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Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking
Octavian-Eugen Ganea, Xinyuan Huang, Charlotte Bunne +4
Protein complex formation is a central problem in biology, being involved in most of the cell's processes, and essential for applications, e.g. drug design or protein engineering.…
Fragment-based Sequential Translation for Molecular Optimization
Benson Chen, Xiang Fu, Regina Barzilay +1
Searching for novel molecular compounds with desired properties is an important problem in drug discovery. Many existing frameworks generate molecules one atom at a time. We instea…
Understanding Interlocking Dynamics of Cooperative Rationalization
Mo Yu, Yang Zhang, Shiyu Chang +1
Selective rationalization explains the prediction of complex neural networks by finding a small subset of the input that is sufficient to predict the neural model output. The selec…
Learning Representations that Support Robust Transfer of Predictors
Yilun Xu, Tommi Jaakkola
Ensuring generalization to unseen environments remains a challenge. Domain shift can lead to substantially degraded performance unless shifts are well-exercised within the availabl…
Crystal Diffusion Variational Autoencoder for Periodic Material Generation
Tian Xie, Xiang Fu, Octavian-Eugen Ganea +2
Generating the periodic structure of stable materials is a long-standing challenge for the material design community. This task is difficult because stable materials only exist in…
Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design
Wengong Jin, Jeremy Wohlwend, Regina Barzilay +1
Antibodies are versatile proteins that bind to pathogens like viruses and stimulate the adaptive immune system. The specificity of antibody binding is determined by complementarity…