Low dimensional representation of multi-patient flow cytometry datasets using optimal transport for minimal residual disease detection in leukemia

• URL: http://arxiv.org/abs/2407.17329v1
• Date: Wed, 24 Jul 2024 14:53:01 GMT
• Title: Low dimensional representation of multi-patient flow cytometry datasets using optimal transport for minimal residual disease detection in leukemia
• Authors: Erell Gachon, Jérémie Bigot, Elsa Cazelles, Aguirre Mimoun, Jean-Philippe Vial,
• Abstract summary: Representing and Minimal Residual Disease (MRD) in Acute Myeloid Leukemia (AML) is essential in prognosis and follow-up of patients. In this paper, we explore statistical learning methods based on optimal transport (OT) to achieve a relevant low-dimensional representation of flow measurements. In particular, our OT-based approach allows a relevant and informative two-dimensional representation of the results of the FlowSom algorithm.
• Score: 1.3980986259786223
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Representing and quantifying Minimal Residual Disease (MRD) in Acute Myeloid Leukemia (AML), a type of cancer that affects the blood and bone marrow, is essential in the prognosis and follow-up of AML patients. As traditional cytological analysis cannot detect leukemia cells below 5\%, the analysis of flow cytometry dataset is expected to provide more reliable results. In this paper, we explore statistical learning methods based on optimal transport (OT) to achieve a relevant low-dimensional representation of multi-patient flow cytometry measurements (FCM) datasets considered as high-dimensional probability distributions. Using the framework of OT, we justify the use of the K-means algorithm for dimensionality reduction of multiple large-scale point clouds through mean measure quantization by merging all the data into a single point cloud. After this quantization step, the visualization of the intra and inter-patients FCM variability is carried out by embedding low-dimensional quantized probability measures into a linear space using either Wasserstein Principal Component Analysis (PCA) through linearized OT or log-ratio PCA of compositional data. Using a publicly available FCM dataset and a FCM dataset from Bordeaux University Hospital, we demonstrate the benefits of our approach over the popular kernel mean embedding technique for statistical learning from multiple high-dimensional probability distributions. We also highlight the usefulness of our methodology for low-dimensional projection and clustering patient measurements according to their level of MRD in AML from FCM. In particular, our OT-based approach allows a relevant and informative two-dimensional representation of the results of the FlowSom algorithm, a state-of-the-art method for the detection of MRD in AML using multi-patient FCM.

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