FraGNNet (main): MassSpecGym · main
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
Evaluation procedure
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
- Configuration
- FraGNNet (main)
- Protocol
- MassSpecGym · main (MassSpecGym Spectrum simulation)
- Dataset
- MassSpecGym · main
- origin
- Author-reported evaluation
- configuration
- MassSpecGym spectrum simulation: molecule and measurement-condition input; main retrieval candidates
- protocol id
- paper-protocol-8c192f6451f321879d
- dataset version
- Not reported
- split
- MCES single-linkage molecular clustering at threshold 10; fixed held-out test split
- subset
- main
- population
- Not reported
- aggregation
- Not reported
- inputs
- Not reported
- adaptation
- MassSpecGym spectrum simulation: molecule and measurement-condition input; main retrieval candidates
- 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 · 5 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| FraGNNet (main): MassSpecGym · main Configuration: FraGNNet (main)Protocol: MassSpecGym · main (MassSpecGym Spectrum simulation)Dataset: MassSpecGym · main 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 Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.63 (0.63-0.64) Jensen-Shannon similarity Unit: dimensionless · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 0.63; upper: 0.64 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, main challenge, FraGNNet, Jensen-Shannon similarity Source checking is not independent reproduction. |
| 0.52 (0.51-0.53) Cosine similarity Unit: dimensionless · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 0.51; upper: 0.53 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, main challenge, FraGNNet, Cosine similarity Source checking is not independent reproduction. |
| 83.58 (82.34-84.75)% Hit rate @20 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 82.34; upper: 84.75 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, main challenge, FraGNNet, Hit rate @20 Source checking is not independent reproduction. |
| 72.56 (71.18-74.00)% Hit rate @5 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 71.18; upper: 74.00 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, main challenge, FraGNNet, Hit rate @5 Source checking is not independent reproduction. |
| 46.64 (44.98-48.26)% Hit rate @1 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 44.98; upper: 48.26 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, main challenge, FraGNNet, Hit rate @1 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 spectrum simulation: molecule and measurement-condition input; main retrieval candidates Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 4: Cosine similarity, main 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 4: Cosine similarity, main 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 4: Cosine similarity, main 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 4: Cosine similarity, main 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 4: Cosine similarity, main 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 4: Cosine similarity, main 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 4: Cosine similarity, main 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-8c192f6451f321879d Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 4: Cosine similarity, main 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 4: Cosine similarity, main 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 main Context-only references | MassSpecGym: A benchmark for the discovery and identification of molecules Table 4: Cosine similarity, main 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-269be32b01b3a5ae0e
- areas
- metabolomics
- origin
- author_reported
- protocol
- 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
- version
- MassSpecGym spectrum simulation: molecule and measurement-condition input; main retrieval candidates
- comparison
- protocol id: paper-protocol-8c192f6451f321879d; dataset version: Not reported; split: MCES single-linkage molecular clustering at threshold 10; fixed held-out test split; subset: main; population: Not reported; aggregation: Not reported; inputs: Not reported; adaptation: MassSpecGym spectrum simulation: molecule and measurement-condition input; main retrieval candidates; budget: Not reported; metric implementation: Not reported
- source locator
- Table 4: Cosine similarity, main
- missing metadata
- checkpoint revision: unextracted; budget: unreported; split manifest: unextracted
Related records
- model: FraGNNet (main)
- benchmark: MassSpecGym · main (MassSpecGym Spectrum simulation)
- dataset: MassSpecGym · main
- evaluation: FraGNNet: Jensen-Shannon similarity on MassSpecGym · main
- evaluation: FraGNNet: Cosine similarity on MassSpecGym · main
- evaluation: FraGNNet: Hit rate @20 on MassSpecGym · main
- evaluation: FraGNNet: Hit rate @5 on MassSpecGym · main
- evaluation: FraGNNet: Hit rate @1 on MassSpecGym · main