Tommi Jaakkola

Computer Science · Physical Sciences

92h-index43.6kcitations450works17.02yr avg
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Research Topics

Computational Drug Discovery Methods(85), Machine Learning in Materials Science(82), Topic Modeling(64), Machine Learning and Algorithms(52), Bayesian Modeling and Causal Inference(40)

Publications446 total

PackFlow: Generative Molecular Crystal Structure Prediction via Reinforcement Learning Alignment
ArXiv.org·2026Open Access
PackFlow: Generative Molecular Crystal Structure Prediction via Reinforcement Learning Alignment
arXiv (Cornell University)·2026Open Access
Rethinking Diffusion Models with Symmetries through Canonicalization with Applications to Molecular Graph Generation
arXiv (Cornell University)·2026Open Access
Rethinking Diffusion Models with Symmetries through Canonicalization with Applications to Molecular Graph Generation
ArXiv.org·2026Open Access
Diamond Maps: Efficient Reward Alignment via Stochastic Flow Maps
ArXiv.org·2026Open Access
Diamond Maps: Efficient Reward Alignment via Stochastic Flow Maps
arXiv (Cornell University)·2026Open Access
Turbulence teaches equivariance to neural networks
ArXiv.org·2026Open Access
Turbulence teaches equivariance to neural networks
arXiv (Cornell University)·2026Open Access
FragmentFlow: Scalable Transition State Generation for Large Molecules
arXiv (Cornell University)·2026Open Access
FragmentFlow: Scalable Transition State Generation for Large Molecules
ArXiv.org·2026Open Access
Atom-level enzyme active site scaffolding using RFdiffusion2
Nature Methods·2025· 10 citedOpen Access
BoltzGen: Toward Universal Binder Design
2025· 10 citedOpen Access
HarnessLLM: Automatic Testing Harness Generation via Reinforcement Learning
arXiv (Cornell University)·2025Open Access
SPG: Sandwiched Policy Gradient for Masked Diffusion Language Models
arXiv (Cornell University)·2025Open Access
Next Semantic Scale Prediction via Hierarchical Diffusion Language Models
arXiv (Cornell University)·2025Open Access
Coevolutionary Continuous Discrete Diffusion: Make Your Diffusion Language Model a Latent Reasoner
arXiv (Cornell University)·2025Open Access
Implicit Augmentation from Distributional Symmetry in Turbulence Super-Resolution
arXiv (Cornell University)·2025Open Access
Structural constraint integration in a generative model for the discovery of quantum materials
Nature Materials·2025· 3 cited
AI-based Methods for Simulating, Sampling, and Predicting Protein Ensembles
arXiv (Cornell University)·2025· 1 citedOpen Access
Continuously Tempered Diffusion Samplers
arXiv (Cornell University)·2025Open Access
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Frequent Co-authors

Regina Barzilay(18), Michael I. Jordan(8), Wengong Jin(7), David K. Gifford(7), Klavs F. Jensen(6), Connor W. Coley(5), Satinder Singh(5), William H. Green(4), Gabriele Corso(4), H. Stärk(4), Kevin Yang(3), Kyle Swanson(3), Anush Chiappino-Pepe(3), James J. Collins(3), David Haussler(3), Nathan Srebro(3), Martin J. Wainwright(3), Alan S. Willsky(3), Ziv Bar‐Joseph(3), Zoubin Ghahramani(2)