Papers by Sukwon Yun
DALK: Dynamic Co-Augmentation of LLMs and KG to answer Alzheimer’s Disease Questions with Scientific Literature (2024.findings-emnlp)
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Dawei Li, Shu Yang, Zhen Tan, Jae Baik, Sukwon Yun, Joseph Lee, Aaron Chacko, Bojian Hou, Duy Duong-Tran, Ying Ding, Huan Liu, Li Shen, Tianlong Chen
| Challenge: | Recent advances in large language models have achieved promising performances across various applications, but the challenge of integrating long-tail knowledge continues to impede the seamless adoption of LLMs in specialized domains. |
| Approach: | They propose a dynamic co-augmentation framework for the refinement of large language models and knowledge graphs in the context of Alzheimer's Disease. |
| Outcome: | The proposed framework can be used to study Alzheimer's Disease (AD) using LLMs and KGs. |
GRNFormer: A Biologically-Guided Framework for Integrating Gene Regulatory Networks into RNA Foundation Models (2025.findings-acl)
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Mufan Qiu, Xinyu Hu, Fengwei Zhan, Sukwon Yun, Jie Peng, Ruichen Zhang, Bhavya Kailkhura, Jiekun Yang, Tianlong Chen
| Challenge: | Foundation models for single-cell RNA sequencing ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals. |
| Approach: | They propose a framework that integrates multi-scale gene regulatory networks into RNA foundation model training. |
| Outcome: | The proposed framework improves on state-of-the-art models on three downstream tasks . it integrates multi-scale gene regulatory networks (GRNs) from multi-omics data into training . |
Agents Under Siege: Breaking Pragmatic Multi-Agent LLM Systems with Optimized Prompt Attacks (2025.acl-long)
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| Challenge: | Multi-agent LLMs are prone to adversarial attacks because of constraints such as limited token bandwidth and latency between message delivery. |
| Approach: | They propose a permutation-invariant adversarial attack that optimizes prompt distribution across latency and bandwidth constraints to bypass distributed safety mechanisms within the system. |
| Outcome: | The proposed method outperforms conventional attacks by up to 7 on multiple models. |
Spatial Coordinates as a Cell Language: A Multi-Sentence Framework for Imaging Mass Cytometry Analysis (2025.findings-acl)
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| Challenge: | Existing single-cell LLMs struggle to integrate spatial information into natural language, limiting their ability to capture biological relationships. |
| Approach: | They propose a framework that integrates both single-cell expression and spatial information into natural language using a multi-sentence approach. |
| Outcome: | The proposed framework outperforms existing single-cell LLMs on preprocessed IMC datasets for diabetes and brain tumors while improving interpretability. |