1 code implementation • 7 Feb 2024 • Andrew Campbell, Jason Yim, Regina Barzilay, Tom Rainforth, Tommi Jaakkola
Our approach achieves state-of-the-art co-design performance while allowing the same multimodal model to be used for flexible generation of the sequence or structure.
1 code implementation • 8 Jan 2024 • 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
The first is motif amortization, in which FrameFlow is trained with the motif as input using a data augmentation strategy.
1 code implementation • 5 Dec 2023 • John J. Yang, Jason Yim, Regina Barzilay, Tommi Jaakkola
Generating protein sequences that fold into a intended 3D structure is a fundamental step in de novo protein design.
1 code implementation • 8 Oct 2023 • Jason Yim, Andrew Campbell, Andrew Y. K. Foong, Michael Gastegger, José Jiménez-Luna, Sarah Lewis, Victor Garcia Satorras, Bastiaan S. Veeling, Regina Barzilay, Tommi Jaakkola, Frank Noé
We present FrameFlow, a method for fast protein backbone generation using SE(3) flow matching.
1 code implementation • 2 Jul 2023 • Andrew Kirjner, Jason Yim, Raman Samusevich, Shahar Bracha, Tommi Jaakkola, Regina Barzilay, Ila Fiete
The ability to engineer novel proteins with higher fitness for a desired property would be revolutionary for biotechnology and medicine.
1 code implementation • 5 Feb 2023 • Jason Yim, Brian L. Trippe, Valentin De Bortoli, Emile Mathieu, Arnaud Doucet, Regina Barzilay, Tommi Jaakkola
The design of novel protein structures remains a challenge in protein engineering for applications across biomedicine and chemistry.
1 code implementation • 8 Jun 2022 • Brian L. Trippe, Jason Yim, Doug Tischer, David Baker, Tamara Broderick, Regina Barzilay, Tommi Jaakkola
Construction of a scaffold structure that supports a desired motif, conferring protein function, shows promise for the design of vaccines and enzymes.
2 code implementations • 10 Jun 2015 • Tyler M. Tomita, James Browne, Cencheng Shen, Jaewon Chung, Jesse L. Patsolic, Benjamin Falk, Jason Yim, Carey E. Priebe, Randal Burns, Mauro Maggioni, Joshua T. Vogelstein
Unfortunately, these extensions forfeit one or more of the favorable properties of decision forests based on axis-aligned splits, such as robustness to many noise dimensions, interpretability, or computational efficiency.