Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Protocol
MassSpecGym · formula (MassSpecGym Spectrum simulation)
MassSpecGym · formula · Table 4. 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
MassSpecGym: A benchmark for the discovery and identification of molecules · Table 4: Cosine similarity, formulaAt a glance
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.
How it works
Evaluation in this paper
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
MassSpecGym: A benchmark for the discovery and identification of molecules · Table 4: Cosine similarity, formulaEvaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Benchmarks
Tasks
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
Published comparisons
Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies.
MassSpecGym · formula · Table 4
Hit rate @1 (percent) · Higher values are better for this metric.
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
- Precursor m/z (formula) · Configuration · Author-reported evaluation2.09 (1.66-2.59)
- FFN Fingerprint (formula) · Configuration · Author-reported evaluation7.62 (6.77-8.54)
- GNN (formula) · Configuration · Author-reported evaluation3.63 (3.05-4.29)
- FraGNNet (formula) · Configuration · Author-reported evaluation31.93 (30.40-33.50)
Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.
MassSpecGym: A benchmark for the discovery and identification of molecules · Table 4: Hit rate @1, formulaValues, uncertainty and evidence
| Tested entity | Printed value | Uncertainty | Evidence |
|---|---|---|---|
| Precursor m/z (formula) · Configuration | 2.09 (1.66-2.59) percent | type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 1.66; upper: 2.59 | Author-reported evaluation · source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, Precursor m/z, Hit rate @1 |
| FFN Fingerprint (formula) · Configuration | 7.62 (6.77-8.54) percent | type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 6.77; upper: 8.54 | Author-reported evaluation · source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, FFN Fingerprint, Hit rate @1 |
| GNN (formula) · Configuration | 3.63 (3.05-4.29) percent | type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 3.05; upper: 4.29 | Author-reported evaluation · source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, GNN, Hit rate @1 |
| FraGNNet (formula) · Configuration | 31.93 (30.40-33.50) percent | type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 30.40; upper: 33.50 | Author-reported evaluation · source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, FraGNNet, Hit rate @1 |
Scope and limitations
- Source metric equations define hit rates as fractions, while table values use percentage scale; recorded values are not rescaled.
- Zero generation accuracy is a reported result, not missingness.
- No checkpoint revision inferred from method name.
- Bootstrap CIs reflect resampling of this test set; not independently reproduced and not seed standard deviations.
- Full table retained, including weaker/random methods and unavailable formula-simulation similarity cells.
Source transcription and grouping reviewed by automated source review on 2026-09-17. These experiments were not independently reproduced by rewire.
Tested entities and results
Release 2026-09-17-d277315f7d76 · 4 evaluations · 20 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| Precursor m/z (formula): MassSpecGym · formula Configuration: Precursor m/z (formula)Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation)Dataset: 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 Author-reported evaluation · Evaluation metadata: needs review | ||
| 2.09 (1.66-2.59)% Hit rate @1 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 1.66; upper: 2.59 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, Precursor m/z, Hit rate @1 Source checking is not independent reproduction. |
| 8.52 (7.65-9.53)% Hit rate @5 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 7.65; upper: 9.53 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, Precursor m/z, Hit rate @5 Source checking is not independent reproduction. |
| - Jensen-Shannon similarity Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, Precursor m/z, Jensen-Shannon similarity Source checking is not independent reproduction. |
| - Cosine similarity Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, Precursor m/z, Cosine similarity Source checking is not independent reproduction. |
| 22.65 (21.26-24.01)% Hit rate @20 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 21.26; upper: 24.01 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, Precursor m/z, Hit rate @20 Source checking is not independent reproduction. |
| GNN (formula): MassSpecGym · formula Configuration: GNN (formula)Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation)Dataset: 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 Author-reported evaluation · Evaluation metadata: needs review | ||
| - Jensen-Shannon similarity Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, GNN, Jensen-Shannon similarity Source checking is not independent reproduction. |
| 33.77 (32.26-35.37)% Hit rate @20 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 32.26; upper: 35.37 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, GNN, Hit rate @20 Source checking is not independent reproduction. |
| 3.63 (3.05-4.29)% Hit rate @1 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 3.05; upper: 4.29 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, GNN, Hit rate @1 Source checking is not independent reproduction. |
| - Cosine similarity Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, GNN, Cosine similarity Source checking is not independent reproduction. |
| 13.55 (12.46-14.68)% Hit rate @5 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 12.46; upper: 14.68 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, GNN, Hit rate @5 Source checking is not independent reproduction. |
| FFN Fingerprint (formula): MassSpecGym · formula Configuration: FFN Fingerprint (formula)Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation)Dataset: 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 Author-reported evaluation · Evaluation metadata: needs review | ||
| - Jensen-Shannon similarity Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, FFN Fingerprint, Jensen-Shannon similarity Source checking is not independent reproduction. |
| 22.70 (21.32-24.12)% Hit rate @5 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 21.32; upper: 24.12 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, FFN Fingerprint, Hit rate @5 Source checking is not independent reproduction. |
| 44.12 (42.51-45.75)% Hit rate @20 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 42.51; upper: 45.75 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, FFN Fingerprint, Hit rate @20 Source checking is not independent reproduction. |
| - Cosine similarity Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, FFN Fingerprint, Cosine similarity Source checking is not independent reproduction. |
| 7.62 (6.77-8.54)% Hit rate @1 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 6.77; upper: 8.54 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, FFN Fingerprint, Hit rate @1 Source checking is not independent reproduction. |
| FraGNNet (formula): MassSpecGym · formula Configuration: FraGNNet (formula)Protocol: MassSpecGym · formula (MassSpecGym Spectrum simulation)Dataset: 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 Author-reported evaluation · Evaluation metadata: needs review | ||
| - Cosine similarity Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, FraGNNet, Cosine similarity Source checking is not independent reproduction. |
| 31.93 (30.40-33.50)% Hit rate @1 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 30.40; upper: 33.50 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, FraGNNet, Hit rate @1 Source checking is not independent reproduction. |
| 82.70 (81.45-83.93)% Hit rate @20 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 81.45; upper: 83.93 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, FraGNNet, Hit rate @20 Source checking is not independent reproduction. |
| - Jensen-Shannon similarity Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, FraGNNet, Jensen-Shannon similarity Source checking is not independent reproduction. |
| 63.20 (61.64-64.76)% Hit rate @5 Unit: percent · Direction: higher | Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 61.64; upper: 64.76 Scored: Not reported · Eligible: Not reported | source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 4, bonus formula challenge, FraGNNet, Hit rate @5 Source checking is not independent reproduction. |
Papers and result coverage
Last literature check: 2026-09-17. Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
| Paper or primary resource | Version | Reference |
|---|---|---|
| MassSpecGym: A benchmark for the discovery and identification of molecules | 2410.23326v1 | Read source |
What is still missing
- Independent batch review before import; preserve existing observation identities.
Search and extraction details
complete comparison tables extracted pending publication review
Searches
- MassSpecGym 2410.23326 benchmark results Table 1 Table 2
Evidence locations
- Table 4: Cosine similarity, formula
Strengths and limitations
Limitations and conditions
No source-reviewed explanatory claims are recorded here yet.
Profile review details
Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.
Stable record: paper-protocol-5d8ed22461594b6dbeEvidence 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.
4 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Evaluation in this paper 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 Individual claims | MassSpecGym: A benchmark for the discovery and identification of molecules Table 4: Cosine similarity, formula 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 MassSpecGym · formula · Table 4. 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 Individual claims | MassSpecGym: A benchmark for the discovery and identification of molecules Table 4: Cosine similarity, formula 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. |
| Relationship: evaluates task discovery-benchmark-massspecgym-spectrum-simulation Individual claims | MassSpecGym: A benchmark for the discovery and identification of molecules Table 4: Cosine similarity, formula Version: 2410.23326v1 | source checked automated source review · 2026-09-17 Audit detailsField: Claim: paper-claim-92c18257e25792da5d Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: part of discovery-benchmark-massspecgym Individual claims | MassSpecGym: A benchmark for the discovery and identification of molecules Table 4: Cosine similarity, formula Version: 2410.23326v1 | source checked automated source review · 2026-09-17 Audit detailsField: Claim: paper-claim-3b04717de32e0edb0a 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-protocol-5d8ed22461594b6dbe
- areas
- metabolomics
- entity level
- protocol
- 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
- comparison panels
- id: part2-massspecgym-table4-ac4b0b4611; title: MassSpecGym · formula · Table 4; protocol id: paper-protocol-5d8ed22461594b6dbe; dataset id: paper-dataset-712fb45862f6d8614f; metric: Hit rate @1; unit: percent; direction: higher; result ids: paper-result-0eb930d3d87c1554c8; paper-result-e0a2ae6ef5e9dac842; paper-result-e1dad4454a489eea14; paper-result-89bc901270255db9e9; source ids: part2-massspecgym-arxiv-v1; source locator: Table 4: Hit rate @1, formula; context: 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; caveats: Source metric equations define hit rates as fractions, while table values use percentage scale; recorded values are not rescaled.; Zero generation accuracy is a reported result, not missingness.; No checkpoint revision inferred from method name.; Bootstrap CIs reflect resampling of this test set; not independently reproduced and not seed standard deviations.; Full table retained, including weaker/random methods and unavailable formula-simulation similarity cells.; review: method: automated_source_review; date: 2026-09-17; id: part2-massspecgym-table4-a71e8b64c9; title: MassSpecGym · formula · Table 4; protocol id: paper-protocol-5d8ed22461594b6dbe; dataset id: paper-dataset-712fb45862f6d8614f; metric: Hit rate @5; unit: percent; direction: higher; result ids: paper-result-23f54c2046394a9849; paper-result-2f03b245ed9e4e81e9; paper-result-f1dea3c2c74bc24384; paper-result-f6cbe952ed6e6a1568; source ids: part2-massspecgym-arxiv-v1; source locator: Table 4: Hit rate @5, formula; context: 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; caveats: Source metric equations define hit rates as fractions, while table values use percentage scale; recorded values are not rescaled.; Zero generation accuracy is a reported result, not missingness.; No checkpoint revision inferred from method name.; Bootstrap CIs reflect resampling of this test set; not independently reproduced and not seed standard deviations.; Full table retained, including weaker/random methods and unavailable formula-simulation similarity cells.; review: method: automated_source_review; date: 2026-09-17; id: part2-massspecgym-table4-8dc4756cf6; title: MassSpecGym · formula · Table 4; protocol id: paper-protocol-5d8ed22461594b6dbe; dataset id: paper-dataset-712fb45862f6d8614f; metric: Hit rate @20; unit: percent; direction: higher; result ids: paper-result-a0d4a99203b52c3a11; paper-result-5db072c636cb16b724; paper-result-23d5f2a3887e324717; paper-result-9e337171088dfc4bc7; source ids: part2-massspecgym-arxiv-v1; source locator: Table 4: Hit rate @20, formula; context: 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; caveats: Source metric equations define hit rates as fractions, while table values use percentage scale; recorded values are not rescaled.; Zero generation accuracy is a reported result, not missingness.; No checkpoint revision inferred from method name.; Bootstrap CIs reflect resampling of this test set; not independently reproduced and not seed standard deviations.; Full table retained, including weaker/random methods and unavailable formula-simulation similarity cells.; review: method: automated_source_review; date: 2026-09-17
- benchmark research
- review date: 2026-09-17; status: complete_comparison_tables_extracted_pending_publication_review; primary sources: part2-massspecgym-arxiv-v1; inspected locators: Table 4: Cosine similarity, formula; searched queries: MassSpecGym 2410.23326 benchmark results Table 1 Table 2; gaps: Independent batch review before import; preserve existing observation identities.; claim scope: Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
- legacy kinds
- benchmark
- entity classification
- review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: part2-massspecgym-arxiv-v1; source locator: Table 4: Cosine similarity, formula; ambiguities: None recorded
Related records
- evaluates task: MassSpecGym Spectrum simulation
- part of: MassSpecGym
- subject: MassSpecGym · formula (MassSpecGym Spectrum simulation): links:part_of:discovery-benchmark-massspecgym
- subject: MassSpecGym · formula (MassSpecGym Spectrum simulation): links:evaluates_task:discovery-benchmark-massspecgym-spectrum-simulation
- benchmark: GNN (formula): MassSpecGym · formula
- benchmark: FFN Fingerprint (formula): MassSpecGym · formula
- benchmark: FraGNNet (formula): MassSpecGym · formula
- benchmark: Precursor m/z (formula): MassSpecGym · formula