Jason Yim

17 papers A* 7Journal 10
YearRankTypeTitle / Venue / Authors
2025 A* conf
Generator Matching: Generative modeling with arbitrary Markov processes.
ICLR
Peter Holderrieth, Marton Havasi, Jason Yim, Neta Shaul, Itai Gat, Tommi S. Jaakkola, Brian Karrer, Ricky T. Q. Chen, Yaron Lipman
2025 J jnl
MotifBench: A standardized protein design benchmark for motif-scaffolding problems.
CoRR
Zhuoqi Zheng, Bo Zhang, Kieran Didi, Kevin K. Yang, Jason Yim, Joseph L. Watson, Hai-Feng Chen, Brian L. Trippe
2025 A* conf
ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids.
ICLR
Hannes Stärk, Bowen Jing, Tomas Geffner, Jason Yim, Tommi S. Jaakkola, Arash Vahdat, Karsten Kreis
2025 A* conf
Proteina: Scaling Flow-based Protein Structure Generative Models.
ICLR
Tomas Geffner, Kieran Didi, Zuobai Zhang, Danny Reidenbach, Zhonglin Cao, Jason Yim, Mario Geiger, Christian Dallago, Emine Küçükbenli, Arash Vahdat, Karsten Kreis
2025 J jnl
Proteina: Scaling Flow-based Protein Structure Generative Models.
CoRR
Tomas Geffner, Kieran Didi, Zuobai Zhang, Danny Reidenbach, Zhonglin Cao, Jason Yim, Mario Geiger, Christian Dallago, Emine Küçükbenli, Arash Vahdat, Karsten Kreis
2024 A* conf
Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design.
ICML
Andrew Campbell, Jason Yim, Regina Barzilay, Tom Rainforth, Tommi S. Jaakkola
2024 J jnl
Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design.
CoRR
Andrew Campbell, Jason Yim, Regina Barzilay, Tom Rainforth, Tommi S. Jaakkola
2024 J jnl
Generator Matching: Generative modeling with arbitrary Markov processes.
CoRR
Peter Holderrieth, Marton Havasi, Jason Yim, Neta Shaul, Itai Gat, Tommi S. Jaakkola, Brian Karrer, Ricky T. Q. Chen, Yaron Lipman
2024 J jnl
Improved motif-scaffolding with SE(3) flow matching.
CoRR
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
2024 J jnl
Improved motif-scaffolding with SE(3) flow matching.
Trans. Mach. Learn. Res.
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
2024 A* conf
Improving protein optimization with smoothed fitness landscapes.
ICLR
Andrew Kirjner, Jason Yim, Raman Samusevich, Shahar Bracha, Tommi S. Jaakkola, Regina Barzilay, Ila R. Fiete
2023 A* conf
Diffusion Probabilistic Modeling of Protein Backbones in 3D for the motif-scaffolding problem.
ICLR
Brian L. Trippe, Jason Yim, Doug Tischer, David Baker, Tamara Broderick, Regina Barzilay, Tommi S. Jaakkola
2023 J jnl
Optimizing protein fitness using Gibbs sampling with Graph-based Smoothing.
CoRR
Andrew Kirjner, Jason Yim, Raman Samusevich, Tommi S. Jaakkola, Regina Barzilay, Ila Fiete
2023 A* conf
SE(3) diffusion model with application to protein backbone generation.
ICML
Jason Yim, Brian L. Trippe, Valentin De Bortoli, Emile Mathieu, Arnaud Doucet, Regina Barzilay, Tommi S. Jaakkola
2023 J jnl
SE(3) diffusion model with application to protein backbone generation.
CoRR
Jason Yim, Brian L. Trippe, Valentin De Bortoli, Emile Mathieu, Arnaud Doucet, Regina Barzilay, Tommi S. Jaakkola
2022 J jnl
Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem.
CoRR
Brian L. Trippe, Jason Yim, Doug Tischer, David Baker, Tamara Broderick, Regina Barzilay, Tommi S. Jaakkola
2020 J jnl
Sparse Projection Oblique Randomer Forests.
J. Mach. Learn. Res.
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