MassSpecGym mass-based retrieval, Hit rate@5 (MassSpecGym in the Wild Table 2); MassSpecGym as audited in arXiv:2606.19624v1

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6 recorded evaluations, 6 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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6 evaluations · 6 results. Different protocols are not a single leaderboard.

Protocol: MassSpecGym mass-based retrieval, Hit rate@5 (MassSpecGym in the Wild Table 2) · Dataset: MassSpecGym test fold, mass-based retrieval candidates (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)
MIST retrieval with the ground-truth formula (MassSpecGym in the Wild)Evaluation	66.25 (65.12–67.46)% (best in column)
MIST retrieval with top-1 formula from MIST-CF trained on train and test data (MassSpecGym in the Wild)Evaluation	47.97 (46.75–49.21)%
MIST retrieval with top-1 formula from MIST-CF trained on test data only (MassSpecGym in the Wild)Evaluation	43.32 (42.06–44.51)%
Random ranking among candidates filtered by the ground-truth formula (MassSpecGym in the Wild)Evaluation	39.09 (37.94-40.31)%
MIST retrieval with MIST-CF top-1 predicted formula (MassSpecGym in the Wild)Evaluation	38.47 (37.21–39.68)%
Random ranking (MassSpecGym in the Wild)Evaluation	2.01 (1.68-2.38)%

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: MIST retrieval with MIST-CF top-1 predicted formula (MassSpecGym in the Wild)	Protocol: MassSpecGym mass-based retrieval, Hit rate@5 (MassSpecGym in the Wild Table 2) Dataset: MassSpecGym test fold, mass-based retrieval candidates (MassSpecGym in the Wild)	38.47 (37.21–39.68)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 37.21 to 39.68. 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 MIST retrieval with MIST-CF top-1 predicted formula on MassSpecGym mass-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-mass-retrieval-hit-rate-5 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 2, row 'MIST (MIST-CF top-1 formula)', column 'Hit rate@5'
Configuration: MIST retrieval with the ground-truth formula (MassSpecGym in the Wild)	Protocol: MassSpecGym mass-based retrieval, Hit rate@5 (MassSpecGym in the Wild Table 2) Dataset: MassSpecGym test fold, mass-based retrieval candidates (MassSpecGym in the Wild)	66.25 (65.12–67.46)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 65.12 to 67.46. 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 MIST retrieval with the ground-truth formula on MassSpecGym mass-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-mass-retrieval-hit-rate-5 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 2, row 'MIST (ground-truth formula)', column 'Hit rate@5'
Configuration: MIST retrieval with top-1 formula from MIST-CF trained on test data only (MassSpecGym in the Wild)	Protocol: MassSpecGym mass-based retrieval, Hit rate@5 (MassSpecGym in the Wild Table 2) Dataset: MassSpecGym test fold, mass-based retrieval candidates (MassSpecGym in the Wild)	43.32 (42.06–44.51)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 42.06 to 44.51. 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 MIST retrieval with top-1 formula from MIST-CF trained on test data only on MassSpecGym mass-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-mass-retrieval-hit-rate-5 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 2, row 'MIST (MIST-CF test-only top-1 formula)', column 'Hit rate@5'
Configuration: MIST retrieval with top-1 formula from MIST-CF trained on train and test data (MassSpecGym in the Wild)	Protocol: MassSpecGym mass-based retrieval, Hit rate@5 (MassSpecGym in the Wild Table 2) Dataset: MassSpecGym test fold, mass-based retrieval candidates (MassSpecGym in the Wild)	47.97 (46.75–49.21)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 46.75 to 49.21. 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 MIST retrieval with top-1 formula from MIST-CF trained on train and test data on MassSpecGym mass-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-mass-retrieval-hit-rate-5 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 2, row 'MIST (MIST-CF train-test top-1 formula)', column 'Hit rate@5'
Configuration: Random ranking among candidates filtered by the ground-truth formula (MassSpecGym in the Wild)	Protocol: MassSpecGym mass-based retrieval, Hit rate@5 (MassSpecGym in the Wild Table 2) Dataset: MassSpecGym test fold, mass-based retrieval candidates (MassSpecGym in the Wild)	39.09 (37.94-40.31)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 37.94 to 40.31. 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 checked Methods, coverage and source Random ranking among candidates filtered by the ground-truth formula on MassSpecGym mass-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-mass-retrieval-hit-rate-5 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 2, row 'Random w/ ground-truth formula', column 'Hit rate@5'
Configuration: Random ranking (MassSpecGym in the Wild)	Protocol: MassSpecGym mass-based retrieval, Hit rate@5 (MassSpecGym in the Wild Table 2) Dataset: MassSpecGym test fold, mass-based retrieval candidates (MassSpecGym in the Wild)	2.01 (1.68-2.38)% Top-5 accuracy (retrieval) percent · higher Uncertainty: 99.9% CI 1.68 to 2.38. 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 Random ranking on MassSpecGym mass-retrieval (Hit rate@5) lit-otheromics-20261011-msgwild-protocol-mass-retrieval-hit-rate-5 Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 2, row 'Random', 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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Technical metadata and extraction receipts

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

areas: metabolomics
contexts: research
protocol: MassSpecGym mass-based retrieval; 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 2 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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