Thank you!

It was a pleasure!!

This project would not be possible without our amazing team: @anton-bushuiev.bsky.social, Raman Samusevich, Corinna Brungs, Josef Sivic, @pluskal-lab.org based at @iocbprague.bsky.social and CIIRC CTU

All models and datasets are freely available to the community under the MIT license 💚
📄 Paper: www.nature.com/articles/s41...
💻 Code: github.com/pluskal-lab/...
💡 Tutorials: dreams-docs.readthedocs.io/en/latest/
📊 Dataset: huggingface.co/datasets/rom...

We also introduce the DreaMS Atlas: a large-scale molecular network built from 200 million mass spectra, providing a new way to connect and analyze thousands of distinct scientific studies.

When fine-tuned, DreaMS achieves state-of-the-art performance across a range of molecule annotation tasks (e.g., predicting chemical similarity of molecular structures based on their mass spectra).

Trained in a self-supervised way on tens of millions of mass spectra from diverse samples (e.g., plants, human tissues, microbes, foods, soil samples), DreaMS learns rich representations ("embeddings") of molecular structures.

Check out the leaderboard paperswithcode.com/sota/de-novo... and MassSpecGym github.com/pluskal-lab/...

⭐ DiffMS (Connor Coley group, MIT) predicts molecular graph edges from a set of nodes (i.e., chemical formula atoms) using discrete diffusion. Conditioning on mass spectra is achieved by incorporating the MIST encoder.
📄 arxiv.org/abs/2502.09571

⭐ MADGEN (Soha Hassoun group, Tufts) retrieves molecular scaffold from a mass spectrum and a corresponding molecular formula using contrastive learning, then refines it with discrete diffusion and classifier-free guidance from mass spectrum.
📄 arxiv.org/abs/2501.01950

Did you experiment with 1D CNN? It should be very similar to GAT in this setup up to some normalizations. Also, would GAT outperform SetTransformer with the same number of parameters/layers?

Marcus Ludwig,Nils Haupt,Apurva Kalia,Corinna Brungs,Robin Schmid,Russell Greiner,Bo Wang,David Wishart,Li-Ping Liu,Juho Rousu,Wout Bittremieux,Hannes Rost,Tytus Mak,Soha Hassoun, @me-datapoint.bsky.social , @jjjvanderhooft.bsky.social ,Michael Stravs,Sebastian Böcker,Josef Sivic, @pluskal-lab.org

This project would not have been possible without the amazing collaboration of our incredible team: @roman-bushuiev.bsky.social, @anton-bushuiev.bsky.social , Niek F. de Jonge, Adamo Young, Fleming Kretschmer, Raman Samusevich, Janne Heirman, Fei Wang, Luke Zhang, Kai Dührkop,
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GitHub: github.com/pluskal-lab/....
Paper: arxiv.org/abs/2410.23326.
Polaris Hub (now officially certified 😍): polarishub.io/datasets/rom....
Hugging Face Hub: huggingface.co/datasets/rom....
Papers with Code leaderboard: paperswithcode.com/dataset/mass....
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