MD4‑MS/MS: Masked Diffusion for Tandem‑MS Structural Elucidation

A fork of MD4: Simplified and Generalized Masked Diffusion for Discrete Data
extended to large‑scale pre‑training on SMILES, conditioned on Morgan fingerprints predicted from MS/MS spectra with the MIST model.

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🛠️ Installation

Create a fresh environment (GPU example shown):

uv sync

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Acknowledgement

@inproceedings{shi2024simplified,
  title={Simplified and Generalized Masked Diffusion for Discrete Data},
  author={Shi, Jiaxin and Han, Kehang and Wang, Zhe and Doucet, Arnaud and Titsias, Michalis K.},
  booktitle={Advances in Neural Information Processing Systems},
  year={2024}
}

Goldman, S., Wohlwend, J., Stražar, M. et al. Annotating metabolite mass spectra with domain-inspired chemical formula transformers. Nat Mach Intell (2023). https://doi.org/10.1038/s42256-023-00708-3