Jaesik Kim

PhD student, University of Pennsylvania

Joined

September 2023

Names

Jaesik Kim (Preferred)

Emails

****@gmail.com (Confirmed)

****@pennmedicine.upenn.edu (Confirmed)

Personal Links

Career & Education History

PhD student

University of Pennsylvania (pennmedicine.upenn.edu)

2022 – Present

MS student

Ajou University (ajou.ac.kr)

2018 – 2021

Advisors, Relations & Conflicts

No relations added

Expertise

virtual cell

Present

single cell foundation

Present

AI Agent for biology

Present

Publications

Interpreting Genomic Language Models using Sparse Autoencoders
Akira A Nair, Jaehyun Joo, Jonghyun Lee, Lina Takemaru, Yidi Huang, Manu Shivakumar, Matthew Eric Lee, Jaesik Kim, Sokratis Apostolidis, Dokyoon Kim
- Mech Interp Workshop ICML 2026 viafasttrackPoster
- Readers: Everyone
Interpreting Genomic Language Models using Sparse Autoencoders
Akira A Nair, Jaehyun Joo, Jonghyun Lee, Lina Takemaru, Yidi Huang, Manu Shivakumar, Matthew Eric Lee, Jaesik Kim, Sokratis Apostolidis, Dokyoon Kim
- ICML 2026 regular
- Readers: Everyone
Evaluation of Multi-Agent LLMs in Multidisciplinary Team Decision-Making for Challenging Cancer Cases
Jaesik Kim, Byounghan Lee, Kyung-Ah Sohn, Dokyoon Kim, Young Chan Lee
- MLHC 2025
- Readers: Everyone
GeOKG: geometry-aware knowledge graph embedding for Gene Ontology and genes
Chang-Uk Jeong, Jaesik Kim, Dokyoon Kim, Kyung-Ah Sohn
- Bioinform. 2025
- Readers: Everyone
MAESTRO: Masked Encoding Set Transformer with Self-Distillation
Matthew Eric Lee, Jaesik Kim, Matei Ionita, Jonghyun Lee, Michelle L. McKeague, Yonghyun Nam, Irene Khavin, Yidi Huang, Victoria Fang, Sokratis Apostolidis, Divij Mathew, Shwetank, Ajinkya Pattekar, Zahabia Rangwala, Amit Bar-Or, Benjamin A. Fensterheim, Benjamin A. Abramoff, Rennie L. Rhee, Damian Maseda, Allison R. Greenplate et al. (1 additional authors not shown)
- ICLR 2025
- Readers: Everyone
Clinically aligned multi-modal image-text model for pan-cancer prognosis prediction
Jonghyun Lee, Jacob S. Leiby, Lina Takemaru, Yidi Huang, Myung-Giun Noh, Jaesik Kim, Byonghan Lee, Mattew E. Lee, Derek A. Oldridge, Young-Gyu Eun, Hyun Jee Lee, Young Chan Lee, Dokyoon Kim
- BioData Min. 2025
- Readers: Everyone
MAESTRO: Masked Encoding Set Transformer with Self-Distillation
Matthew Eric Lee, Jaesik Kim, Matei Ionita, Jonghyun Lee, Michelle L. McKeague, YONGHYUN NAM, Irene Khavin, Yidi Huang, Victoria Fang, Sokratis Apostolidis, Divij Mathew, Shwetank, Ajinkya Pattekar, Zahabia Rangwala, Amit Bar-Or, Benjamin A Fensterheim, Benjamin A. Abramoff, Rennie L. Rhee, Damian Maseda, Allison R Greenplate et al. (2 additional authors not shown)
- ICLR 2025 Poster
- Readers: Everyone
Single-cell Masked Autoencoder: An Accurate and Interpretable Automated Immunophenotyper
Jaesik Kim, Matei Ionita, Matthew Eric Lee, Michelle McKeague, Ajinkya Pattekar, Mark Painter, Joost Wagenaar, Van Quynh-Thi 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
- NeurIPS2023-AI4Science Poster
- Readers: Everyone
Improving Unsupervised Out-of-domain detection through Pseudo Labeling and Learning
Byounghan Lee, Jaesik Kim, Junekyu Park, Kyung-ah Sohn
- EACL (Findings) 2023
- Readers: Everyone
Interpretable temporal graph neural network for prognostic prediction of Alzheimer's disease using longitudinal neuroimaging data
Mansu Kim, Jaesik Kim, Jeffrey Qu, Heng Huang, Qi Long, Kyung-Ah Sohn, Dokyoon Kim, Li Shen
- 2021 (modified: 24 Apr 2023)
- BIBM 2021
- Readers: Everyone

View all 11 publications

Co-Authors

View all 55 co-authors