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Tong Group

Research

Generative modeling, flow models, optimal transport, and protein design at the intersection of machine learning and life sciences

Sampling and Boltzmann Generators Active

Sampling and Boltzmann Generators

Developing generative models for sampling from Boltzmann distributions—combining normalizing flows, diffusion, and autoregressive models to generate equilibrium samples of molecular systems.

boltzmann-generators molecular-sampling normalizing-flows statistical-physics
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Generative Modeling Active

Generative Modeling

Developing state-of-the-art generative models including diffusion models and flow-based approaches with applications to molecular design, language modeling, and scientific computing.

diffusion-models flow-models deep-learning
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Optimal Transport & Geometry Active

Optimal Transport & Geometry

Developing efficient computational methods for optimal transport with applications to single-cell biology, trajectory inference, and generative modeling.

optimal-transport differential-geometry machine-learning computational-biology
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Protein Design & Molecular Structure

Applying generative modeling to protein design, molecular structure prediction, and crystal structure prediction using SE(3)-invariant flow matching and all-atom diffusion models.

proteins structure-prediction molecular-design diffusion-models
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Sequence Modeling Active

Sequence Modeling

Developing generative models for discrete sequences—including diffusion language models, masked discrete diffusion, and one-step discrete generation—for language modeling and biological sequence design.

discrete-diffusion language-models sequence-generation generative-modeling
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Single-Cell Biology & Dynamics Active

Single-Cell Biology & Dynamics

Developing machine learning methods to understand cellular development, state transitions, and responses to stimuli using single-cell omics data.

single-cell transcriptomics cellular-dynamics inference
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