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Protocol

MassSpecGym · main (MassSpecGym De novo molecule generation)

MassSpecGym · main · Table 2. 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

MassSpecGym: A benchmark for the discovery and identification of molecules · Table 2: Top-1 accuracy, main

3 evaluations · 18 metric rows

At 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

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

MassSpecGym: A benchmark for the discovery and identification of molecules · Table 2: Top-1 accuracy, main

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

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 · main · Table 2

Top-1 accuracy (fraction) · Higher values are better for this metric.

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

Evaluation protocol · MassSpecGym · main

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 2: Top-1 accuracy, main
Values, uncertainty and evidence
Top-1 accuracy: original source values
Tested entityPrinted valueUncertaintyEvidence
Random chemical generation (main) · Configuration0.00 fractionNot reportedAuthor-reported evaluation · source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, Random chemical generation, Top-1 accuracy
SMILES Transformer (main) · Configuration0.00 fractionNot reportedAuthor-reported evaluation · source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, SMILES Transformer, Top-1 accuracy
SELFIES Transformer (main) · Configuration0.00 fractionNot reportedAuthor-reported evaluation · source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, SELFIES Transformer, Top-1 accuracy
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 · 3 evaluations · 18 metric rows. Different protocols are not a single leaderboard.

Results grouped by the exact reported evaluation
Metric and findingCoverage and uncertaintyEvidence
SMILES Transformer (main): MassSpecGym · main

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

Author-reported evaluation · Evaluation metadata: needs review

0.00 Top-1 accuracy

Unit: fraction · Direction: higher

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, SMILES Transformer, Top-1 accuracy

Source checking is not independent reproduction.

53.80 (52.95-54.61) Top-1 MCES

Unit: edge-edit distance · Direction: lower

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 52.95; upper: 54.61

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, SMILES Transformer, Top-1 MCES

Source checking is not independent reproduction.

0.00 Top-10 accuracy

Unit: fraction · Direction: higher

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, SMILES Transformer, Top-10 accuracy

Source checking is not independent reproduction.

0.07 (0.07 - 0.08) Top-1 Tanimoto

Unit: dimensionless · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 0.07; upper: 0.08

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, SMILES Transformer, Top-1 Tanimoto

Source checking is not independent reproduction.

0.17 (0.17 - 0.17) Top-10 Tanimoto

Unit: dimensionless · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 0.17; upper: 0.17

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, SMILES Transformer, Top-10 Tanimoto

Source checking is not independent reproduction.

21.97 (21.79-22.16) Top-10 MCES

Unit: edge-edit distance · Direction: lower

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 21.79; upper: 22.16

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, SMILES Transformer, Top-10 MCES

Source checking is not independent reproduction.

SELFIES Transformer (main): MassSpecGym · main

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

Author-reported evaluation · Evaluation metadata: needs review

0.00 Top-1 accuracy

Unit: fraction · Direction: higher

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, SELFIES Transformer, Top-1 accuracy

Source checking is not independent reproduction.

21.84 (21.67-22.00) Top-10 MCES

Unit: edge-edit distance · Direction: lower

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 21.67; upper: 22.00

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, SELFIES Transformer, Top-10 MCES

Source checking is not independent reproduction.

0.00 Top-10 accuracy

Unit: fraction · Direction: higher

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, SELFIES Transformer, Top-10 accuracy

Source checking is not independent reproduction.

33.28 (33.00-33.57) Top-1 MCES

Unit: edge-edit distance · Direction: lower

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 33.00; upper: 33.57

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, SELFIES Transformer, Top-1 MCES

Source checking is not independent reproduction.

0.15 (0.15 - 0.15) Top-10 Tanimoto

Unit: dimensionless · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 0.15; upper: 0.15

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, SELFIES Transformer, Top-10 Tanimoto

Source checking is not independent reproduction.

0.10 (0.10 - 0.10) Top-1 Tanimoto

Unit: dimensionless · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 0.10; upper: 0.10

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, SELFIES Transformer, Top-1 Tanimoto

Source checking is not independent reproduction.

Random chemical generation (main): MassSpecGym · main

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

Author-reported evaluation · Evaluation metadata: needs review

28.59 (28.33-28.84) Top-1 MCES

Unit: edge-edit distance · Direction: lower

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 28.33; upper: 28.84

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, Random chemical generation, Top-1 MCES

Source checking is not independent reproduction.

0.00 Top-10 accuracy

Unit: fraction · Direction: higher

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, Random chemical generation, Top-10 accuracy

Source checking is not independent reproduction.

25.72 (25.49-25.95) Top-10 MCES

Unit: edge-edit distance · Direction: lower

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 25.49; upper: 25.95

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, Random chemical generation, Top-10 MCES

Source checking is not independent reproduction.

0.10 (0.10 - 0.10) Top-10 Tanimoto

Unit: dimensionless · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 0.10; upper: 0.10

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, Random chemical generation, Top-10 Tanimoto

Source checking is not independent reproduction.

0.00 Top-1 accuracy

Unit: fraction · Direction: higher

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, Random chemical generation, Top-1 accuracy

Source checking is not independent reproduction.

0.07 (0.07 - 0.07) Top-1 Tanimoto

Unit: dimensionless · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 0.07; upper: 0.07

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 2, main challenge, Random chemical generation, Top-1 Tanimoto

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.

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 2: Top-1 accuracy, main

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

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-9e2c05cdecc9a3241c

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.

4 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
Property and statementOriginal source and locationReview and provenance
Evaluation in this paper

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

Individual claims
MassSpecGym: A benchmark for the discovery and identification of molecules

Original source ↗

Table 2: Top-1 accuracy, main

Version: 2410.23326v1
Retrieved: 2026-09-17T07:56:11.146650+00:00

source checked

automated source review · 2026-09-17

Audit details

Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.

Field: attributes.profile.sections.0.body

Source artifact SHA-256: 82176d50e8947c8b9baa2a0d91493f5680c0e4c7e25a2266ff7879f48a58c40c

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Introduction

MassSpecGym · main · Table 2. 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

Individual claims
MassSpecGym: A benchmark for the discovery and identification of molecules

Original source ↗

Table 2: Top-1 accuracy, main

Version: 2410.23326v1
Retrieved: 2026-09-17T07:56:11.146650+00:00

source checked

automated source review · 2026-09-17

Audit details

Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.

Field: attributes.profile.summary

Source artifact SHA-256: 82176d50e8947c8b9baa2a0d91493f5680c0e4c7e25a2266ff7879f48a58c40c

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Relationship: evaluates task

discovery-benchmark-massspecgym-de-novo-molecule-generation

Individual claims
MassSpecGym: A benchmark for the discovery and identification of molecules

Original source ↗

Table 2: Top-1 accuracy, main

Version: 2410.23326v1
Retrieved: 2026-09-17T07:56:11.146650+00:00

source checked

automated source review · 2026-09-17

Audit details

Field: links:evaluates_task:discovery-benchmark-massspecgym-de-novo-molecule-generation

Claim: paper-claim-9131dcecc02ad9e836

Source artifact SHA-256: 82176d50e8947c8b9baa2a0d91493f5680c0e4c7e25a2266ff7879f48a58c40c

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Relationship: part of

discovery-benchmark-massspecgym

Individual claims
MassSpecGym: A benchmark for the discovery and identification of molecules

Original source ↗

Table 2: Top-1 accuracy, main

Version: 2410.23326v1
Retrieved: 2026-09-17T07:56:11.146650+00:00

source checked

automated source review · 2026-09-17

Audit details

Field: links:part_of:discovery-benchmark-massspecgym

Claim: paper-claim-7f96e8ca23e2f2304d

Source artifact SHA-256: 82176d50e8947c8b9baa2a0d91493f5680c0e4c7e25a2266ff7879f48a58c40c

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Sources and history

Release 2026-09-17-d277315f7d76 · Record review: needs review

Download this release
Technical metadata and extraction receipts

Stable ID: paper-protocol-9e2c05cdecc9a3241c

areas
metabolomics
entity level
protocol
protocol
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
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
benchmark research
review date: 2026-09-17; status: complete_comparison_tables_extracted_pending_publication_review; primary sources: part2-massspecgym-arxiv-v1; inspected locators: Table 2: Top-1 accuracy, main; 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 2: Top-1 accuracy, main; ambiguities: None recorded
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