Automated Identification of Cell Populations in Flow Cytometry Data with Transformers [article]

Matthias Wödlinger, Michael Reiter, Lisa Weijler, Margarita Maurer-Granofszky, Angela Schumich, Michael Dworzak
2021 arXiv   pre-print
Acute Lymphoblastic Leukemia (ALL) is the most frequent hematologic malignancy in children and adolescents. A strong prognostic factor in ALL is given by the Minimal Residual Disease (MRD), which is a measure for the number of leukemic cells persistent in a patient. Manual MRD assessment from Multiparameter Flow Cytometry (FCM) data after treatment is time-consuming and subjective. In this work, we present an automated method to compute the MRD value directly from FCM data. We present a novel
more » ... ural network approach based on the transformer architecture that learns to directly identify blast cells in a sample. We train our method in a supervised manner and evaluate it on publicly available ALL FCM data from three different clinical centers. Our method reaches a median f1 score of ~0.93 when tested on 200 B-ALL samples.
arXiv:2108.10072v1 fatcat:bhb2x6ybv5h7dfxi4txg4zlaoy