In Cytometry. Part A : the journal of the International Society for Analytical Cytology
Technologies for single-cell profiling of the immune system have enabled researchers to extract rich interconnected networks of cellular abundance, phenotypical and functional cellular parameters. These studies can power machine learning approaches to understand the role of the immune system in various diseases. However, the performance of these approaches and the generalizability of the findings have been hindered by limited cohort sizes in translational studies, partially due to logistical demands and costs associated with longitudinal data collection in sufficiently large patient cohorts. An evolving challenge is the requirement for ever-increasing cohort sizes as the dimensionality of datasets grows. We propose a deep learning model derived from a novel pipeline of optimal temporal cell matching and overcomplete autoencoders that uses data from a small subset of patients to learn to forecast an entire patient's immune response in a high dimensional space from one timepoint to another. In our analysis of 1.08 million cells from patients pre- and post-surgical intervention, we demonstrate that the generated patient-specific data are qualitatively and quantitatively similar to real patient data by demonstrating fidelity, diversity, and usefulness. This article is protected by copyright. All rights reserved.
Fallahzadeh Ramin, Bidoki Neda H, Stelzer Ina A, Becker Martin, Marić Ivana, Chang Alan L, Culos Anthony, Phongpreecha Thanaphong, Xenochristou Maria, De Francesco Davide, Espinosa Camilo, Berson Eloise, Verdonk Franck, Angst Martin S, Gaudilliere Brice, Aghaeepour Nima
2022-Dec-12
Autoencoders, Deep Learning, Generative Modeling, Mass Cytometry, Single-Cell Immunome, Surgery
