40 citations · 58 across the 4 of their papers we have counts for
6 papers · 1 filter
Protein Representation Learning by Geometric Structure Pretraining
Zuobai Zhang, Minghao Xu, Arian Jamasb +4
Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain prote…
Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design
Yue Cao, Payel Das, Vijil Chenthamarakshan +3
Designing novel protein sequences for a desired 3D topological fold is a fundamental yet non-trivial task in protein engineering. Challenges exist due to the complex sequence--fold…
Optimizing Molecules using Efficient Queries from Property Evaluations
Samuel Hoffman, Vijil Chenthamarakshan, Kahini Wadhawan +2
Machine learning based methods have shown potential for optimizing existing molecules with more desirable properties, a critical step towards accelerating new chemical discovery. H…
Accelerating Antimicrobial Discovery with Controllable Deep Generative Models and Molecular Dynamics
Payel Das, Tom Sercu, Kahini Wadhawan +12
De novo therapeutic design is challenged by a vast chemical repertoire and multiple constraints, e.g., high broad-spectrum potency and low toxicity. We propose CLaSS (Controlled La…
CogMol: Target-Specific and Selective Drug Design for COVID-19 Using Deep Generative Models
Vijil Chenthamarakshan, Payel Das, Samuel C. Hoffman +8
The novel nature of SARS-CoV-2 calls for the development of efficient de novo drug design approaches. In this study, we propose an end-to-end framework, named CogMol (Controlled Ge…
A Sequential Set Generation Method for Predicting Set-Valued Outputs
Tian Gao, Jie Chen, Vijil Chenthamarakshan +1
Consider a general machine learning setting where the output is a set of labels or sequences. This output set is unordered and its size varies with the input. Whereas multi-label c…