ArticleCell reports. Medicine2024
Cytometry masked autoencoder: An accurate and interpretable automated immunophenotyper.
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Article in Cell reports. Medicine, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2citing papers in PubMed
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Who cites it
2 citing papers in PubMed.
- Deep learning representations of human Immune Health for precision immunology.bioRxiv : the preprint server for biology · 2026Article
- AUTOENCODIX: a generalized and versatile framework to train and evaluate autoencoders for biological representation learning and beyond.Nature computational science · 2026Article
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Authors and funding
37 authors.
Jaesik KimDepartment of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Matei IonitaInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Matthew LeeInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Michelle L McKeagueInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Ajinkya PattekarInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Mark M PainterInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Joost WagenaarInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Van TruongInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Dylan T NortonInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Divij MathewInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Yonghyun NamInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Sokratis A ApostolidisInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Rheumatology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Cynthia ClendeninInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Patryk OrzechowskiInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Automatics and Robotics, AGH University of Science and Technology, al. Mickiewicza 30, 30-059 Kraków, Poland.
Sang-Hyuk JungInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Jakob WoernerInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Caroline A G IttnerDivision of Pulmonary and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Alexandra P TurnerDivision of Pulmonary and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Mika EsperanzaDivision of Pulmonary and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Thomas G DunnDivision of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Nilam S MangalmurtiInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
John P ReillyInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Nuala J MeyerDivision of Pulmonary and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Carolyn S CalfeeDepartment of Anesthesia and Perioperative Care, University of California, San Francisco, School of Medicine, San Francisco, CA 94143, USA; Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, School of Medicine, San Francisco, CA 94143, USA; Cardiovascular Research Institute, Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, CA 94158, USA.
Kathleen D LiuDivision of Nephrology and Critical Care Medicine, University of California, San Francisco, School of Medicine, San Francisco, CA 94143, USA.
Michael A MatthyCardiovascular Research Institute, Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, CA 94158, USA.
Lamorna Brown SwigartDepartment of Laboratory Medicine, University of California, San Francisco, School of Medicine, San Francisco, CA 94143, USA.
Ellen L BurnhamDivision of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA.
Jeffrey McKeehanDivision of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA.
Sheetal GandotraDivision of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
Derek W RusselDivision of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Pulmonary Section, Birmingham Veteran's Affairs Medical Center, Birmingham, AL 35233, USA.
Kevin W GibbsSection on Pulmonary and Critical Care, Allergy, and Immunology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
Karl W ThomasSection on Pulmonary and Critical Care, Allergy, and Immunology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
Harsh BarotSection on Hospital Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
Allison R GreenplateInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: allie.greenplate@pennmedicine.upenn.edu.
E John WherryInstitute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: wherry@pennmedicine.upenn.edu.
Dokyoon KimDepartment of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology & Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: dokyoon.kim@pennmedicine.upenn.edu.
Funding
Virology CoreU19AI082630 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI RAYMOND T CHUNG · 2009 to 2026
$48.1MInvestigating Individual Susceptibility and Host Response in Acute Respiratory Distress SyndromeR35HL161196 · NHLBI · UNIVERSITY OF PENNSYLVANIA · PI Nuala Jennings Meyer · 2022 to 2026
$4.8MNHLBI NIH HHS R35 HL161196NIAID NIH HHS U19 AI082630
Abstract
Single-cell cytometry data are crucial for understanding the role of the immune system in diseases and responses to treatment. However, traditional methods for annotating cytometry data face challenges in scalability, robustness, and accuracy. We propose a cytometry masked autoencoder (cyMAE), which automates immunophenotyping tasks including cell type annotation. The model upholds user-defined cell type definitions, facilitating interpretability and cross-study comparisons. The training of cyMAE has a self-supervised phase, which leverages large amounts of unlabeled data, followed by fine-tuning on specialized tasks using smaller amounts of annotated data. The cost of training a new model is amortized over repeated inferences on new datasets using the same panel. Through validation across multiple studies using the same panel, we demonstrate that cyMAE delivers accurate and interpretable cellular immunophenotyping and improves the prediction of subject-level metadata. This proof of concept marks a significant step forward for large-scale immunology studies.
Indexed as
Flow CytometryImmunophenotypingAlgorithmsHumansSingle-Cell Analysisautomated gatingdeep learninghigh-dimensional cytometryimmunophenotypingmachine learningmass cytometryrepresentation learning
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