HemaGraph: Breaking Barriers in Hematologic Single Cell Classification with Graph Attention

Abstract

In the realm of hematologic cell populations classification, the intricate patterns within flow cytometry data necessitate advanced analytical tools. This paper presents 'HemaGraph', a novel framework based on Graph Attention Networks (GATs) for single-cell multi-class classification of hematological cells from flow cytometry data. Harnessing the power of GATs, our method captures subtle cell relationships, offering highly accurate patient profiling. Based on evaluation of data from 30 patients, HemaGraph demonstrates classification performance across five different cell classes, outperforming traditional methodologies and state-of-the-art methods. Moreover, the uniqueness of this framework lies in the training and testing phase of HemaGraph, where it has been applied for extremely large graphs, containing up to hundreds of thousands of nodes and two million edges, to detect low frequency cell populations (e.g. 0.01% for one population), with accuracies reaching 98%. Our findings underscore the potential of HemaGraph in improving hematoligic multi-class classification, paving the way for patient-personalized interventions. To the best of our knowledge, this is the first effort to use GATs, and Graph Neural Networks (GNNs) in general, to classify cell populations from single-cell flow cytometry data. We envision applying this method to single-cell data from larger cohort of patients and on other hematologic diseases.