publications

2025

1. 

   Efficient and Transferable Agentic Knowledge Graph RAG via Reinforcement Learning

   Jinyeop Song, Shuo Wang, Julian Shun, and 1 more author

   arXiv preprint, 2025

   Bib

   @article{song2025kgrag,
     title = {Efficient and Transferable Agentic Knowledge Graph RAG via Reinforcement Learning},
     author = {Song, Jinyeop and Wang, Shuo and Shun, Julian and Zhu, Yada},
     journal = {arXiv preprint},
     year = {2025},
   }

2. 

   Estimating Empowerment of Language Model Agents

   Jinyeop Song, Jeff Gore, and Max Kleiman-Weiner

   arXiv preprint arXiv:2509.22504, 2025

   Bib

   @article{song2025empowerment,
     title = {Estimating Empowerment of Language Model Agents},
     author = {Song, Jinyeop and Gore, Jeff and Kleiman-Weiner, Max},
     journal = {arXiv preprint arXiv:2509.22504},
     year = {2025},
   }

3. 

   When Do LLMs Improve Bayesian Optimization? A Systematic Comparison Across Molecular and Protein Design

   M. Akke, S. Yang, J. Ruža, and 3 more authors

   In NeurIPS 2025 AI4Science Workshop, 2025

   Bib

   @inproceedings{akke2025bayesian,
     title = {When Do LLMs Improve Bayesian Optimization? A Systematic Comparison Across Molecular and Protein Design},
     author = {Akke, M. and Yang, S. and Ruža, J. and Song, Jinyeop and Pan, E. and Gómez-Bombarelli, Rafael},
     booktitle = {NeurIPS 2025 AI4Science Workshop},
     year = {2025},
   }

4. 

   When AI Co-Scientists Fail: SPOT - Benchmark for Automated Verification of Scientific Research

   G. Son, J. Hong, H. Fan, and 8 more authors

   arXiv preprint, 2025

   Bib

   @article{son2025spot,
     title = {When AI Co-Scientists Fail: SPOT - Benchmark for Automated Verification of Scientific Research},
     author = {Son, G. and Hong, J. and Fan, H. and Nam, H. and Ko, H. and Lim, S. and Song, Jinyeop and Choi, J. and Paulo, G. and Yu, Y. and Biderman, S.},
     journal = {arXiv preprint},
     year = {2025},
   }

2024

1. 

   Context to Concept: Concept Encoding in In-context Learning

   Jinyeop Song, Sumin Han, P. Argawal, and 1 more author

   2024

   ICML 2025 spotlight

   Bib

   @article{song2024context,
     title = {Context to Concept: Concept Encoding in In-context Learning},
     author = {Song, Jinyeop and Han, Sumin and Argawal, P. and Gore, Jeffrey},
     note = {ICML 2025 spotlight},
     year = {2024},
   }

2. 

   Probing the Embedding Space of Protein Foundation Models through Intrinsic Dimension Analysis

   Seungwoo Yang, Jiho Nam, Tomas Perez, and 3 more authors

   In NeurIPS 2025 AIDrugX Workshop, 2024

   Bib

   @inproceedings{yang2024embedding,
     title = {Probing the Embedding Space of Protein Foundation Models through Intrinsic Dimension Analysis},
     author = {Yang, Seungwoo and Nam, Jiho and Perez, Tomas and Song, Jinyeop and Du, Xiao and Gomez-Bombarelli, Rafael},
     booktitle = {NeurIPS 2025 AIDrugX Workshop},
     year = {2024},
   }

3. 

   MethylGPT: Foundational GPT-like Model for Human Methylation Data

   Alex Ying, Jinyeop Song, Haoran Cui, and 1 more author

   2024

   Under review in Nature Methods

4. 

   Reconciling Kaplan and Chinchilla Scaling Laws

   Tim Pearce, and Jinyeop Song

   TMLR, 2024

5. 

   A resource model for neural scaling law

   Jinyeop Song, Ziming Liu, Max Tegmark, and 1 more author

   ICLR BGPT workshop, 2024

2023

1. 

   Additivity and asymmetricity in microbial community coalescence

   Jinyeop Song, Jiliang Hu, and Jeff Gore

   In APS March Meeting, 2023

2. 

   Noncovalent antibody catenation on a target surface greatly increases the antigen-binding avidity

   Jinyeop Song, Bo-Seong Jeong, Seong-Woo Kim, and 7 more authors

   Elife, 2023

2022

1. 

   Rapid and label-free identification of individual bacterial pathogens exploiting three-dimensional quantitative phase imaging and deep learning

   Geon Kim, Daewoong Ahn, Minhee Kang, and 7 more authors

   Light: Science & Applications, 2022

2020

1. 

   Deep-learning based three-dimensional label-free tracking and analysis of immunological synapses of CAR-T cells

   Moosung Lee, Young-Ho Lee, Jinyeop Song, and 5 more authors

   Elife, 2020