Sparse Projection Oblique Randomer Forests. - Tyler M. Tomita; James Browne; Cencheng Shen; Jaewon Chung; Jesse Patsolic; Benjamin Falk; Carey E. Priebe; Jason Yim; Randal C. Burns; Mauro Maggioni; Joshua T. Vogelstein (J. Mach. Learn. Res., 2020)

Diffusion Probabilistic Modeling of Protein Backbones in 3D for the motif-scaffolding problem. - Brian L. Trippe; Jason Yim; Doug Tischer; David Baker 001; Tamara Broderick; Regina Barzilay; Tommi S. Jaakkola (ICLR, 2023)

SE(3) diffusion model with application to protein backbone generation. - Jason Yim; Brian L. Trippe; Valentin De Bortoli; Emile Mathieu; Arnaud Doucet; Regina Barzilay; Tommi S. Jaakkola (ICML, 2023)

Optimizing protein fitness using Gibbs sampling with Graph-based Smoothing. - Andrew Kirjner; Jason Yim; Raman Samusevich; Tommi S. Jaakkola; Regina Barzilay; Ila Fiete (CoRR, 2023)

Improving protein optimization with smoothed fitness landscapes. - Andrew Kirjner; Jason Yim; Raman Samusevich; Shahar Bracha; Tommi S. Jaakkola; Regina Barzilay; Ila R. Fiete (ICLR, 2024)

Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design. - Andrew Campbell; Jason Yim; Regina Barzilay; Tom Rainforth; Tommi S. Jaakkola (ICML, 2024)

Improved motif-scaffolding with SE(3) flow matching. - Jason Yim; Andrew Campbell; Emile Mathieu; Andrew Y. K. Foong; Michael Gastegger; José Jiménez-Luna; Sarah Lewis; Victor Garcia Satorras; Bastiaan S. Veeling; Frank Noé; Regina Barzilay; Tommi S. Jaakkola (Trans. Mach. Learn. Res., 2024)

Proteina: Scaling Flow-based Protein Structure Generative Models. - Tomas Geffner; Kieran Didi; Zuobai Zhang; Danny Reidenbach; Zhonglin Cao; Jason Yim; Mario Geiger; Christian Dallago; Emine Küçükbenli; Arash Vahdat; Karsten Kreis (ICLR, 2025)

Generator Matching: Generative modeling with arbitrary Markov processes. - Peter Holderrieth; Marton Havasi; Jason Yim; Neta Shaul; Itai Gat; Tommi S. Jaakkola; Brian Karrer; Ricky T. Q. Chen; Yaron Lipman (ICLR, 2025)

ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids. - Hannes Stärk; Bowen Jing; Tomas Geffner; Jason Yim; Tommi S. Jaakkola; Arash Vahdat; Karsten Kreis (ICLR, 2025)

MotifBench: A standardized protein design benchmark for motif-scaffolding problems. - Zhuoqi Zheng; Bo Zhang; Kieran Didi; Kevin K. Yang; Jason Yim; Joseph L. Watson; Hai-Feng Chen; Brian L. Trippe (CoRR, 2025)