{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/low-dimensional-representation-of-multi","title":"Low dimensional representation of multi-patient flow cytometry datasets using optimal transport for minimal residual disease detection in leukemia","arxiv_id":"2407.17329","date":"2024-07-24","proceeding":null,"authors":["Erell Gachon","Jérémie Bigot","Elsa Cazelles","Audrey Bidet","Jean-Philippe Vial","Pierre-Yves Dumas","Aguirre Mimoun"],"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.","url_abs":"https://arxiv.org/abs/2407.17329v3","url_pdf":"https://arxiv.org/pdf/2407.17329v3.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"low-dimensional-representation-of-multi","repo_url":"https://github.com/erellgachon/cytolot","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[{"task_slug":"dimensionality-reduction","task_name":"Dimensionality Reduction"},{"task_slug":"prognosis","task_name":"Prognosis"},{"task_slug":"quantization","task_name":"Quantization"}],"methods":[{"method_slug":"pca","method_name":"PCA"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}