Datasets › MassSpecGym
MassSpecGym (MassSpecGym: A benchmark for the discovery and identification of molecules)
MassSpecGym provides three challenges for benchmarking the discovery and identification of new molecules from MS/MS spectra:
- 💥 De novo molecule generation (MS/MS spectrum → molecular structure)
- ✨ Bonus chemical formulae challenge (MS/MS spectrum + chemical formula → molecular structure)
- 💥 Molecule retrieval (MS/MS spectrum → ranked list of candidate molecular structures)
- ✨ Bonus chemical formulae challenge (MS/MS spectrum → ranked list of candidate molecular structures with ground-truth chemical formulae)
- 💥 Spectrum simulation (molecular structure → MS/MS spectrum)
- ✨ Bonus chemical formulae challenge (molecular structure → MS/MS spectrum; evaluated on the retrieval of molecular structures with ground-truth chemical formulae)
The provided challenges abstract the process of scientific discovery from biological and environmental samples into well-defined machine learning problems with pre-defined datasets, data splits, and evaluation metrics.
Benchmarks archive 2025-07-28
All 6 leaderboards whose dataset resolves to this page shown (sort by any header). "First row" is the archive's own first row at snapshot, in the archive's row order; nothing here re-ranks and metric direction is not asserted.
Papers archive 2025-07-28
4 shown of 4 papers with a leaderboard row on this dataset's benchmarks, newest first. The archive's own "papers using this dataset" list was never published, so this is the benchmark-backed subset; the archive's count for this dataset is 4. The Syntology column is from Syntology's graph (read 2026-09-24), stated per sample; it is not part of any archive number.
| Date | Samples run Syntology | |||
|---|---|---|---|---|
| DiffMS: Diffusion Generation of Molecules Conditioned on Mass Spectra | 1 | 2 | 13 Feb 2025 | ran 1 of 1 samples (0 unverified) |
| MADGEN: Mass-Spec attends to De Novo Molecular generation | 1 | 2 | 3 Jan 2025 | ran 2 of 2 samples (0 unverified) |
| JESTR: Joint Embedding Space Technique for Ranking Candidate Molecules for the Annotation of Untargeted Metabolomics Data | 0 | 6 | 18 Nov 2024 | not harvested |
| MassSpecGym: A benchmark for the discovery and identification of molecules | 1 | 24 | 30 Oct 2024 | ran 2 of 6 samples (4 unverified) |
Dataset loaders archive 2025-07-28
1 loader as listed in the archive; links are outbound and not re-checked here.
Tasks archive 2025-07-28
License archive 2025-07-28
MIT
Modalities archive 2025-07-28
Languages archive 2025-07-28
Variants archive 2025-07-28
- MassSpecGym
1 variant name, as the archive lists them.
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