We discuss how gene-gene interaction graphs (same pathway, protein-protein, co-expression, or research paper text association) can be used to impose a bias on a deep neural network model similar to the spatial bias imposed by convolutions on an image. We find this approach provides an advantage for particular tasks in a low data regime but is very dependent on the quality of the graph used. More info: Paper Slides Code
Dutil, Francis, et al. “Towards Gene Expression Convolutions Using Gene Interaction Graphs.” International Conference on Machine Learning (ICML) Workshop on Computational Biology (WCB), 2018, http://arxiv.org/abs/1806.06975.
Oct, 24th 2018: Martin Weiss received the “Best Presentation Award” for presenting this project at the 2018 IRIC symposium