Using Interpretable Machine Learning to Massively Increase the Number of Antibody-Virus Interactions Across Studies

TL;DR

This paper introduces an interpretable machine learning framework that predicts antibody-virus interactions across diverse studies, greatly expanding datasets and enabling better understanding of influenza immunity and pandemic preparedness.

Contribution

The authors develop a novel computational method that predicts antibody inhibition for any virus variant across studies, even with minimal data overlap, enhancing data integration and analysis.

Findings

Validated on 200,000 measurements, predicting 2 million new values.

Quantified transferability between multiple influenza studies.

Identified correlations between serum potency and breadth.

Abstract

A central challenge in every field of biology is to use existing measurements to predict the outcomes of future experiments. In this work, we consider the wealth of antibody inhibition data against variants of the influenza virus. Due to this viru's genetic diversity and evolvability, the variants examined in one study will often have little-to-no overlap with other studies, making it difficult to discern common patterns or unify datasets for further analysis. To that end, we develop a computational framework that predicts how an antibody or serum would inhibit any variant from any other study. We use this framework to greatly expand seven influenza datasets utilizing hemagglutination inhibition, validating our method upon 200,000 existing measurements and predicting 2,000,000 new values along with their uncertainties. With these new values, we quantify the transferability between seven vaccination and infection studies in humans and ferrets, show that the serum potency is negatively correlated with breadth, and present a tool for pandemic preparedness. This data-driven approach does not require any information beyond each virus's name and measurements, and even datasets with as few as 5 viruses can be expanded, making this approach widely applicable. Future influenza studies using hemagglutination inhibition can directly utilize our curated datasets to predict newly measured antibody responses against ~80 H3N2 influenza viruses from 1968-2011, whereas immunological studies utilizing other viruses or a different assay only need a single partially-overlapping dataset to extend their work. In essence, this approach enables a shift in perspective when analyzing data from "what you see is what you get" into "what anyone sees is what everyone gets."