4 papers
On the Design Space of Discrete Diffusion Online Adaptation for Molecular Optimization
Trevor Chen, Ariel Dai, Jason Yang +8
Molecular optimization often starts from a pretrained generative model that captures a broad prior over valid molecular structures. At test time, however, the goal is not to sample…
General Multimodal Protein Design Enables DNA-Encoding of Chemistry
Jarrid Rector-Brooks, Théophile Lambert, Marta Skreta +15
Evolution is an extraordinary engine for enzymatic diversity, yet the chemistry it has explored remains a narrow slice of what DNA can encode. Deep generative models can design new…
Steering Generative Models with Experimental Data for Protein Fitness Optimization
Jason Yang, Wenda Chu, Daniel Khalil +4
Protein fitness optimization involves finding a protein sequence that maximizes desired quantitative properties in a combinatorially large design space of possible sequences. Recen…
CARE: a Benchmark Suite for the Classification and Retrieval of Enzymes
Jason Yang, Ariane Mora, Shengchao Liu +4
Enzymes are important proteins that catalyze chemical reactions. In recent years, machine learning methods have emerged to predict enzyme function from sequence; however, there are…