Yim, Jason

14 publications

ICLR 2025 Generator Matching: Generative Modeling with Arbitrary Markov Processes Peter Holderrieth, Marton Havasi, Jason Yim, Neta Shaul, Itai Gat, Tommi Jaakkola, Brian Karrer, Ricky T. Q. Chen, Yaron Lipman

ICLRW 2025 Hierarchical Protein Backbone Generation with Latent and Structure Diffusion Jason Yim, Marouane Jaakik, Ge Liu, Jacob Gershon, Karsten Kreis, David Baker, Regina Barzilay, Tommi Jaakkola

ICLR 2025 ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids Hannes Stark, Bowen Jing, Tomas Geffner, Jason Yim, Tommi Jaakkola, Arash Vahdat, Karsten Kreis

ICLR 2025 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 Kucukbenli, Arash Vahdat, Karsten Kreis

ICML 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 Jaakkola

ICLRW 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 Jaakkola

TMLR 2024 Improved Motif-Scaffolding with SE(3) Flow Matching Jason Yim, Andrew Campbell, Emile Mathieu, Andrew Y. K. Foong, Michael Gastegger, Jose Jimenez-Luna, Sarah Lewis, Victor Garcia Satorras, Bastiaan S. Veeling, Frank Noe, Regina Barzilay, Tommi Jaakkola

ICLRW 2024 Improved Motif-Scaffolding with SE(3) Flow Matching Jason Yim, Andrew Campbell, Emile Mathieu, Andrew Y. K. Foong, Michael Gastegger, Jose Jimenez-Luna, Sarah Lewis, Victor Garcia Satorras, Bastiaan S. Veeling, Frank Noe, Regina Barzilay, Tommi Jaakkola

ICLR 2024 Improving Protein Optimization with Smoothed Fitness Landscapes Andrew Kirjner, Jason Yim, Raman Samusevich, Shahar Bracha, Tommi S. Jaakkola, Regina Barzilay, Ila R Fiete

ICLR 2023 Diffusion Probabilistic Modeling of Protein Backbones in 3D for the Motif-Scaffolding Problem Brian L. Trippe, Jason Yim, Doug Tischer, David Baker, Tamara Broderick, Regina Barzilay, Tommi S. Jaakkola

ICMLW 2023 Optimizing Protein Fitness Using Gibbs Sampling with Graph-Based Smoothing Andrew Kirjner, Jason Yim, Raman Samusevich, Tommi S. Jaakkola, Regina Barzilay, Ila R Fiete

ICMLW 2023 Optimizing Protein Fitness Using Gibbs Sampling with Graph-Based Smoothing Andrew Kirjner, Jason Yim, Raman Samusevich, Tommi S. Jaakkola, Regina Barzilay, Ila R Fiete

ICML 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 Jaakkola

JMLR 2020 Sparse Projection Oblique Randomer Forests Tyler M. Tomita, James Browne, Cencheng Shen, Jaewon Chung, Jesse L. Patsolic, Benjamin Falk, Carey E. Priebe, Jason Yim, Randal Burns, Mauro Maggioni, Joshua T. Vogelstein