MassSpecGym De novo molecule generation

Stable ID: discovery-benchmark-massspecgym-de-novo-molecule-generation

areas

metabolomics

entity level

task

scope note

Specialist molecular or omics evaluation; protocol details require review before numerical comparison.

task

Generate molecular structures from tandem mass spectra

version

Not reported

comparison panels

id: part2-massspecgym-table2-eaf9691d7e; title: MassSpecGym · main · Table 2; protocol id: paper-protocol-9e2c05cdecc9a3241c; dataset id: paper-dataset-c25f9f3bb2961b23d5; metric: Top-1 accuracy; unit: fraction; direction: higher; result ids: paper-result-cdb00f17075ddae1d4; paper-result-001ce58c5292191491; paper-result-114b6658eaef67bace; source ids: part2-massspecgym-arxiv-v1; source locator: Table 2: Top-1 accuracy, main; context: 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; 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-table2-09fb9292ad; title: MassSpecGym · main · Table 2; protocol id: paper-protocol-9e2c05cdecc9a3241c; dataset id: paper-dataset-c25f9f3bb2961b23d5; metric: Top-1 MCES; unit: edge-edit distance; direction: lower; result ids: paper-result-5e7fd1597e90064dde; paper-result-5dbec6173d09a309db; paper-result-39e03e2651a3119076; source ids: part2-massspecgym-arxiv-v1; source locator: Table 2: Top-1 MCES, main; context: 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; 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-table2-f34201e2e4; title: MassSpecGym · main · Table 2; protocol id: paper-protocol-9e2c05cdecc9a3241c; dataset id: paper-dataset-c25f9f3bb2961b23d5; metric: Top-1 Tanimoto; unit: dimensionless; direction: higher; result ids: paper-result-fe122a4b95cfa19aec; paper-result-d8b7f603a24a1acf17; paper-result-a8a01911a2a38153bb; source ids: part2-massspecgym-arxiv-v1; source locator: Table 2: Top-1 Tanimoto, main; context: 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; 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-table2-363b3d3145; title: MassSpecGym · main · Table 2; protocol id: paper-protocol-9e2c05cdecc9a3241c; dataset id: paper-dataset-c25f9f3bb2961b23d5; metric: Top-10 accuracy; unit: fraction; direction: higher; result ids: paper-result-bc4465183b3bdd05e9; paper-result-b11072597f662ee8a3; paper-result-26d9400143fc2fd637; source ids: part2-massspecgym-arxiv-v1; source locator: Table 2: Top-10 accuracy, main; context: 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; 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-table2-9a67349dfe; title: MassSpecGym · main · Table 2; protocol id: paper-protocol-9e2c05cdecc9a3241c; dataset id: paper-dataset-c25f9f3bb2961b23d5; metric: Top-10 MCES; unit: edge-edit distance; direction: lower; result ids: paper-result-c4d079d645b148475c; paper-result-ef245bf2ce8115f850; paper-result-198ffa156afdd9aafa; source ids: part2-massspecgym-arxiv-v1; source locator: Table 2: Top-10 MCES, main; context: 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; 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-table2-8afdec59d8; title: MassSpecGym · main · Table 2; protocol id: paper-protocol-9e2c05cdecc9a3241c; dataset id: paper-dataset-c25f9f3bb2961b23d5; metric: Top-10 Tanimoto; unit: dimensionless; direction: higher; result ids: paper-result-c8b08ae7e71a836a51; paper-result-ddf10b5e3e4f655b34; paper-result-724980ddce45409480; source ids: part2-massspecgym-arxiv-v1; source locator: Table 2: Top-10 Tanimoto, main; context: 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; 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-table2-c5487be6c0; title: MassSpecGym · formula · Table 2; protocol id: paper-protocol-5d42ac5481b1c071e4; dataset id: paper-dataset-3f9a5b3d0316153887; metric: Top-1 accuracy; unit: fraction; direction: higher; result ids: paper-result-cb2bbb66e78675cc68; paper-result-cedb7d744e7a1a1270; paper-result-52e51c1dd59d05f572; source ids: part2-massspecgym-arxiv-v1; source locator: Table 2: Top-1 accuracy, formula; context: 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; 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-table2-eef6fb998a; title: MassSpecGym · formula · Table 2; protocol id: paper-protocol-5d42ac5481b1c071e4; dataset id: paper-dataset-3f9a5b3d0316153887; metric: Top-1 MCES; unit: edge-edit distance; direction: lower; result ids: paper-result-a3823cbc55713c1741; paper-result-f9e0659ed6de1857f1; paper-result-38f0c179e79c4c9dac; source ids: part2-massspecgym-arxiv-v1; source locator: Table 2: Top-1 MCES, formula; context: 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; 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-table2-78affa9e01; title: MassSpecGym · formula · Table 2; protocol id: paper-protocol-5d42ac5481b1c071e4; dataset id: paper-dataset-3f9a5b3d0316153887; metric: Top-1 Tanimoto; unit: dimensionless; direction: higher; result ids: paper-result-0ac9b7767e0fd6ca67; paper-result-7f9cce726b4019f851; paper-result-96030a32c14aaf11c3; source ids: part2-massspecgym-arxiv-v1; source locator: Table 2: Top-1 Tanimoto, formula; context: 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; 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-table2-daa1fccabf; title: MassSpecGym · formula · Table 2; protocol id: paper-protocol-5d42ac5481b1c071e4; dataset id: paper-dataset-3f9a5b3d0316153887; metric: Top-10 accuracy; unit: fraction; direction: higher; result ids: paper-result-57c8c3eaa6c96fd115; paper-result-252d625fb1507235e2; paper-result-23eb570af16987191b; source ids: part2-massspecgym-arxiv-v1; source locator: Table 2: Top-10 accuracy, formula; context: 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; 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-table2-c877ae5cd5; title: MassSpecGym · formula · Table 2; protocol id: paper-protocol-5d42ac5481b1c071e4; dataset id: paper-dataset-3f9a5b3d0316153887; metric: Top-10 MCES; unit: edge-edit distance; direction: lower; result ids: paper-result-b288a91a9b8d3c0ac3; paper-result-0cba6df8abf3e80c3e; paper-result-041cb47a464089a409; source ids: part2-massspecgym-arxiv-v1; source locator: Table 2: Top-10 MCES, formula; context: 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; 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-table2-c39edfb769; title: MassSpecGym · formula · Table 2; protocol id: paper-protocol-5d42ac5481b1c071e4; dataset id: paper-dataset-3f9a5b3d0316153887; metric: Top-10 Tanimoto; unit: dimensionless; direction: higher; result ids: paper-result-20160e960ae3bce164; paper-result-cc841777ec02cbc26d; paper-result-50fe2681b8dc27e6a7; source ids: part2-massspecgym-arxiv-v1; source locator: Table 2: Top-10 Tanimoto, formula; context: 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; 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: Tables2–4; task definitions and supplementary split table; 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.

historical missing metadata

dataset release: unextracted; metric implementation: unextracted; split manifest: unextracted; version: unextracted

metadata review scope

historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.

legacy kinds

benchmark

entity classification

review date: 2026-09-17; rationale: This record identifies the biological prediction question or a suite-specific task, rather than a uniquely fixed evaluated procedure. Preserve its task identity and leave split, model adaptation and scoring details on linked protocols/evaluations.; source ids: src-discovery-pluskal-lab-massspecgym; evidence-benchmark-massspecgym-de-novo-base-py; source locator: Pinned README: three challenges; dataset and DataModule; evaluation base classes; pinned massspecgym/models/de_novo/base.py evaluation methods; ambiguities: A paper- or suite-specific task may constrain some inputs or metrics; that alone does not make it interchangeable with a complete versioned protocol. No protocol equivalence is inferred.

• parent: MassSpecGym
• part of: MassSpecGym
• evaluates task: MassSpecGym · formula (MassSpecGym De novo molecule generation)
• evaluates task: MassSpecGym · main (MassSpecGym De novo molecule generation)
• subject: MassSpecGym De novo molecule generation: part of MassSpecGym