MassSpecGym test fold; retrieval with bonus information: candidates restricted to the ground-truth molecular formula.
72 evaluations · 72 results. Different protocols are not a single leaderboard.
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), Hit rate@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 8.2 (7.53-8.89)% Top-1 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 7.53 to 8.89. 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-hit-rate-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 'Hit rate@1' |
| Configuration: ChemBERTa SMILES classifier (spectrum-free), corrected candidate canonicalization (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@20 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 38.14 (36.96-39.36)% Top-20 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 36.96 to 39.36. 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 checkedMethods, coverage and sourcelit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-20 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@20' |
| 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 checkedMethods, coverage and sourcelit-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), 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), Hit rate@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 99.66 (99.50-99.79)% Top-1 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 99.50 to 99.79. 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-hit-rate-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 'Hit rate@1' |
| Configuration: ChemBERTa SMILES classifier (spectrum-free), original candidate canonicalization (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@20 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 99.99 (99.95-100.00)% Top-20 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 99.95 to 100.00. 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-hit-rate-20 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@20' |
| 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 checkedMethods, coverage and sourcelit-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: 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), Hit rate@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 7.60 (6.94-8.31)% Top-1 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 6.94 to 8.31. 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-hit-rate-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 'Hit rate@1' |
| Configuration: ChemFormer two-stage retrieval, corrected candidate canonicalization (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@20 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 39.31 (38.16-40.53)% Top-20 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 38.16 to 40.53. 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-hit-rate-20 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@20' |
| 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 checkedMethods, coverage and sourcelit-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, 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), Hit rate@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 63.89 (62.71-65.03)% Top-1 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 62.71 to 65.03. 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-hit-rate-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 'Hit rate@1' |
| Configuration: ChemFormer two-stage retrieval, original candidate canonicalization (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@20 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 75.86 (74.79-76.89)% Top-20 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 74.79 to 76.89. 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-hit-rate-20 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@20' |
| 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 checkedMethods, coverage and sourcelit-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: 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), Hit rate@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 32.29 (31.13-33.45)% Top-1 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 31.13 to 33.45. 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 checkedMethods, coverage and sourceDiffMS generative retrieval on MassSpecGym formula-retrieval (Hit rate@1) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-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 'Hit rate@1' |
| Configuration: DiffMS generative retrieval (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@20 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 75.47 (74.38-76.55)% Top-20 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 74.38 to 76.55. 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 (Hit rate@20) lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-20 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@20' |
| 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 checkedMethods, coverage and sourceDiffMS 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: 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), Hit rate@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 6.70 (6.09-7.35)% Top-1 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 6.09 to 7.35. 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-hit-rate-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 'Hit rate@1' |
| Configuration: DreaMS spectral encoder aligned to frozen ChemBERTa, corrected candidate canonicalization (MassSpecGym in the Wild) | Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@20 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 40.62 (39.44-41.79)% Top-20 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 39.44 to 41.79. 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-hit-rate-20 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@20' |
| 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 checkedMethods, coverage and sourcelit-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, 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), Hit rate@1 (MassSpecGym in the Wild Table 3) Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) | 82.41 (81.46-83.33)% Top-1 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 81.46 to 83.33. 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 | Author-reported evaluation · Source checkedMethods, coverage and sourcelit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-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 'Hit rate@1' |
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| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Source location Table 3 caption and section headers Context-only references | MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery Table 3 caption and section headers Version: arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Split Test fold Context-only references | MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery Table 3 caption and section headers Version: arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Version MassSpecGym as used in each cited work; corrected rows use uniform RDKit canonicalization (MassSpecGym v1.5) Context-only references | MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery Table 3 caption and section headers Version: arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Description MassSpecGym test fold; retrieval with bonus information: candidates restricted to the ground-truth molecular formula. Context-only references | MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery Table 3 caption and section headers Version: arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Name MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild) Context-only references | MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery Table 3 caption and section headers Version: arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-10-23-5347695500ed · Record review: source checked
Stable ID: lit-otheromics-20261011-msgwild-data-formula-retrieval