Papers by Hongyi Yu
SHAPE: Unifying Safety, Helpfulness and Pedagogy for Educational LLMs (2026.acl-long)
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| Challenge: | Existing educational LLMs are vulnerable to pedagogical jailbreaks where students use answer-inducing prompts to elicit solutions rather than scaffolded instructions. |
| Approach: | They propose a graph-augmented tutoring pipeline that infers prerequisite concepts from queries and identifies mastery gaps. |
| Outcome: | The proposed method improves safety under two pedagogical jailbreak scenarios while maintaining near-ceiling helpfulness under the same evaluation protocol. |
Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning (2022.naacl-main)
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| Challenge: | Generative methods for biomedical entity linking (EL) use synonyms knowledge from knowledge bases (KB) this is not trivial to inject into a generative method, but it is cost-effective. |
| Approach: | They propose to inject synonyms knowledge into a generative model of biomedical EL by constructing synthetic samples with synonyms and definitions from KB and requiring the model to recover concept names. |
| Outcome: | The proposed method achieves state-of-the-art results on several biomedical EL tasks without candidate selection. |
AgentThink: A Unified Framework for Tool-Augmented Chain-of-Thought Reasoning in Vision-Language Models for Autonomous Driving (2025.findings-emnlp)
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Kangan Qian, Sicong Jiang, Yang Zhong, Ziang Luo, Zilin Huang, Tianze Zhu, Kun Jiang, Mengmeng Yang, Zheng Fu, Jinyu Miao, Yining Shi, He Zhe Lim, Li Liu, Tianbao Zhou, Hongyi Wang, Huang Yu, Yifei Hu, Guang Li, Guang Chen, Hao Ye, Lijun Sun, Diange Yang
| Challenge: | Vision-Language Models struggle with hallucinations, inefficient reasoning, and limited real-world validation hinders accurate perception and robust step-by-step reasoning. |
| Approach: | AgentThink integrates Chain-of-Thought reasoning with dynamic, agent-style tool invocation for autonomous driving tasks. |
| Outcome: | Experiments on the DriveLMM-o1 benchmark show AgentThink significantly boosts overall reasoning scores by 53.91% and enhances answer accuracy by 33.54% . |
Identifying Cellular Niches in Spatial Transcriptomics: An Investigation into the Capabilities of Large Language Models (2025.acl-long)
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Huanhuan Wei, Xiao Luo, Hongyi Yu, Jinping Liang, Luning Yang, Lixing Lin, Alexandra Popa, Xiting Yan
| Challenge: | Spatial transcriptomic technologies allow measuring gene expression profile and spatial information of cells in tissues simultaneously. |
| Approach: | They propose a spatial transcriptomic approach to identify spatial niches using a zero-shot large language models by transforming spatial transcriptomics data into spatial context prompts. |
| Outcome: | The proposed model improves performance by leveraging gene expression of neighboring cells/spots, cell type composition, tissue information, and external knowledge. |
Efficient Federated Learning on Knowledge Graphs via Privacy-preserving Relation Embedding Aggregation (2022.findings-emnlp)
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| Challenge: | Existing frameworks that share entity embeddings of knowledge graphs (KGs) would incur a severe privacy leakage. |
| Approach: | They propose a new attack method that aims to recover the original embedding information based on the known entity embeddables of FedE. |
| Outcome: | The proposed framework can be used to infer whether a specific relation exists in a private client. |
TOREE: Evaluating Topic Relevance of Student Essays for Chinese Primary and Middle School Education (2024.findings-acl)
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Xinlin Zhuang, Hongyi Wu, Xinshu Shen, Peimin Yu, Gaowei Yi, Xinhao Chen, Tu Hu, Yang Chen, Yupei Ren, Yadong Zhang, Youqi Song, Binxuan Liu, Man Lan
| Challenge: | Existing research on Automatic Essay Scoring (AES) for Chinese essays has overlooked topic relevance and lacks detailed feedback. |
| Approach: | They propose to use TOREE to assess topic relevance in Chinese primary and middle school students’ essays to improve automatic and human evaluations. |
| Outcome: | The proposed method significantly improves both automatic and human evaluations across four diverse LLMs. |