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@tuftsrobotics @KrishnaswamyLab @DiffEqML @DISCO-design

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atong01/README.md

Alex Tong πŸ‘‹

Principal Investigator at Aithyra in Vienna, working on generative models for proteins and cells.

Website Lab Scholar Bluesky Twitter


About

I'm a PI at Aithyra (a research institute at the intersection of ML and life sciences in Vienna, led by Michael Bronstein), where I build generative models for proteins and cells. My research focuses on:

  • Flow matching β€” simulation-free training of continuous normalizing flows
  • Protein design β€” generative models over SE(3) and sequence spaces
  • Boltzmann sampling β€” scalable methods for sampling from molecular distributions
  • Single-cell dynamics β€” modeling cellular trajectories and causal discovery

Before Aithyra, I was a postdoc with Yoshua Bengio at Mila, and I completed my PhD at Yale advised by Smita Krishnaswamy. I also cofounded Dreamfold.


Featured Projects

Project Description Stars
TorchCFM Conditional Flow Matching library for training flow models Stars
Open-dLLM Open diffusion language model for code generation Stars
FoldFlow SE(3)-stochastic flow matching for protein backbone generation Stars
DISCO General multimodal protein design with DNA-encoded chemistry Stars
transferable-samplers Amortized sampling of molecular systems with normalizing flows Stars

GitHub Stats

GitHub Stats

πŸ“š Check out my publications β€” including work on FALCON, PAPL, and PITA.

πŸ‡¦πŸ‡Ή Based in Vienna, Austria Β· πŸ‡ΊπŸ‡Έ Grew up in Seattle

Pinned Loading

  1. conditional-flow-matching conditional-flow-matching Public

    TorchCFM: a Conditional Flow Matching library

    Python 2.5k 220

  2. pengzhangzhi/Open-dLLM pengzhangzhi/Open-dLLM Public

    Open diffusion language model for code generation β€” releasing pretraining, evaluation, inference, and checkpoints.

    Python 645 50

  3. DreamFold/FoldFlow DreamFold/FoldFlow Public

    FoldFlow: SE(3)-Stochastic Flow Matching for Protein Backbone Generation

    Jupyter Notebook 293 25

  4. DISCO-design/DISCO DISCO-design/DISCO Public

    Code for the DISCO model: General Multimodal Protein Design Enables DNA-Encoding of Chemistry

    Python 210 23

  5. jarridrb/DEM jarridrb/DEM Public

    Code for the paper Iterated Denoising Energy Matching for Sampling from Boltzmann Densities.

    Python 71 11

  6. transferable-samplers/transferable-samplers transferable-samplers/transferable-samplers Public

    A repo for transferable sampling of molecular systems

    Python 49 8