A Chunking-for-Pooling Strategy for Cytometric Representation Learning for Automatic Hematologic Malignancy Classification

Jeng Lin Li, Yun Chun Lin, Yu Fen Wang, Sara A. Monaghan, Bor Sheng Ko, Chi Chun Lee

Research output: Contribution to journalArticlepeer-review


Differentiating types of hematologic malignancies is vital to determine therapeutic strategies for the newly diagnosed patients. Flow cytometry (FC) can be used as diagnostic indicator by measuring the multi-parameter fluorescent markers on thousands of antibody-bound cells, but the manual interpretation of large scale flow cytometry data has long been a time-consuming and complicated task for hematologists and laboratory professionals. Past studies have led to the development of representation learning algorithms to perform sample-level automatic classification. In this work, we propose a chunking-for-pooling strategy to include large-scale FC data into a supervised deep representation learning procedure for automatic hematologic malignancy classification. The use of discriminatively-trained representation learning strategy and the fixed-size chunking and pooling design are key components of this framework. It improves the discriminative power of the FC sample-level embedding and simultaneously addresses the robustness issue due to an inevitable use of down-sampling in conventional distribution based approaches for deriving FC representation. We evaluated our framework on two datasets. Our framework outperformed other baseline methods and achieved 92.3% unweighted average recall (UAR) for four-class recognition on the UPMC dataset and 85.0% UAR for five-class recognition on the hema.to dataset. We further compared the robustness of our proposed framework with that of the traditional downsampling approach. Analysis of the effects of the chunk size and the error cases revealed further insights about different hematologic malignancy characteristics in the FC data.

Original languageEnglish (US)
Pages (from-to)1
Number of pages1
JournalIEEE Journal of Biomedical and Health Informatics
StateAccepted/In press - 2022
Externally publishedYes


  • Cells (biology)
  • Data models
  • ensemble
  • flow cytometry
  • hematologic malignancy
  • Manuals
  • pooling
  • Representation learning
  • representation learning
  • Robustness
  • Sociology
  • Statistics

ASJC Scopus subject areas

  • Biotechnology
  • Computer Science Applications
  • Electrical and Electronic Engineering
  • Health Information Management


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