MassSpecGym · main
Dataset and cohort used in the cited comparison. Dataset population counts do not establish successful prediction coverage.
Dataset and evaluation context
A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.
Evaluation results
Release 2026-09-17-d277315f7d76 · 5 evaluations · 20 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| Random (main): MassSpecGym · main Configuration: Random (main)Protocol: MassSpecGym · main (MassSpecGym Molecule retrieval)Dataset: MassSpecGym · main Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Author-reported evaluation · Evaluation metadata: needs review | ||
| 30.81 (30.40-31.21) MCES @1 Unit: edge-edit distance · Direction: lower | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 30.40; upper: 31.21 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, Random, MCES @1 Source checking is not independent reproduction. |
| 2.01 (1.68-2.39)% Hit rate @5 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 1.68; upper: 2.39 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, Random, Hit rate @5 Source checking is not independent reproduction. |
| 0.37 (0.24-0.54)% Hit rate @1 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 0.24; upper: 0.54 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, Random, Hit rate @1 Source checking is not independent reproduction. |
| 8.22 (7.53-8.89)% Hit rate @20 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 7.53; upper: 8.89 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, Random, Hit rate @20 Source checking is not independent reproduction. |
| DeepSets + Fourier features (main): MassSpecGym · main Configuration: DeepSets + Fourier features (main)Protocol: MassSpecGym · main (MassSpecGym Molecule retrieval)Dataset: MassSpecGym · main Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Author-reported evaluation · Evaluation metadata: needs review | ||
| 22.13 (21.85-22.43) MCES @1 Unit: edge-edit distance · Direction: lower | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 21.85; upper: 22.43 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, DeepSets + Fourier features, MCES @1 Source checking is not independent reproduction. |
| 12.58 (11.80-13.42)% Hit rate @5 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 11.80; upper: 13.42 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, DeepSets + Fourier features, Hit rate @5 Source checking is not independent reproduction. |
| 28.21 (27.10-29.36)% Hit rate @20 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 27.10; upper: 29.36 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, DeepSets + Fourier features, Hit rate @20 Source checking is not independent reproduction. |
| 5.24 (4.71-5.83)% Hit rate @1 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 4.71; upper: 5.83 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, DeepSets + Fourier features, Hit rate @1 Source checking is not independent reproduction. |
| Fingerprint FFN (main): MassSpecGym · main Configuration: Fingerprint FFN (main)Protocol: MassSpecGym · main (MassSpecGym Molecule retrieval)Dataset: MassSpecGym · main Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Author-reported evaluation · Evaluation metadata: needs review | ||
| 20.00 (19.01-20.98)% Hit rate @20 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 19.01; upper: 20.98 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, Fingerprint FFN, Hit rate @20 Source checking is not independent reproduction. |
| 7.59 (6.96-8.28)% Hit rate @5 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 6.96; upper: 8.28 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, Fingerprint FFN, Hit rate @5 Source checking is not independent reproduction. |
| 24.66 (24.38-24.94) MCES @1 Unit: edge-edit distance · Direction: lower | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 24.38; upper: 24.94 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, Fingerprint FFN, MCES @1 Source checking is not independent reproduction. |
| 2.54 (2.17-2.99)% Hit rate @1 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 2.17; upper: 2.99 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, Fingerprint FFN, Hit rate @1 Source checking is not independent reproduction. |
| DeepSets (main): MassSpecGym · main Configuration: DeepSets (main)Protocol: MassSpecGym · main (MassSpecGym Molecule retrieval)Dataset: MassSpecGym · main Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Author-reported evaluation · Evaluation metadata: needs review | ||
| 6.21 (5.64-6.82)% Hit rate @5 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 5.64; upper: 6.82 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, DeepSets, Hit rate @5 Source checking is not independent reproduction. |
| 25.11 (24.84-25.39) MCES @1 Unit: edge-edit distance · Direction: lower | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 24.84; upper: 25.39 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, DeepSets, MCES @1 Source checking is not independent reproduction. |
| 1.47 (1.18-1.77)% Hit rate @1 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 1.18; upper: 1.77 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, DeepSets, Hit rate @1 Source checking is not independent reproduction. |
| 19.23 (18.24-20.26)% Hit rate @20 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 18.24; upper: 20.26 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, DeepSets, Hit rate @20 Source checking is not independent reproduction. |
| MIST (main): MassSpecGym · main Configuration: MIST (main)Protocol: MassSpecGym · main (MassSpecGym Molecule retrieval)Dataset: MassSpecGym · main Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Author-reported evaluation · Evaluation metadata: needs review | ||
| 59.15 (57.89-60.39)% Hit rate @20 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 57.89; upper: 60.39 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, MIST, Hit rate @20 Source checking is not independent reproduction. |
| 15.37 (15.12-15.62) MCES @1 Unit: edge-edit distance · Direction: lower | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 15.12; upper: 15.62 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, MIST, MCES @1 Source checking is not independent reproduction. |
| 14.64 (13.82-15.54)% Hit rate @1 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 13.82; upper: 15.54 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, MIST, Hit rate @1 Source checking is not independent reproduction. |
| 34.87 (33.69-36.10)% Hit rate @5 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 33.69; upper: 36.10 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, MIST, Hit rate @5 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.
6 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.reported_population No value recorded Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 3: Hit rate @1, main Version: 2410.23326v1 | missing or unspecified No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.source_locator Table 3: Hit rate @1, main Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 3: Hit rate @1, main Version: 2410.23326v1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.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 3: Hit rate @1, main Version: 2410.23326v1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.subset main Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 3: Hit rate @1, main Version: 2410.23326v1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| description Dataset and cohort used in the cited comparison. Dataset population counts do not establish successful prediction coverage. Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 3: Hit rate @1, main Version: 2410.23326v1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| name MassSpecGym · main Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 3: Hit rate @1, main Version: 2410.23326v1 | not individually reviewed No individual claim review recorded 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-dataset-43f783b5d7a7151aa9
- areas
- metabolomics
- split
- MCES single-linkage molecular clustering at threshold 10; fixed held-out test split
- subset
- main
- reported population
- Not reported
- source locator
- Table 3: Hit rate @1, main
- missing metadata
- manifest: unextracted; scored count: unreported
- entity classification
- review date: 2026-09-17; rationale: This record identifies a biological data collection or source-labelled evaluation cohort. Keep its dataset identity; split, assay, taxonomic level, candidate restrictions and comparison context remain attributes rather than automatically becoming new entity kinds.; source ids: part2-massspecgym-arxiv-v1; source locator: Table 3: Hit rate @1, main; ambiguities: The formula/main label describes task input or candidate constraints in some MassSpecGym tables, not necessarily a different biological population. Preserve the paper-specific data identity and do not infer subset equivalence.