Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states

Single-cell RNA-seq (scRNA-seq) has become a prominent tool for studying human biology and disease. The availability of massive scRNA-seq datasets and advanced machine learning techniques has recently driven the development of single-cell foundation models that provide informative and versatile cell representations based on expression profiles. However, to understand disease states, we need to consider entire tissue ecosystems, simultaneously considering many different interacting cells. Here, we tackle this challenge by generating patient-level representations derived from multi-cellular expression context measured with scRNA-seq of tissues. We develop PaSCient, a novel model that employs a multi-level representation learning paradigm and provides importance scores at the individual cell and gene levels for fine-grained analysis across multiple cell types and gene programs characteristic of a given disease. We apply PaSCient to learn a disease model across a large-scale scRNA-seq atlas of 24.3 million cells from over 5,000 patients. Comprehensive and rigorous benchmarking demonstrates the superiority of PaSCient in disease classification and its multiple downstream applications, including dimensionality reduction, gene/cell type prioritization, and patient subgroup discovery.