Deep generative selection models of T and B cell receptor repertoires with soNNia

Subclasses of immune B and T-cells have different functional roles to work together to produce an immune response and lasting immunity.
Additionally to these functional roles, T and B-cell lymphocytes rely on the diversity of their receptor chains to recognize different pathogens.
The lymphocyte subclasses emerge from common ancestors generated with the same diversity of receptors during selection processes.
I will show how to leverage biophysical models of receptor generation with machine learning models of selection to identify specific sequence features characteristic of functional lymphocyte repertoires and subrepertoires.
Specifically using only repertoire level sequence information, we classify CD4 and CD8 T-cells, find correlations between receptor chains arising during selection and identify T-cells subsets that are targets of pathogenic epitopes.
I also show examples of when linear classifiers do as well as deep methods.