MassSpecGym de novo generation with formula (bonus), Top-1 MCES (MassSpecGym in the Wild Table 9)
MassSpecGym de novo generation with formula (bonus) on the test fold, scored by Top-1 MCES; mean over test spectra.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
10 recorded evaluations, 10 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
10 evaluations · 10 results. Different protocols are not a single leaderboard.
Protocol: MassSpecGym de novo generation with formula (bonus), Top-1 MCES (MassSpecGym in the Wild Table 9) · Dataset: MassSpecGym test fold, de novo generation with formula (bonus) (MassSpecGym in the Wild)
Sorted by Top-1 MCES (de novo) (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
All 10 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
Source checking is not independent reproduction. Release 2026-10-23-5347695500ed.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- DiffMS on MassSpecGym denovo-bonus (Top-1 MCES)
- FOAM (DiffMS + PubChem) on MassSpecGym denovo-bonus (Top-1 MCES)
- FRIGID on MassSpecGym denovo-bonus (Top-1 MCES)
- MADGEN on MassSpecGym denovo-bonus (Top-1 MCES)
- MIST + MolForge, reimplemented by the authors, batched inference bug (batch size 24) on MassSpecGym denovo-bonus (Top-1 MCES)
- MIST + MolForge, reimplemented by the authors, corrected on MassSpecGym denovo-bonus (Top-1 MCES)
- MIST + MSNovelist on MassSpecGym denovo-bonus (Top-1 MCES)
- MIST + Neuraldecipher on MassSpecGym denovo-bonus (Top-1 MCES)
- MS-BART on MassSpecGym denovo-bonus (Top-1 MCES)
- Spec2Mol on MassSpecGym denovo-bonus (Top-1 MCES)
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- External evaluations
- 2
- paper compilation
- 8
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Select a task-valid null control after reviewing inputs and metric
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Select an upstream conventional reference after reviewing the full protocol
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-23-5347695500ed. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
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Sources and history
Release 2026-10-23-5347695500ed · Record review: source checked
1 source record and release history
- MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Original source · arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering
Technical metadata and extraction receipts
Stable ID: lit-otheromics-20261011-msgwild-protocol-denovo-bonus-top-1-mces
- areas
- metabolomics
- contexts
- research
- protocol
- MassSpecGym de novo generation with formula (bonus); Top-1 MCES
- version
- MassSpecGym as audited in arXiv:2606.19624v1
- metric
- top-1-mces
- metric direction
- lower
- unit
- unitless
- metric qualifier
- de novo
- source locator
- Table 9 column 'Top-1 MCES'; Appendix 'Confidence Intervals'
- limitations
- Rows mix values copied from the literature with the authors' own runs; see each evaluation's origin.; Grey rows are results the authors consider leaking or inflated.
Related records
- part of: MassSpecGym
- evaluates task: MassSpecGym De novo molecule generation
- uses data: MassSpecGym test fold, de novo generation with formula (bonus) (MassSpecGym in the Wild)
- assessment: DiffMS on MassSpecGym denovo-bonus (Top-1 MCES)
- assessment: FOAM (DiffMS + PubChem) on MassSpecGym denovo-bonus (Top-1 MCES)
- assessment: FRIGID on MassSpecGym denovo-bonus (Top-1 MCES)
- assessment: MADGEN on MassSpecGym denovo-bonus (Top-1 MCES)
- assessment: MIST + MolForge, reimplemented by the authors, batched inference bug (batch size 24) on MassSpecGym denovo-bonus (Top-1 MCES)
- assessment: MIST + MolForge, reimplemented by the authors, corrected on MassSpecGym denovo-bonus (Top-1 MCES)
- assessment: MIST + MSNovelist on MassSpecGym denovo-bonus (Top-1 MCES)
- assessment: MIST + Neuraldecipher on MassSpecGym denovo-bonus (Top-1 MCES)
- assessment: MS-BART on MassSpecGym denovo-bonus (Top-1 MCES)
- assessment: Spec2Mol on MassSpecGym denovo-bonus (Top-1 MCES)