Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Configuration
SMILES Transformer (formula)
SMILES Transformer as evaluated in the cited study. MassSpecGym paper baseline; spectrum-conditioned Transformer; molecular formula provided
Sources
MassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, bonus formula challenge, SMILES Transformer, Top-1 accuracyOverview
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
Evaluations and results
1 evaluation · 6 results. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: SMILES Transformer (formula) | Protocol: MassSpecGym · formula (MassSpecGym De novo molecule generation) Dataset: MassSpecGym · formula | 0.03 (0.03 - 0.04) Top-1 Tanimoto dimensionless · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 0.03; upper: 0.04 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSMILES Transformer (formula): MassSpecGym · formula Generate candidate molecules from an input spectrum. Compare within the same main/formula challenge and metric. Main random generation uses precursor mass; the Transformer consumes the spectrum. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, bonus formula challenge, SMILES Transformer, Top-1 Tanimoto |
| Configuration: SMILES Transformer (formula) | Protocol: MassSpecGym · formula (MassSpecGym De novo molecule generation) Dataset: MassSpecGym · formula | 0.10 (0.09 - 0.10) Top-10 Tanimoto dimensionless · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 0.09; upper: 0.10 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSMILES Transformer (formula): MassSpecGym · formula Generate candidate molecules from an input spectrum. Compare within the same main/formula challenge and metric. Main random generation uses precursor mass; the Transformer consumes the spectrum. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, bonus formula challenge, SMILES Transformer, Top-10 Tanimoto |
| Configuration: SMILES Transformer (formula) | Protocol: MassSpecGym · formula (MassSpecGym De novo molecule generation) Dataset: MassSpecGym · formula | 0 Top-10 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSMILES Transformer (formula): MassSpecGym · formula Generate candidate molecules from an input spectrum. Compare within the same main/formula challenge and metric. Main random generation uses precursor mass; the Transformer consumes the spectrum. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, bonus formula challenge, SMILES Transformer, Top-10 accuracy |
| Configuration: SMILES Transformer (formula) | Protocol: MassSpecGym · formula (MassSpecGym De novo molecule generation) Dataset: MassSpecGym · formula | 79.39 (78.64-80.08) Top-1 MCES edge-edit distance · lower Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 78.64; upper: 80.08 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSMILES Transformer (formula): MassSpecGym · formula Generate candidate molecules from an input spectrum. Compare within the same main/formula challenge and metric. Main random generation uses precursor mass; the Transformer consumes the spectrum. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, bonus formula challenge, SMILES Transformer, Top-1 MCES |
| Configuration: SMILES Transformer (formula) | Protocol: MassSpecGym · formula (MassSpecGym De novo molecule generation) Dataset: MassSpecGym · formula | 52.13 (51.45-52.81) Top-10 MCES edge-edit distance · lower Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 51.45; upper: 52.81 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSMILES Transformer (formula): MassSpecGym · formula Generate candidate molecules from an input spectrum. Compare within the same main/formula challenge and metric. Main random generation uses precursor mass; the Transformer consumes the spectrum. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, bonus formula challenge, SMILES Transformer, Top-10 MCES |
| Configuration: SMILES Transformer (formula) | Protocol: MassSpecGym · formula (MassSpecGym De novo molecule generation) Dataset: MassSpecGym · formula | 0 Top-1 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSMILES Transformer (formula): MassSpecGym · formula Generate candidate molecules from an input spectrum. Compare within the same main/formula challenge and metric. Main random generation uses precursor mass; the Transformer consumes the spectrum. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, bonus formula challenge, SMILES Transformer, Top-1 accuracy |
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Evaluation in this paper
MassSpecGym paper baseline; spectrum-conditioned Transformer; molecular formula provided
Sources
MassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, bonus formula challenge, SMILES Transformer, Top-1 accuracyStrengths, limitations and unresolved questions
Strengths and limitations
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Stable record: paper-model-71ed4dc46bc632a2a7Specifications
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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.
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2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Evaluation in this paper MassSpecGym paper baseline; spectrum-conditioned Transformer; molecular formula provided Individual claims | MassSpecGym: A benchmark for the discovery and identification of molecules Table 2, bonus formula challenge, SMILES Transformer, Top-1 accuracy 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 SMILES Transformer as evaluated in the cited study. MassSpecGym paper baseline; spectrum-conditioned Transformer; molecular formula provided Individual claims | MassSpecGym: A benchmark for the discovery and identification of molecules Table 2, bonus formula challenge, SMILES Transformer, Top-1 accuracy 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. |
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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-model-71ed4dc46bc632a2a7
- areas
- metabolomics
- entity level
- method
- configuration type
- reported_configuration
- version
- MassSpecGym paper baseline; spectrum-conditioned Transformer; molecular formula provided
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- entity classification
- review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: part2-massspecgym-arxiv-v1; source locator: Table 2, bonus formula challenge, SMILES Transformer, Top-1 accuracy; ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.