General
Solving Inverse Problems with Conditional Diffusion Models
What is an inverse problem, and where do inverse problems appear in chemistry? In deep learning for chemistry, it is common to train a classifier
July 11, 2022
Data Science
Coarse-grained Molecular Dynamics with Geometric Machine Learning
We live an a world where chemistry computation is increasingly competitive with experimentation. AlphaFold predicts protein structure with accuracy sufficient for many applications. In the
June 27, 2022
Data Science
SELFIES and the future of molecular string representations
Neural sequence models have recently produced astonishing results in domains ranging from natural language to proteins and biochemistry. Current sequence models trained on text can explain
June 16, 2022
Data Science
Machine Learning for Drug Discovery at ICLR 2022
For the last decade, the field of deep learning and AI has been dominated by applications to images and text. However, in the past two
May 12, 2022
Data Science
Fragment Ligand Generation
Extremely data-efficient ligand generation What is a sufficient number of data points to train a deep learning algorithm? 1,000? 1 million? 1 billion? Of course,
May 5, 2022
Data Science
Protein Representation Learning by Geometric Structure Pretraining
The study of structural biochemistry is based on the axiom that “structure determines function”. A corollary of that axiom is that, for proteins, “function is
April 28, 2022
Data Science
A new state-of-the-art model for molecular conformer generation
In structure-based drug discovery, most methods rely on two key elements of accuracy: accurate protein structure modeling and accurate drug structure modeling. AlphaFold is able to predict
April 21, 2022
Data Science
Deep learning methods for designing proteins scaffolding functional sites
In a recent preprint from the Baker Lab, Jue Wang et. al. outlined a framework for protein design that uses protein structure prediction neural networks. This framework defines
April 14, 2022
Data Science
Design of protein binding proteins from target structure alone
How do you design a protein that binds to another protein given only the target protein structure? Until recently, you could use Rosetta to manually
April 8, 2022
Data Science
Data2Vec: A General Training Algorithm for Self-supervised Learning
What would you give to be able to train a neural network with 5% of the labels that you thought you needed? In the context
April 2, 2022