecGym in the Wild)Evaluation	36.88 (35.71-38.02)%
JESTR (MassSpecGym in the Wild)Evaluation	33.48 (32.33-34.68)%
Nearest neighbour, reimplemented by the authors (MassSpecGym in the Wild)Evaluation	22.26 (21.25-23.33)%
DreaMS spectral encoder aligned to frozen ChemBERTa, corrected candidate canonicalization (MassSpecGym in the Wild)Evaluation	19.82 (18.89-20.83)%
ChemFormer two-stage retrieval, corrected candidate canonicalization (MassSpecGym in the Wild)Evaluation	19.12 (18.18-20.11)%
ChemBERTa SMILES classifier (spectrum-free), corrected candidate canonicalization (MassSpecGym in the Wild)Evaluation	18.39 (17.38-19.36)%
Ranking by number of chiral atoms (spectrum-blind) (MassSpecGym in the Wild)Evaluation	16.85 (15.92-17.79)%

All 18 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
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), Hit rate@5 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)	18.39 (17.38-19.36)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 17.38 to 19.36. 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 checked Methods, coverage and source ChemBERTa SMILES classifier (spectrum-free), corrected candidate canonicalization on MassSpecGym formula-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5 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 'Hit rate@5'
Configuration: ChemBERTa SMILES classifier (spectrum-free), original candidate canonicalization (MassSpecGym in the Wild)	Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)	99.84 (99.72-99.92)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 99.72 to 99.92. 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 checked Methods, coverage and source ChemBERTa SMILES classifier (spectrum-free), original candidate canonicalization on MassSpecGym formula-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5 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 'Hit rate@5'
Configuration: ChemFormer two-stage retrieval, corrected candidate canonicalization (MassSpecGym in the Wild)	Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)	19.12 (18.18-20.11)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 18.18 to 20.11. 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 checked Methods, coverage and source ChemFormer two-stage retrieval, corrected candidate canonicalization on MassSpecGym formula-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5 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 'Hit rate@5'
Configuration: ChemFormer two-stage retrieval, original candidate canonicalization (MassSpecGym in the Wild)	Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)	70.52 (69.37-71.70)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 69.37 to 71.70. 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 checked Methods, coverage and source ChemFormer two-stage retrieval, original candidate canonicalization on MassSpecGym formula-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5 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 'Hit rate@5'
Configuration: DiffMS generative retrieval (MassSpecGym in the Wild)	Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)	54.36 (53.11-55.58)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 53.11 to 55.58. 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 checked Methods, coverage and source DiffMS generative retrieval on MassSpecGym formula-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5 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 'Hit rate@5'
Configuration: DreaMS spectral encoder aligned to frozen ChemBERTa, corrected candidate canonicalization (MassSpecGym in the Wild)	Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)	19.82 (18.89-20.83)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 18.89 to 20.83. 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 checked Methods, coverage and source DreaMS spectral encoder aligned to frozen ChemBERTa, corrected candidate canonicalization on MassSpecGym formula-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5 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 'Hit rate@5'
Configuration: DreaMS spectral encoder aligned to frozen ChemBERTa, original candidate canonicalization (MassSpecGym in the Wild)	Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)	92.57 (91.91-93.21)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 91.91 to 93.21. 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 checked Methods, coverage and source DreaMS spectral encoder aligned to frozen ChemBERTa, original candidate canonicalization on MassSpecGym formula-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5 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 'Hit rate@5'
Configuration: FLARE (MassSpecGym in the Wild)	Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)	50.00 (48.78–51.22)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 48.78 to 51.22. 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 checked Methods, coverage and source FLARE on MassSpecGym formula-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5 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 'Hit rate@5'
Configuration: FRIGID generative retrieval (MassSpecGym in the Wild)	Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)	58.30 (57.02-59.48)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 57.02 to 59.48. 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 checked Methods, coverage and source FRIGID generative retrieval on MassSpecGym formula-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5 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 'Hit rate@5'
Configuration: ICEBERG forward-model retrieval with imputed collision energies (MassSpecGym in the Wild)	Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)	60.70 (59.58–61.86)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 59.58 to 61.86. 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 checked Methods, coverage and source ICEBERG forward-model retrieval with imputed collision energies on MassSpecGym formula-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5 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 'Hit rate@5'
Configuration: JESTR (MassSpecGym in the Wild)	Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)	33.48 (32.33-34.68)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 32.33 to 34.68. 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 checked Methods, coverage and source JESTR on MassSpecGym formula-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5 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 'Hit rate@5'
Configuration: MIST, DiffMS checkpoint (vDiffMS) (MassSpecGym in the Wild)	Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)	54.74 (53.43-55.96)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 53.43 to 55.96. 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 checked Methods, coverage and source MIST, DiffMS checkpoint (vDiffMS) on MassSpecGym formula-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5 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 'Hit rate@5'
Configuration: MIST, FRIGID checkpoint (vFRIGID) (MassSpecGym in the Wild)	Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)	65.32 (64.09-66.45)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 64.09 to 66.45. 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 checked Methods, coverage and source MIST, FRIGID checkpoint (vFRIGID) on MassSpecGym formula-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5 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 'Hit rate@5'
Configuration: MIST + MolForge generative retrieval, reimplemented by the authors (MassSpecGym in the Wild)	Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)	49.25 (47.98-50.48)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 47.98 to 50.48. 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 checked Methods, coverage and source MIST + MolForge generative retrieval, reimplemented by the authors on MassSpecGym formula-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5 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 'Hit rate@5'
Configuration: MVP (MassSpecGym in the Wild)	Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)	36.88 (35.71-38.02)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 35.71 to 38.02. 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 checked Methods, coverage and source MVP on MassSpecGym formula-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5 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 'Hit rate@5'
Configuration: Nearest neighbour, reimplemented by the authors (MassSpecGym in the Wild)	Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)	22.26 (21.25-23.33)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 21.25 to 23.33. 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 checked Methods, coverage and source Nearest neighbour, reimplemented by the authors on MassSpecGym formula-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5 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 'Hit rate@5'
Configuration: PubChem default ranking (spectrum-blind) (MassSpecGym in the Wild)	Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)	54.13 (52.93-55.28)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 52.93 to 55.28. 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 checked Methods, coverage and source PubChem default ranking (spectrum-blind) on MassSpecGym formula-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5 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 'Hit rate@5'
Configuration: Ranking by number of chiral atoms (spectrum-blind) (MassSpecGym in the Wild)	Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@5 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)	16.85 (15.92-17.79)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 15.92 to 17.79. 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 checked Methods, coverage and source Ranking by number of chiral atoms (spectrum-blind) on MassSpecGym formula-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5 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 'Hit rate@5'

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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

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Stable ID: lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-5

areas: metabolomics
contexts: research
protocol: MassSpecGym formula-known retrieval (bonus); Hit rate@5
version: MassSpecGym as audited in arXiv:2606.19624v1
metric: top-5-accuracy
metric direction: higher
unit: percent
metric qualifier: retrieval
source locator: Table 3 column 'Hit rate@5'; 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.

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