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Journal Articles
- 2024
[j2]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:
Improved motif-scaffolding with SE(3) flow matching. Trans. Mach. Learn. Res. 2024 (2024)- 2020
- [j1]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:
Sparse Projection Oblique Randomer Forests. J. Mach. Learn. Res. 21: 104:1-104:39 (2020)
Conference and Workshop Papers
- 2024
- [c4]Andrew Kirjner, Jason Yim, Raman Samusevich, Shahar Bracha, Tommi S. Jaakkola, Regina Barzilay, Ila R. Fiete:
Improving protein optimization with smoothed fitness landscapes. ICLR 2024 - [c3]Andrew Campbell, Jason Yim, Regina Barzilay, Tom Rainforth, Tommi S. Jaakkola:
Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design. ICML 2024 - 2023
- [c2]Brian L. Trippe, Jason Yim, Doug Tischer, David Baker, Tamara Broderick, Regina Barzilay, Tommi S. Jaakkola:
Diffusion Probabilistic Modeling of Protein Backbones in 3D for the motif-scaffolding problem. ICLR 2023 - [c1]Jason Yim, Brian L. Trippe, Valentin De Bortoli, Emile Mathieu, Arnaud Doucet, Regina Barzilay, Tommi S. Jaakkola:
SE(3) diffusion model with application to protein backbone generation. ICML 2023: 40001-40039
Informal and Other Publications
- 2024
- [i5]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:
Improved motif-scaffolding with SE(3) flow matching. CoRR abs/2401.04082 (2024) - [i4]Andrew Campbell, Jason Yim, Regina Barzilay, Tom Rainforth, Tommi S. Jaakkola:
Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design. CoRR abs/2402.04997 (2024) - 2023
- [i3]Jason Yim, Brian L. Trippe, Valentin De Bortoli, Emile Mathieu, Arnaud Doucet, Regina Barzilay, Tommi S. Jaakkola:
SE(3) diffusion model with application to protein backbone generation. CoRR abs/2302.02277 (2023) - [i2]Andrew Kirjner, Jason Yim, Raman Samusevich
, Tommi S. Jaakkola, Regina Barzilay, Ila Fiete:
Optimizing protein fitness using Gibbs sampling with Graph-based Smoothing. CoRR abs/2307.00494 (2023) - 2022
- [i1]Brian L. Trippe, Jason Yim, Doug Tischer, David Baker, Tamara Broderick, Regina Barzilay, Tommi S. Jaakkola:
Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem. CoRR abs/2206.04119 (2022)
Coauthor Index
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