5 papers
Protein FID: Improved Evaluation of Protein Structure Generative Models
Felix Faltings, Hannes Stark, Tommi Jaakkola +1
Protein structure generative models have seen a recent surge of interest, but meaningfully evaluating them computationally is an active area of research. While current metrics have…
ProxelGen: Generating Proteins as 3D Densities
Felix Faltings, Hannes Stark, Regina Barzilay +1
We develop ProxelGen, a protein structure generative model that operates on 3D densities as opposed to the prevailing 3D point cloud representations. Representing proteins as voxel…
Identifying biological perturbation targets through causal differential networks
Menghua Wu, Umesh Padia, Sean H. Murphy +2
Identifying variables responsible for changes to a biological system enables applications in drug target discovery and cell engineering. Given a pair of observational and intervent…
Predicting sub-population specific viral evolution
Wenxian Shi, Menghua Wu, Regina Barzilay
Forecasting the change in the distribution of viral variants is crucial for therapeutic design and disease surveillance. This task poses significant modeling challenges due to the…
Hierarchical protein backbone generation with latent and structure diffusion
Jason Yim, Marouane Jaakik, Ge Liu +5
We propose a hierarchical protein backbone generative model that separates coarse and fine-grained details. Our approach called LSD consists of two stages: sampling latents which a…