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John Ingraham

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3 papers

2 author rows

NeurIPS Conference 2019 Conference Paper

Generative Models for Graph-Based Protein Design

John Ingraham
Vikas Garg
Regina Barzilay
Tommi Jaakkola

Engineered proteins offer the potential to solve many problems in biomedicine, energy, and materials science, but creating designs that succeed is difficult in practice. A significant aspect of this challenge is the complex coupling between protein sequence and 3D structure, with the task of finding a viable design often referred to as the inverse protein folding problem. We develop relational language models for protein sequences that directly condition on a graph specification of the target structure. Our approach efficiently captures the complex dependencies in proteins by focusing on those that are long-range in sequence but local in 3D space. Our framework significantly improves in both speed and robustness over conventional and deep-learning-based methods for structure-based protein sequence design, and takes a step toward rapid and targeted biomolecular design with the aid of deep generative models.

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ICLR Conference 2019 Conference Paper

Learning Protein Structure with a Differentiable Simulator

John Ingraham
Adam J. Riesselman
Chris Sander
Debora S. Marks

The Boltzmann distribution is a natural model for many systems, from brains to materials and biomolecules, but is often of limited utility for fitting data because Monte Carlo algorithms are unable to simulate it in available time. This gap between the expressive capabilities and sampling practicalities of energy-based models is exemplified by the protein folding problem, since energy landscapes underlie contemporary knowledge of protein biophysics but computer simulations are challenged to fold all but the smallest proteins from first principles. In this work we aim to bridge the gap between the expressive capacity of energy functions and the practical capabilities of their simulators by using an unrolled Monte Carlo simulation as a model for data. We compose a neural energy function with a novel and efficient simulator based on Langevin dynamics to build an end-to-end-differentiable model of atomic protein structure given amino acid sequence information. We introduce techniques for stabilizing backpropagation under long roll-outs and demonstrate the model's capacity to make multimodal predictions and to, in some cases, generalize to unobserved protein fold types when trained on a large corpus of protein structures.

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ICML Conference 2017 Conference Paper

Variational Inference for Sparse and Undirected Models

John Ingraham
Debora S. Marks

Undirected graphical models are applied in genomics, protein structure prediction, and neuroscience to identify sparse interactions that underlie discrete data. Although Bayesian methods for inference would be favorable in these contexts, they are rarely used because they require doubly intractable Monte Carlo sampling. Here, we develop a framework for scalable Bayesian inference of discrete undirected models based on two new methods. The first is Persistent VI, an algorithm for variational inference of discrete undirected models that avoids doubly intractable MCMC and approximations of the partition function. The second is Fadeout, a reparameterization approach for variational inference under sparsity-inducing priors that captures a posteriori correlations between parameters and hyperparameters with noncentered parameterizations. We find that, together, these methods for variational inference substantially improve learning of sparse undirected graphical models in simulated and real problems from physics and biology.

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