Uncovering Effective Explanations for Interactive Genomic Data Analysis

Summary Better tools are needed to enable researchers to quickly identify and explore effective and interpretable feature-based explanations for discriminating multi-class genomic datasets, e.g., healthy versus diseased samples. We develop an interactive exploration tool, GENVISAGE, which rapidly discovers the most discriminative feature pairs that separate two classes of genomic objects and then displays the corresponding visualizations. Since quickly finding top feature pairs is computationally challenging, especially for large numbers of objects and features, we propose a suite of optimizations to make GENVISAGE responsive at scale and demonstrate that our optimizations lead to a 400× speedup over competitive baselines for multiple biological datasets. We apply our rapid and interpretable tool to identify literature-supported pairs of genes whose transcriptomic responses significantly discriminate several chemotherapy drug treatments. With its generalizable optimizations and framework, GENVISAGE opens up real-time feature-based explanation generation to data from massive sequencing efforts, as well as many other scientific domains.