SMILES 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
Evaluation procedure
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
- Configuration
- SMILES Transformer (formula)
- Protocol
- MassSpecGym · formula (MassSpecGym De novo molecule generation)
- Dataset
- MassSpecGym · formula
- origin
- Author-reported evaluation
- configuration
- MassSpecGym paper baseline; spectrum-conditioned Transformer; molecular formula provided
- protocol id
- paper-protocol-5d42ac5481b1c071e4
- dataset version
- Not reported
- split
- MCES single-linkage molecular clustering at threshold 10; fixed held-out test split
- subset
- formula
- population
- Not reported
- aggregation
- Not reported
- inputs
- Not reported
- adaptation
- MassSpecGym paper baseline; spectrum-conditioned Transformer; molecular formula provided
- budget
- Not reported
- metric implementation
- Not reported
Metadata review: needs review. Unreported conditions prevent automatic comparisons.
Evaluation results
Release 2026-09-17-d277315f7d76 · 1 evaluation · 6 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| SMILES Transformer (formula): MassSpecGym · formula Configuration: SMILES Transformer (formula)Protocol: MassSpecGym · formula (MassSpecGym De novo molecule generation)Dataset: 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 Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.03 (0.03 - 0.04) Top-1 Tanimoto Unit: dimensionless · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 0.03; upper: 0.04 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, bonus formula challenge, SMILES Transformer, Top-1 Tanimoto Source checking is not independent reproduction. |
| 0.10 (0.09 - 0.10) Top-10 Tanimoto Unit: dimensionless · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 0.09; upper: 0.10 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, bonus formula challenge, SMILES Transformer, Top-10 Tanimoto Source checking is not independent reproduction. |
| 0.00 Top-10 accuracy Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, bonus formula challenge, SMILES Transformer, Top-10 accuracy Source checking is not independent reproduction. |
| 79.39 (78.64-80.08) Top-1 MCES Unit: edge-edit distance · Direction: lower | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 78.64; upper: 80.08 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, bonus formula challenge, SMILES Transformer, Top-1 MCES Source checking is not independent reproduction. |
| 52.13 (51.45-52.81) Top-10 MCES Unit: edge-edit distance · Direction: lower | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 51.45; upper: 52.81 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, bonus formula challenge, SMILES Transformer, Top-10 MCES Source checking is not independent reproduction. |
| 0.00 Top-1 accuracy Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, bonus formula challenge, SMILES Transformer, Top-1 accuracy Source checking is not independent reproduction. |
Evidence table
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
19 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.comparison.adaptation MassSpecGym paper baseline; spectrum-conditioned Transformer; molecular formula provided Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 2: Top-1 accuracy, formula Version: 2410.23326v1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.aggregation No value recorded Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 2: Top-1 accuracy, formula Version: 2410.23326v1 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.budget No value recorded Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 2: Top-1 accuracy, formula Version: 2410.23326v1 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.dataset_version No value recorded Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 2: Top-1 accuracy, formula Version: 2410.23326v1 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.inputs No value recorded Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 2: Top-1 accuracy, formula Version: 2410.23326v1 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.metric_implementation No value recorded Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 2: Top-1 accuracy, formula Version: 2410.23326v1 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.population No value recorded Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 2: Top-1 accuracy, formula Version: 2410.23326v1 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.protocol_id paper-protocol-5d42ac5481b1c071e4 Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 2: Top-1 accuracy, formula Version: 2410.23326v1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.split MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 2: Top-1 accuracy, formula Version: 2410.23326v1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.subset formula Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 2: Top-1 accuracy, formula Version: 2410.23326v1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
- MassSpecGym: A benchmark for the discovery and identification of molecules · Original source · 2410.23326v1
Technical metadata and extraction receipts
Stable ID: paper-evaluation-04a2b8bffb7c43a77e
- areas
- metabolomics
- origin
- author_reported
- protocol
- 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
- version
- MassSpecGym paper baseline; spectrum-conditioned Transformer; molecular formula provided
- comparison
- protocol id: paper-protocol-5d42ac5481b1c071e4; dataset version: Not reported; split: MCES single-linkage molecular clustering at threshold 10; fixed held-out test split; subset: formula; population: Not reported; aggregation: Not reported; inputs: Not reported; adaptation: MassSpecGym paper baseline; spectrum-conditioned Transformer; molecular formula provided; budget: Not reported; metric implementation: Not reported
- source locator
- Table 2: Top-1 accuracy, formula
- missing metadata
- checkpoint revision: unextracted; budget: unreported; split manifest: unextracted
Related records
- model: SMILES Transformer (formula)
- benchmark: MassSpecGym · formula (MassSpecGym De novo molecule generation)
- dataset: MassSpecGym · formula
- evaluation: SMILES Transformer: Top-1 Tanimoto on MassSpecGym · formula
- evaluation: SMILES Transformer: Top-10 Tanimoto on MassSpecGym · formula
- evaluation: SMILES Transformer: Top-10 accuracy on MassSpecGym · formula
- evaluation: SMILES Transformer: Top-1 MCES on MassSpecGym · formula
- evaluation: SMILES Transformer: Top-10 MCES on MassSpecGym · formula
- evaluation: SMILES Transformer: Top-1 accuracy on MassSpecGym · formula