Jason Yim


Email: jyim [at] mit.edu

Stata center

32 Vassar St

Cambridge, MA 02139

Hi! I am a 3rd year EECS PhD candidate at MIT CSAIL advised by Tommi Jaakkola and Regina Barzilay. Previously, I was as a research engineer at DeepMind and obtained my B.S. from Johns Hopkins University in Computer Science and Applied Mathematics. My research is partially funded by NSF graduate research fellowship (GRFP).

My research aims to develop machine learning methods in scientific domains such as biology and chemistry. I am passionate about applications to medicine, environmentalism, and advancing scientific knowledge.

I enjoy learning the science behind each problem and developing practical algorithms that reflect the underlying structure and mechanism. I do not limit myself to specific techniques but instead look for the right foundation in mathematics, statistics, optimization and aim to develop novel machine learning methods from them. I have research experience in the following:

  • Applications: medical imaging, protein structure modeling, protein fitness optimization, de novo protein design.

  • Methods: geometric deep learning, generative (diffusion and flow) models, discrete optimization, Riemannian manifolds.

In addition, I value strong research engineering of moving fast and efficiently (i.e. minimizing bugs). See my publications page for my recent work. You can hear about my work from my CSAIL student spotlight.


Apr 8, 2024
  • MIT news ran a article on our protein sequence optimization method.
  • Our review of diffusion models in protein structure generation and docking is out on WIREs advanced reviews.
Jan 16, 2024
Jul 13, 2023
Jan 21, 2023
Dec 9, 2022