FOAM (DiffMS + PubChem) (MassSpecGym in the Wild)

Overview

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Evaluations and results

6 evaluations · 6 results. Different protocols are not a single leaderboard.

Dataset: MassSpecGym test fold, de novo generation with formula (bonus) (MassSpecGym in the Wild)

Sorted by Top-1 accuracy (de novo, exact match) (higher 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.

Tested configuration	Protocol and dataset	Top-1 accuracy (de novo, exact match)	Top-1 MCES (de novo)	Top-1 tanimoto (de novo)	Top-10 accuracy (de novo, exact match)	Top-10 MCES (de novo)	Top-10 tanimoto (de novo)
FOAM (DiffMS + PubChem) (MassSpecGym in the Wild)Evaluation	MassSpecGym de novo generation with formula (bonus), Top-1 Accuracy (MassSpecGym in the Wild Table 9)	1.5%	Not reported	Not reported	Not reported	Not reported	Not reported
FOAM (DiffMS + PubChem) (MassSpecGym in the Wild)Evaluation	MassSpecGym de novo generation with formula (bonus), Top-1 MCES (MassSpecGym in the Wild Table 9)	Not reported	12.2	Not reported	Not reported	Not reported	Not reported
FOAM (DiffMS + PubChem) (MassSpecGym in the Wild)Evaluation	MassSpecGym de novo generation with formula (bonus), Top-1 Tanimoto (MassSpecGym in the Wild Table 9)	Not reported	Not reported	0.35	Not reported	Not reported	Not reported
FOAM (DiffMS + PubChem) (MassSpecGym in the Wild)Evaluation	MassSpecGym de novo generation with formula (bonus), Top-10 Accuracy (MassSpecGym in the Wild Table 9)	Not reported	Not reported	Not reported	10.3%	Not reported	Not reported
FOAM (DiffMS + PubChem) (MassSpecGym in the Wild)Evaluation	MassSpecGym de novo generation with formula (bonus), Top-10 MCES (MassSpecGym in the Wild Table 9)	Not reported	Not reported	Not reported	Not reported	6.06	Not reported
FOAM (DiffMS + PubChem) (MassSpecGym in the Wild)Evaluation	MassSpecGym de novo generation with formula (bonus), Top-10 Tanimoto (MassSpecGym in the Wild Table 9)	Not reported	Not reported	Not reported	Not reported	Not reported	0.53

All 6 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: FOAM (DiffMS + PubChem) (MassSpecGym in the Wild)	Protocol: MassSpecGym de novo generation with formula (bonus), Top-1 Accuracy (MassSpecGym in the Wild Table 9) Dataset: MassSpecGym test fold, de novo generation with formula (bonus) (MassSpecGym in the Wild)	1.5% Top-1 accuracy (de novo, exact match) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Result quoted from another source · Source checked Methods, coverage and source FOAM (DiffMS + PubChem) on MassSpecGym denovo-bonus (Top-1 Accuracy) lit-otheromics-20261011-msgwild-protocol-denovo-bonus-top-1-accuracy Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 9, row 'FOAM (DiffMS + PubChem)', column 'Top-1 Accuracy'
Configuration: FOAM (DiffMS + PubChem) (MassSpecGym in the Wild)	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)	12.2 Top-1 MCES (de novo) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Result quoted from another source · Source checked Methods, coverage and source FOAM (DiffMS + PubChem) on MassSpecGym denovo-bonus (Top-1 MCES) lit-otheromics-20261011-msgwild-protocol-denovo-bonus-top-1-mces Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 9, row 'FOAM (DiffMS + PubChem)', column 'Top-1 MCES'
Configuration: FOAM (DiffMS + PubChem) (MassSpecGym in the Wild)	Protocol: MassSpecGym de novo generation with formula (bonus), Top-1 Tanimoto (MassSpecGym in the Wild Table 9) Dataset: MassSpecGym test fold, de novo generation with formula (bonus) (MassSpecGym in the Wild)	0.35 Top-1 tanimoto (de novo) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Result quoted from another source · Source checked Methods, coverage and source FOAM (DiffMS + PubChem) on MassSpecGym denovo-bonus (Top-1 Tanimoto) lit-otheromics-20261011-msgwild-protocol-denovo-bonus-top-1-tanimoto Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 9, row 'FOAM (DiffMS + PubChem)', column 'Top-1 Tanimoto'
Configuration: FOAM (DiffMS + PubChem) (MassSpecGym in the Wild)	Protocol: MassSpecGym de novo generation with formula (bonus), Top-10 Accuracy (MassSpecGym in the Wild Table 9) Dataset: MassSpecGym test fold, de novo generation with formula (bonus) (MassSpecGym in the Wild)	10.3% Top-10 accuracy (de novo, exact match) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Result quoted from another source · Source checked Methods, coverage and source FOAM (DiffMS + PubChem) on MassSpecGym denovo-bonus (Top-10 Accuracy) lit-otheromics-20261011-msgwild-protocol-denovo-bonus-top-10-accuracy Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 9, row 'FOAM (DiffMS + PubChem)', column 'Top-10 Accuracy'
Configuration: FOAM (DiffMS + PubChem) (MassSpecGym in the Wild)	Protocol: MassSpecGym de novo generation with formula (bonus), Top-10 MCES (MassSpecGym in the Wild Table 9) Dataset: MassSpecGym test fold, de novo generation with formula (bonus) (MassSpecGym in the Wild)	6.06 Top-10 MCES (de novo) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Result quoted from another source · Source checked Methods, coverage and source FOAM (DiffMS + PubChem) on MassSpecGym denovo-bonus (Top-10 MCES) lit-otheromics-20261011-msgwild-protocol-denovo-bonus-top-10-mces Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 9, row 'FOAM (DiffMS + PubChem)', column 'Top-10 MCES'
Configuration: FOAM (DiffMS + PubChem) (MassSpecGym in the Wild)	Protocol: MassSpecGym de novo generation with formula (bonus), Top-10 Tanimoto (MassSpecGym in the Wild Table 9) Dataset: MassSpecGym test fold, de novo generation with formula (bonus) (MassSpecGym in the Wild)	0.53 Top-10 tanimoto (de novo) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Result quoted from another source · Source checked Methods, coverage and source FOAM (DiffMS + PubChem) on MassSpecGym denovo-bonus (Top-10 Tanimoto) lit-otheromics-20261011-msgwild-protocol-denovo-bonus-top-10-tanimoto Aggregation: Not reported MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 9, row 'FOAM (DiffMS + PubChem)', column 'Top-10 Tanimoto'

Source checking is not independent reproduction. Release 2026-10-23-5347695500ed.

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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

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Technical metadata and extraction receipts

Stable ID: lit-otheromics-20261011-msgwild-config-foam-diffms-plus-pubchem

areas: metabolomics
contexts: research
method types: supervised_machine_learning
reported name: FOAM (DiffMS + PubChem)
foundation model eligible: false
parameters: FOAM (DiffMS + PubChem)
access reuse: Not stated in the source; see the cited work or https://github.com/pluskal-lab/MassSpecGym
source locator: Table 9 row 'FOAM (DiffMS + PubChem)'
missing metadata: version: reason: unreported; note: Only the printed row label identifies the setup
provenance note: FOAM (DiffMS + PubChem), as listed in MassSpecGym in the Wild Table 9.

Related records

configuration of: FOAM
system: FOAM (DiffMS + PubChem) on MassSpecGym denovo-bonus (Top-1 Accuracy)
system: FOAM (DiffMS + PubChem) on MassSpecGym denovo-bonus (Top-1 MCES)
system: FOAM (DiffMS + PubChem) on MassSpecGym denovo-bonus (Top-1 Tanimoto)
system: FOAM (DiffMS + PubChem) on MassSpecGym denovo-bonus (Top-10 Accuracy)
system: FOAM (DiffMS + PubChem) on MassSpecGym denovo-bonus (Top-10 MCES)
system: FOAM (DiffMS + PubChem) on MassSpecGym denovo-bonus (Top-10 Tanimoto)