About me

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I’m a third-year Bioengineering PhD student in Kim Lab at the University of Pennsylvania. My interests of research are Biomedical Informatics, Artificial Intelligence, Computational Single-cell Immunology, and LLM applications in Biomedical research.

Publication

  • Cytometry Masked Autoencoder: An Accurate and Interpretable Automated Immunophenotyper
    Jaesik Kim§, Matei Ionita§, Matthew Lee, Michelle L. McKeague, Ajinkya Pattekar, Mark M. Painter, Joost Wagenaar, Van Truong, Dylan T. Norton, Divij Mathew, Yonghyun Nam, Sokratis A. Apostolidis, Cynthia Clendenin, Patryk Orzechowski, Sang-Hyuk Jung, Jakob Woerner, Caroline A.G. Ittner, Alexandra P. Turner, Mika Esperanza, Thomas G. Dunn, Nilam S. Mangalmurti, John P. Reilly, Nuala J. Meyer, Carolyn S. Calfee, Kathleen D. Liu, Michael A. Matthy, Lamorna Brown Swigart, Ellen L. Burnham, Jeffrey McKeehan, Sheetal Gandotra, Derek W. Russel, Kevin W. Gibbs, Karl W. Thomas, Harsh Barot, Allison R. Greenplate*, Dokyoon Kim*, John Wherry*
    Cell Reports Medicine 2024 [Paper]

  • Harnessing AI in Multi-Modal Omits Data Integration: Paving the Path for the Next Frontier in Precision Medicine
    Yonghyun Nam, Jaesik Kim, Sang-Hyuk Jung, Jakob Woerner, Erica H. Sue, Dong-gi Lee, Manu Shivakumar, Matthew E. Lee, Dokyoon Kim*
    Annual Review of Biomedical Data Science 2024 [Paper]

  • Improving Unsupervised Out-of-domain detection through Pseudo Labeling and Learning
    Byounghan Lee, Jaesik Kim, Junekyu Park and Kyung-Ah Sohn*
    EACL 2023 [Paper]

  • Enterotypical Prevotella and three novel bacterial biomarkers in preoperative stool predict clinical outcome of colorectal cancer
    Ji-Won Huh, Min Jung Kim, Jaesik Kim, Hyeon Gwon Lee, Seung-Bum Ryoo, Ja-Lok Ku, Seung-Yong Jeong, Kyu Joo Park, Dokyoon Kim, Ji Won Park*, Jihyun F. Kim*
    Microbiome 2022 [Paper]

  • Development and validation of a novel strong prognostic index for colon cancer through a robust combination of laboratory features for systemic inflammation: A prognostic immune nutritional index
    Sang-Hyuk Jung§, Jie Hao§, Manu Shivakumar, Yonghyun Nam, Jaesik Kim, Min Jung Kim, Seung-Bum Ryoo, Eun Kyung Cho, Seung-Yong Jeong, Kyu Joo Park, Sung Chan Park, Dae Kyung Sohn, Jae Hwan Oh, Hong-Hee Won, Dokyoon Kim*, Ji Won Park*
    British Journal of Cancer 2022 [Paper]

  • A Deep Learning Model for Screening Type 2 Diabetes from Retinal Photographs
    Jae-Seung Yun§, Jaesik Kim§, Sang-Hyuk Jung, Seon-Ah Cha, Seung-Hyun Ko, Yu-Bae Ahn, Hong-Hee Won, Kyung-Ah Sohn*, Dokyoon Kim*
    Nutrition, Metabolism, and Cardiovascular Diseases 2022 [Paper]

  • Interpretable temporal graph neural network for prognostic prediction of Alzheimer’s disease using longitudinal neuroimaging data
    Mansu Kim§, Jaesik Kim§, Jeffrey Qu, Heng Huang, Kyung-Ah Sohn, Qi Long, Dokyoon Kim, and Li Shen*
    IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM) 2021 (20% Acceptance rate) [Paper] [Code]

  • A Novel Scoring System for Response of Preoperative Chemoradiotherapy in Locally Advanced Rectal Cancer Using Early-treatment Blood Features Derived from Machine Learning
    Jaesik Kim, Kyung-Ah Sohn, Jung-Hak Kwak, Min Jung Kim, Seung-Bum Ryoo, Seung-Yong Jeong, Kyu Joo Park, Hyun-Cheol Kang, Eui Kyu Chie, Sang-Hyuk Jung, Dokyoon Kim*, Ji Won Park*
    Frontiers in Oncology 2021 [Paper]

  • HiG2Vec: Hierarchical Representations of Gene Ontology and Genes in the Poincaré Ball
    Jaesik Kim, Dokyoon Kim*, Kyung-Ah Sohn*
    Bioinformatics 2021 [Paper] [Code]

  • Robust Pathway-based Multi-Omics Data Integration using Directed Random Walk for Survival Prediction in Multiple Cancer Studies
    So Yeon Kim, Hyun-Hwan Jeong, Jaesik Kim, Jeong-Hyeon Moon and Kyung-Ah Sohn*
    Biology Direct 2019 (presented at the 17th Annual International Conference on Critical Assessment of Massive Data Analysis (CAMDA 2018, ISMB COSI track), Chicago, USA) [Paper]

Conference Oral Presentations

  • Cytometry Masked Autoencoder: An Accurate and Interpretable Automated Immunophenotyper
    Jaesik Kim§, Matei Ionita§, Matthew Lee, Michelle McKeague, Ajinkya Pattekar, Mark Painter, Joost Wagenaar, Van Truong, Dylan Norton, Divij Mathew, Yonghyun Nam, Sokratis Apostolidis, Patryk Orzechowski, Sang-Hyuk Jung, Jakob Woerner, Yidi Huang, Nuala J. Meyer, Allison R. Greenplate, Dokyoon Kim, John Wherry,
    CYTO 2024 (Oral) [SNS]

Conference Poster Presentations

  • Single-cell Masked Autoencoder: An Accurate and Interpretable Automated Immunophenotyper
    Jaesik Kim§, Matei Ionita§, Matthew Lee, Michelle McKeague, Ajinkya Pattekar, Mark Painter, Joost Wagenaar, Van Truong, Dylan Norton, Divij Mathew, Yonghyun Nam, Sokratis Apostolidis, Patryk Orzechowski, Sang-Hyuk Jung, Jakob Woerner, Yidi Huang, Nuala J. Meyer, Allison R. Greenplate, Dokyoon Kim, John Wherry,
    AI4Science@NeurIPS2023 [Link]

  • Artificial Intelligence and Individualized Optimal Glycemic Target in ICU Patients
    Garam Lee, Jaesik Kim, Sang-Hyuk Jung, Kyung-Ah Sohn, Jae-Seung Yun, Dokyoon Kim,
    DBEI & CCEB Research Day 2022 Poster Flash Talk Presenter [Link]

  • HiG2Vec: Hierarchical Representations of Gene Ontology and Genes in the Poincaré Ball
    Jaesik Kim, Dokyoon Kim*, Kyung-Ah Sohn*
    DBEI & CCEB Research Day 2022 Poster [Link]

  • TransformerPRS: a deep learning-based polygenic risk model using bidirectional transformers derived from a language model
    Jaesik Kim§, Sang-Hyuk Jung§, Mansu Kim, Kwangsik Nho, Li Shen, Kyung-Ah Sohn*, Hong-Hee Won*, Dokyoon Kim*
    ASHG 2021 Poster

  • Informative Tumor Mutational Burden (iTMB): integrated multiple scores for missense mutations to predict immunotherapy outcome for non-small cell lung cancer
    Jaesik Kim, Garam Lee, Kyung-Ah Sohn*, Dokyoon Kim*
    ASHG 2020 Poster (Cancer - Posters #2362) [Link]

Experience

  • Bioengineering PhD Student and Research Fellow, Aug. 2022 - Present
    Kim Lab at University of Pennsylvania, Philadelphia, PA, USA

  • Junior Bioinformatician, Feb. 2022 - Jul. 2022 (6m)
    Kim Lab at University of Pennsylvania, Philadelphia, PA, USA

  • BioData Engineer, Sep. 2021 - Jan. 2022 (5m)
    LAMDA lab at Ajou University, Suwon, Korea

  • Visiting Student Intern, Mar. 2020 - Mar. 2021 (1y)
    Kim Lab at University of Pennsylvania, Philadelphia, PA, USA

  • Visiting Student Intern, Jul. 2019 - Aug. 2019 (3m)
    Kim Lab at University of Pennsylvania, Philadelphia, PA, USA

  • Computer Engineering MS Student, Feb. 2018 - Aug. 2021 (3y 6m)
    LAMDA lab at Ajou University, Suwon, Korea

Teaching

  • Teaching Assistant
    Programming practice of Data Structure (Fall 2018)

Awards

  • 2023 Asan Foundation Medical Bioscience Scholarship, Feb. 2023 - Present

  • Best Paper Award (Graduate School Dean’s Award), Ajou University, Feb. 2022

Education

  • M.S., Computer Engineering at Ajou University, 2018 - 2021
    • Thesis: Representation Learning of Biomedical Ontologies using Poincaré Embedding and Application to Genetic Risk Model
    • Advised by Professor Kyung-Ah Sohn
  • B.S., Systems Biology at Yonsei University, 2011 - 2018

Contact me

jaesik.kim@pennmedicine.upenn.edu
jaesik@seas.upenn.edu
happicukki@gmail.com