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Release 2026-09-29-06401fd5b220 · Evidence verified: Not verified
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4 evaluations · 20 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Precursor m/z (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | 2.09 (1.66-2.59)% Hit rate @1 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 1.66; upper: 2.59 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePrecursor m/z (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, Precursor m/z, Hit rate @1 |
| Configuration: GNN (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | - Jensen-Shannon similarity dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGNN (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, GNN, Jensen-Shannon similarity |
| Configuration: GNN (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | 33.77 (32.26-35.37)% Hit rate @20 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 32.26; upper: 35.37 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGNN (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, GNN, Hit rate @20 |
| Configuration: Precursor m/z (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | 8.52 (7.65-9.53)% Hit rate @5 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 7.65; upper: 9.53 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePrecursor m/z (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, Precursor m/z, Hit rate @5 |
| Configuration: FFN Fingerprint (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | - Jensen-Shannon similarity dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceFFN Fingerprint (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, FFN Fingerprint, Jensen-Shannon similarity |
| Configuration: FFN Fingerprint (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | 22.70 (21.32-24.12)% Hit rate @5 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 21.32; upper: 24.12 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceFFN Fingerprint (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, FFN Fingerprint, Hit rate @5 |
| Configuration: FraGNNet (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | - Cosine similarity dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceFraGNNet (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, FraGNNet, Cosine similarity |
| Configuration: FFN Fingerprint (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | 44.12 (42.51-45.75)% Hit rate @20 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 42.51; upper: 45.75 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceFFN Fingerprint (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, FFN Fingerprint, Hit rate @20 |
| Configuration: Precursor m/z (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | - Jensen-Shannon similarity dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePrecursor m/z (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, Precursor m/z, Jensen-Shannon similarity |
| Configuration: FraGNNet (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | 31.93 (30.40-33.50)% Hit rate @1 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 30.40; upper: 33.50 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceFraGNNet (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, FraGNNet, Hit rate @1 |
| Configuration: Precursor m/z (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | - Cosine similarity dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePrecursor m/z (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, Precursor m/z, Cosine similarity |
| Configuration: FraGNNet (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | 82.70 (81.45-83.93)% Hit rate @20 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 81.45; upper: 83.93 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceFraGNNet (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, FraGNNet, Hit rate @20 |
| Configuration: Precursor m/z (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | 22.65 (21.26-24.01)% Hit rate @20 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 21.26; upper: 24.01 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePrecursor m/z (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, Precursor m/z, Hit rate @20 |
| Configuration: FraGNNet (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | - Jensen-Shannon similarity dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceFraGNNet (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, FraGNNet, Jensen-Shannon similarity |
| Configuration: FFN Fingerprint (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | - Cosine similarity dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceFFN Fingerprint (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, FFN Fingerprint, Cosine similarity |
| Configuration: FFN Fingerprint (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | 7.62 (6.77-8.54)% Hit rate @1 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 6.77; upper: 8.54 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceFFN Fingerprint (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, FFN Fingerprint, Hit rate @1 |
| Configuration: GNN (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | 3.63 (3.05-4.29)% Hit rate @1 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 3.05; upper: 4.29 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGNN (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, GNN, Hit rate @1 |
| Configuration: GNN (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | - Cosine similarity dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGNN (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, GNN, Cosine similarity |
| Configuration: GNN (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | 13.55 (12.46-14.68)% Hit rate @5 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 12.46; upper: 14.68 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGNN (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, GNN, Hit rate @5 |
| Configuration: FraGNNet (formula) | Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation) Dataset: MassSpecGym · formula | 63.20 (61.64-64.76)% Hit rate @5 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 61.64; upper: 64.76 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceFraGNNet (formula): MassSpecGym · formula Predict a spectrum from a molecule under measurement conditions. Metadata-complete simulation subset; simulation-derived retrieval is distinct from direct molecule retrieval in Table 3. 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 4, bonus formula challenge, FraGNNet, Hit rate @5 |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
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.
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6 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.reported_population Not reported Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 4: Cosine similarity, formula 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 4: Cosine similarity, formula Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 4: Cosine similarity, formula 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 4: Cosine similarity, formula 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 formula Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 4: Cosine similarity, formula 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 4: Cosine similarity, formula 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 · formula Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 4: Cosine similarity, formula 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. |
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Release 2026-09-29-06401fd5b220 · Record review: needs review
Stable ID: paper-dataset-712fb45862f6d8614f