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Update README
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roman-bushuiev committed Oct 29, 2024
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MassSpecGym provides three challenges for benchmarking the discovery and identification of new molecules from MS/MS spectra:

- 💥 ***De novo* molecular generation** (MS/MS spectrum → molecular structure)
- 🎆 **Bonus chemical formulae challenge** (MS/MS spectrum + chemical formula → molecular structure)
- 💥 **Molecular retrieval** (MS/MS spectrum → ranked list of candidate molecular structures)
- 🎆 **Bonus chemical formulae challenge** (MS/MS spectrum + chemical formula → ranked list of candidate molecular structures)
- 💥 ***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 + chemical formula → ranked list of candidate molecular structures)
- 💥 **Spectrum simulation** (molecular structure → MS/MS spectrum)

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.
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