Publications

All the publications that I have done or collaborated with. (†:Equal contribution)

Preprints

2025

  1. Preprint
    MedRep: Medical Concept Representation for General Electronic Health Record Foundation Models
    Junmo Kim, Namkyeong Lee, Jiwon Kim, and Kwangsoo Kim
    Under Review, 2025
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  2. Preprint
    MolTextQA: A Curated Question-Answering Dataset and Benchmark for Molecular Structure-Text Relationship Learning
    Siddhartha Laghuvarapu, Namkyeong Lee, Chufan Gao, and Jimeng Sun
    Work done as a Visiting Student at UIUC
    Under Review, 2025
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  3. Preprint
    RAG-Enhanced Collaborative LLM Agents for Drug Discovery
    Namkyeong Lee, Edward De Brouwer, Ehsan Hajiramezanali, Chanyoung Park, and Gabriele Scalia
    Work done during the Internship at Genentech
    Under Review, 2025
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  4. Preprint
    3D Interaction Geometric Pre-training for Molecular Relational Learning
    Namkyeong Lee, Yunhak Oh, Heewoong Noh, Gyoung S. Na, Minkai Xu, Hanchen Wang, Tianfan Fu, and Chanyoung Park
    Collaboration with KRICT
    Under Review, 2025
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  5. Preprint
    Protein-Mamba: Biological Mamba Models for Protein Function Prediction
    Bohao Xu, Yingzhou Lu, Yoshitaka Inoue, Namkyeong Lee, Tianfan Fu, and Jintai Chen
    Under Review, 2025
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  6. Preprint
    Compositional Representation of Polymorphic Crystalline Materials
    Namkyeong Lee, Heewoong Noh, Gyoung S. Na, Jimeng Sun, Tianfan Fu, Marinka Zitnik, and Chanyoung Park
    Collaboration with KRICT
    Under Review, 2025
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International Conferences

2025

  1. ICML
    Global Context-aware Representation Learning for Spatially Resolved Transcriptomics
    Yunhak Oh†, Junseok Lee†, Yeongmin Kim, Sangwoo Seo, Namkyeong Lee, and Chanyoung Park
    In International Conference on Machine Learning (ICML), 2025
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  2. ICML
    Thickness-aware E(3)-Equivariant Mesh Neural Networks
    Sungwon Kim, Namkyeong Lee, Yunyoung Doh, Seungmin Shin, Guimok Cho, Seung-Won Jeon, Sangkook Kim, and Chanyoung Park
    Collaboration with LG Electronics
    In International Conference on Machine Learning (ICML), 2025
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  3. ICLR
    Subgraph Federated Learning for Local Generalization
    Sungwon Kim, Yoonho Lee, Yunhak Oh, Namkyeong Lee, Sukwon Yun, Junseok Lee, Sein Kim, Carl Yang, and Chanyoung Park
    In International Conference on Learning Representations (ICLR), 2025
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2024

  1. NeurIPS
    Implicit Precursor Extraction with Expert Retriever for Inorganic Retrosynthesis
    Heewoong Noh, Namkyeong Lee, Gyoung S. Na, and Chanyoung Park
    Collaboration with KRICT
    In Conference on Neural Information Processing Systems (NeurIPS), 2024
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  2. CIKM
    Vision Language Model is NOT All You Need: Augmentation Strategies for Molecule Language Model
    Namkyeong Lee, Siddhartha Laghuvarapu, Chanyoung Park, and Jimeng Sun
    Work done as a Visiting Student at UIUC
    In ACM International Conference on Information and Knowledge Management (CIKM), 2024
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  3. CIKM
    Debiased Graph Poisoning Attack via Contrastive Surrogate Objective
    Kanghoon Yoon, Yeonjun In, Namkyeong Lee, Kibum Kim, and Chanyoung Park
    In ACM International Conference on Information and Knowledge Management (CIKM), 2024
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2023

  1. NeurIPS
    Density of States Prediction of Crystalline Materials via Prompt-guided Multi-Modal Transformer
    Namkyeong Lee†, Heewoong Noh†, Sungwon Kim, Dongmin Hyun, Gyoung S. Na, and Chanyoung Park
    Collaboration with KRICT
    In Conference on Neural Information Processing Systems (NeurIPS), 2023
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  2. KDD
    Shift-Robust Molecular Relational Learning with Causal Substructure
    Namkyeong Lee, Kanghoon Yoon, Gyoung S. Na, Sein Kim, and Chanyoung Park
    Collaboration with KRICT
    In ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD), 2023
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  3. KDD
    Task Relation-aware Continual User Representation Learning
    Sein Kim, Namkyeong Lee, Donghyun Kim, Min-Chul Yang, and Chanyoung Park
    Work done during the Internship at NAVER Corp.
    In ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD), 2023
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  4. KDD
    Task-Equivariant Graph Few-shot Learning
    Sungwon Kim, Junseok Lee, Namkyeong Lee, Wonjoong Kim, Seungyoon Choi, and Chanyoung Park
    In ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD), 2023
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  5. ICML
    Conditional Graph Information Bottleneck for Molecular Relational Learning
    Namkyeong Lee, Dongmin Hyun, Gyoung S. Na, Sungwon Kim, Junseok Lee, and Chanyoung Park
    Collaboration with KRICT
    In International Conference on Machine Learning (ICML), 2023
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  6. AAAI
    Heterogeneous Graph Learning for Multi-modal Medical Data Analysis
    Sein Kim, Namkyeong Lee, Junseok Lee, Dongmin Hyun, and Chanyoung Park
    In AAAI Conference on Artificial Intelligence (AAAI), 2023
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2022

  1. CIKM
    Relational Self-Supervised Learning on Graphs
    Namkyeong Lee, Dongmin Hyun, Junseok Lee, and Chanyoung Park
    In ACM International Conference on Information and Knowledge Management (CIKM), 2022
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  2. SIGIR Short
    GraFN: Semi-Supervised Graph Node Classification with Few Labels via Non-Parametric Distribution Assignment
    Junseok Lee, Yunhak Oh, Yeonjun In, Namkyeong Lee, Dongmin Hyun, and Chanyoung Park
    In ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR), 2022
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  3. AAAI
    Augmentation-Free Self-Supervised Learning on Graphs
    Namkyeong Lee, Junseok Lee, and Chanyoung Park
    In AAAI Conference on Artificial Intelligence (AAAI), 2022
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International Journals

2023

  1. Bioinformatics
    Deep single-cell RNA-seq data clustering with graph prototypical contrastive learning
    Junseok Lee, Sungwon Kim, Dongmin Hyun, Namkyeong Lee, Yejin Kim, and Chanyoung Park
    Bioinformatics, 2023
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2022

  1. Info Sci
    Self-Supervised Graph Representation Learning via Positive Mining
    Namkyeong Lee, Junseok Lee, and Chanyoung Park
    Information Sciences, 2022
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