Papers by Yuan Dong
Biology-Instructions: A Dataset and Benchmark for Multi-Omics Sequence Understanding Capability of Large Language Models (2025.findings-emnlp)
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Haonan He, Yuchen Ren, Yining Tang, Ziyang Xu, Junxian Li, Minghao Yang, Di Zhang, Yuan Dong, Tao Chen, Shufei Zhang, Yuqiang Li, Nanqing Dong, Wanli Ouyang, Dongzhan Zhou, Peng Ye
| Challenge: | Biology-Instructions is the first large-scale instruction-tuning dataset for multi-omics biological sequences. |
| Approach: | They propose a large-scale instruction-tuning dataset for multi-omics biological sequences . they propose 'chatMultiOmics' to overcome limitations of current LLMs on multi-ome tasks . |
| Outcome: | The proposed dataset bridges LLMs and complex biological sequence-related tasks while maintaining conversational fluency. |
Topology Matters: Measuring Memory Leakage in Multi-Agent LLMs (2026.findings-acl)
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| Challenge: | Multi-agent LLMs are rapidly moving from prototype to real-world use . network topology is a first-order security parameter in multi-aggent systems . |
| Approach: | They propose a framework for comparing topology-conditioned memory leakage in multi-agent LLM systems. |
| Outcome: | The proposed framework evaluates topology-conditioned memory leakage in multi-agent LLM systems. |
MinerU2.5: A Decoupled Vision-Language Model for Efficient High-Resolution Document Parsing (2026.acl-industry)
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Junbo Niu, Zheng Liu, Zhuangcheng Gu, Bin Wang, Linke Ouyang, Zhiyuan Zhao, Tao Chu, Tianyao He, Fan Wu, Qintong Zhang, Zhenjiang Jin, Guang Liang, Rui Zhang, Wenzheng Zhang, Yuan Qu, Zhifei Ren, Yuefeng Sun, Zirui Tang, Boyu Niu, Yuanhong Zheng, Dongsheng Ma, Ziyang Miao, Hejun Dong, Siyi Qian, Junyuan Zhang, Fangdong Wang, Jingzhou Chen, Xiaomeng Zhao, Liqun Wei, Wei Li, Shasha Wang, RuiLiang Xu, Yuanyuan Cao, Lu Chen, Qianqian Wu, Huaiyu Gu, Lindong Lu, Dechen Lin, null Shenguanlin, Xuanhe Zhou, Linfeng Zhang, Yuhang Zang, Xiaoyi Dong, Jiaqi Wang, Bo Zhang, Lei Bai, Pei Chu, Weijia Li, Jiang Wu, Lijun Wu, Zhenxiang Li, Guangyu Wang, Zhongying Tu, Chao Xu, Kai Chen, Bowen Zhou, Dahua Lin, Wentao Zhang, Conghui He
| Challenge: | Document images are characterized by higher resolutions, denser content, and more complex structural layouts. |
| Approach: | They propose a 1.2B-parameter document parsing vision-language model that decouples layout analysis from local content recognition. |
| Outcome: | The proposed model surpasses general-purpose and domain-specific models on multiple benchmarks while maintaining significantly lower computational overhead. |
AnyGPT: Unified Multimodal LLM with Discrete Sequence Modeling (2024.acl-long)
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Jun Zhan, Junqi Dai, Jiasheng Ye, Yunhua Zhou, Dong Zhang, Zhigeng Liu, Xin Zhang, Ruibin Yuan, Ge Zhang, Linyang Li, Hang Yan, Jie Fu, Tao Gui, Tianxiang Sun, Yu-Gang Jiang, Xipeng Qiu
| Challenge: | Existing language models that use discrete representations for unified processing of various modalities are limited to text generation and do not include multimodal output. |
| Approach: | They propose a multimodal language model that utilizes discrete representations for unified processing of various modalities. |
| Outcome: | The proposed model can be trained stably without any alterations to existing models or training paradigms. |
A Continued Pretrained LLM Approach for Automatic Medical Note Generation (2024.naacl-short)
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Dong Yuan, Eti Rastogi, Gautam Naik, Sree Prasanna Rajagopal, Sagar Goyal, Fen Zhao, Bharath Chintagunta, Jeffrey Ward
| Challenge: | HEAL is the first continuously trained LLaMA2-based LLM for medical conversations . despite the success of LLMs in general capabilities, they often fall short in niche domains like healthcare . |
| Approach: | They propose a 13B LLaMA2-based LLM that is purpose-built for medical conversations and measured on automated scribing. |
| Outcome: | The HEAL LLM outperforms GPT-4 and PMC-LLaMA in PubMedQA with 78.4% accuracy and parity with GPT-LLAMA in generating medical notes. |
Meta-Information Guided Meta-Learning for Few-Shot Relation Classification (2020.coling-main)
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| Challenge: | Existing meta-learning models rely on implicit instance statistics and are unreliability and weak interpretability. |
| Approach: | They propose a meta-information guided meta-learning framework that uses semantics to guide meta- learning . experimental results demonstrate the effectiveness of the proposed framework . |
| Outcome: | The proposed framework can establish connections between instance-based information and semantic-based data, enabling faster initialization and adaptation. |
Mitigating the Alignment Tax of RLHF (2024.emnlp-main)
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Yong Lin, Hangyu Lin, Wei Xiong, Shizhe Diao, Jianmeng Liu, Jipeng Zhang, Rui Pan, Haoxiang Wang, Wenbin Hu, Hanning Zhang, Hanze Dong, Renjie Pi, Han Zhao, Nan Jiang, Heng Ji, Yuan Yao, Tong Zhang
| Challenge: | Large Language Models (LLMs) acquire a wide range of abilities during pre-training, but aligning LLMs under Reinforcement Learning with Human Feedback (RLHF) can lead to forgetting pretrained abilities, which is also known as the alignment tax. |
| Approach: | They propose to use a model averaging technique to find the most powerful alignment-forging Pareto front among RLHF algorithms. |
| Outcome: | The proposed method achieves the strongest alignment-forging Pareto front among competing methods. |
Prompt Tuning for Discriminative Pre-trained Language Models (2022.findings-acl)
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Yuan Yao, Bowen Dong, Ao Zhang, Zhengyan Zhang, Ruobing Xie, Zhiyuan Liu, Leyu Lin, Maosong Sun, Jianyong Wang
| Challenge: | Recent studies have shown promising results of prompt tuning in stimulating pre-trained language models (PLMs) for natural language processing tasks. |
| Approach: | They propose a prompt tuning framework that reformulates NLP tasks into a discriminative language modeling problem. |
| Outcome: | The proposed framework improves on text classification and question answering tasks and prevents unstable tuning problems in low-resource settings. |
ShopperBench: A Benchmark for Personalized Shopping with Persona-Guided Simulation (2026.eacl-industry)
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| Challenge: | Existing evaluation frameworks lack mechanisms to assess Personalized shopping agents' ability to adapt their strategies to heterogeneous user preferences and decisionmaking patterns. |
| Approach: | They propose a persona-guided benchmark that augments shopping trajectories with personas . they propose persona Fidelity, Persona-Query Alignment, and Path Consistency . |
| Outcome: | The proposed benchmark captures how shopper types navigate product search and selection . it measures persona Fidelity, Persona-Query Alignment, and Path Consistency . |
CLaMP 2: Multimodal Music Information Retrieval Across 101 Languages Using Large Language Models (2025.findings-naacl)
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Shangda Wu, Yashan Wang, Ruibin Yuan, Guo Zhancheng, Xu Tan, Ge Zhang, Monan Zhou, Jing Chen, Xuefeng Mu, Yuejie Gao, Yuanliang Dong, Jiafeng Liu, Xiaobing Li, Feng Yu, Maosong Sun
| Challenge: | Current music information retrieval systems struggle to meet linguistic diversity challenges . current systems struggle with text queries in non-English languages . |
| Approach: | They propose a music information retrieval system that supports both ABC notation and MIDI . CLaMP 2 includes a multilingual text encoder and a multiple-modal music encoder . |
| Outcome: | The proposed system achieves state-of-the-art results in multilingual semantic search and music classification across modalities. |
KELE: A Multi-Agent Framework for Structured Socratic Teaching with Large Language Models (2025.findings-emnlp)
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| Challenge: | Socratic teaching places high demands on teachers’ expertise and real-time feedback capabilities, making it difficult to scale in large educational settings. |
| Approach: | They propose a multi-agent framework for structured Socratic teaching with LLMs that integrates a structured SocRule and a consultant-teacher collaborative teaching mechanism. |
| Outcome: | The proposed framework outperforms existing LLMs in natural language generation and dialogue comprehension in the classroom. |
MuggleMath: Assessing the Impact of Query and Response Augmentation on Math Reasoning (2024.acl-long)
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Chengpeng Li, Zheng Yuan, Hongyi Yuan, Guanting Dong, Keming Lu, Jiancan Wu, Chuanqi Tan, Xiang Wang, Chang Zhou
| Challenge: | In math reasoning with large language models, fine-tuning data augmentation by query evolution and diverse reasoning paths is empirically verified effective. |
| Approach: | They propose to fine-tune data augmentation by query evolution and diverse reasoning paths. |
| Outcome: | The proposed model achieves new state-of-the-art on GSM8K and MATH. |
Curse of Knowledge: Your Guidance and Provided Knowledge are biasing LLM Judges in Complex Evaluation (2025.findings-emnlp)
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| Challenge: | a recent study has focused on simple settings, but their reliability in complex tasks remains understudied. |
| Approach: | They propose to use large language models as judges to evaluate reliability in complex tasks . they use a challenge benchmark to expose and quantify Auxiliary Information Induced Biases . |
| Outcome: | The proposed benchmark exposes and quantifies Auxiliary Information Induced Biases across 12 basic and 3 advanced scenarios. |
Knowledge-to-Verification: Exploring RLVR for LLMs in Knowledge-Intensive Domains (2026.acl-long)
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Zhonghang Yuan, Zhefan Wang, Fang Hu, Zihong Chen, Jinzhe Li, Gang Li, Jie Ying, Huanjun Kong, Songyang Zhang, Nanqing Dong
| Challenge: | Recent large language models (LLMs) have demonstrated remarkable progress in reasoning, but their applications on knowledge-intensive domains have not been explored due to the scarcity of high-quality verifiable data. |
| Approach: | They propose a framework that extends reinforcement learning with verifiable rewards (RLVR) to knowledge-intensive domains through automated verififiability data synthesis while enabling verification of the LLM's reasoning process. |
| Outcome: | Extensive experiments show that the proposed framework enhances the reasoning of large language models in knowledge-intensive domains without significantly compromising the model’s general capabilities. |
How Abilities in Large Language Models are Affected by Supervised Fine-tuning Data Composition (2024.acl-long)
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Guanting Dong, Hongyi Yuan, Keming Lu, Chengpeng Li, Mingfeng Xue, Dayiheng Liu, Wei Wang, Zheng Yuan, Chang Zhou, Jingren Zhou
| Challenge: | supervised fine-tuning (SFT) is a technique used to enhance multiple abilities in large language models. |
| Approach: | They propose to study the interplay of data composition between mathematical reasoning, code generation, and general human-aligning abilities during supervised fine-tuning. |
| Outcome: | The proposed model improves math reasoning and code generation with increasing data amount . the proposed model size and SFT strategies can be used to learn multiple skills with different scaling patterns. |
TableLoRA: Low-rank Adaptation on Table Structure Understanding for Large Language Models (2025.acl-long)
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| Challenge: | Tabular data are crucial in many fields and their understanding by large language models (LLMs) under high parameter efficiency paradigm is important. |
| Approach: | They propose a module that uses 2D LoRA to encode low-rank information on cell positions to improve table serialization and representation of two-dimensional structured information within a one-dimensional sequence. |
| Outcome: | Experiments on four tabular-related datasets show that TableLoRA outperforms vanilla LoRA and surpasses table encoding methods tested in control. |
Language Model Analysis for Ontology Subsumption Inference (2023.findings-acl)
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| Challenge: | Existing studies focus on simple, triple-based, relational KBs but omit more sophisticated, logic-based conceptualised KB. |
| Approach: | They propose to use ontology subsumption axioms to probe LMs' knowledge of ontologies by probing datasets from atomic and complex concepts. |
| Outcome: | The proposed methods encode less background knowledge of Subsumption Inference (SI) than traditional Natural Language Inference but can improve on SI significantly when a small number of samples are given. |
Bringing Structure into Summaries: a Faceted Summarization Dataset for Long Scientific Documents (2021.acl-short)
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| Challenge: | Faceted summarization provides briefings of a document from different perspectives. |
| Approach: | They propose a faceted summarization benchmark built on Emerald journal articles . they propose faceted models that bring structure into faceted documents . |
| Outcome: | The proposed benchmark is based on Emerald journal articles and covers a diverse range of domains. |
R-Judge: Benchmarking Safety Risk Awareness for LLM Agents (2024.findings-emnlp)
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Tongxin Yuan, Zhiwei He, Lingzhong Dong, Yiming Wang, Ruijie Zhao, Tian Xia, Lizhen Xu, Binglin Zhou, Fangqi Li, Zhuosheng Zhang, Rui Wang, Gongshen Liu
| Challenge: | Large language models (LLMs) have shown compelling abilities in reasoning, decision-making, and instruction following. |
| Approach: | They propose a benchmark to evaluate the proficiency of large language models (LLMs) in judging and identifying safety risks given agent interaction records. |
| Outcome: | The proposed model outperforms the best-performing model, GPT-4o, while no other models significantly exceed the random. |
Train in Vain: Functionality-Preserving Poisoning to Prevent Unauthorized Use of Code Datasets (2026.findings-acl)
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Yuan Xiao, Jiaming Wang, Yuchen Chen, Wei Song, Jun Sun, Shiqing Ma, Yanzhou Mu, Juan Zhai, Chunrong Fang, Jin Song Dong, Zhenyu Chen
| Challenge: | Existing methods for dataset poisoning require full-dataset poison, which breaks code compilability. |
| Approach: | They propose a functionality-preserving poisoning approach that injects short, compilable weak-use fragments into executed code paths. |
| Outcome: | The proposed method contaminates 10% of the dataset while maintaining 100% compilability and functional correctness. |
Crafting Customisable Characters with LLMs: A Persona-Driven Role-Playing Agent Framework (2025.findings-emnlp)
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Bohao Yang, Dong Liu, Chenghao Xiao, Kun Zhao, Chen Tang, Chao Li, Lin Yuan, Yang Guang, Chenghua Lin
| Challenge: | Large Language Models (LLMs) are capable of generating human-like text, but the potential for freely customisable characters remains underexplored. |
| Approach: | They propose a framework which employs Large Language Models to create freely customisable characters through personalised characteristic feature injection. |
| Outcome: | The proposed framework provides valuable insights for developing more accurate and customisable human simulacra. |
Collision to Cognition: Hash-Driven Graph Construction for Efficient RAG (2026.acl-long)
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Chuang Zhou, Zheng Yuan, Linhao Luo, Zhaozhuo Xu, Yilin Xiao, Junnan Dong, Siyu An, di Yin, Xing Sun, Xiao Huang
| Challenge: | Retrieval-augmented generation (RAG) has been used for enhancing large language models with external knowledge. |
| Approach: | They propose a framework for mining efficient graph structures via hashing to enhance RAG . they adopt an inductive paradigm where global graph structure emerges from local hash collisions . |
| Outcome: | The proposed framework outperforms existing baselines while requiring no GPU resources or token budget. |
How Far are LLMs from Being Our Digital Twins? A Benchmark for Persona-Based Behavior Chain Simulation (2025.findings-acl)
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| Challenge: | Recent studies have focused on dialogue simulation while overlooking human behavior simulation, which is crucial for digital twins. |
| Approach: | They propose to integrate persona metadata into LLMs and use it to iteratively infer contextually appropriate behaviors within dynamic scenarios. |
| Outcome: | The proposed model is based on 15,846 distinct behaviors across 1,001 unique personas and incorporates persona metadata to iteratively infer appropriate behaviors within dynamic scenarios. |
SeedBench: A Multi-task Benchmark for Evaluating Large Language Models in Seed Science (2025.acl-long)
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Jie Ying, Zihong Chen, Zhefan Wang, Wanli Jiang, Chenyang Wang, Zhonghang Yuan, Haoyang Su, Huanjun Kong, Fan Yang, Nanqing Dong
| Challenge: | Seed science is essential for modern agriculture, but its application in seed science remains limited due to a shortage of experts and limited availability of online resources. |
| Approach: | They evaluate 26 leading large language models and compare them against a set of benchmarks . they find that there is a gap between the power of LLMs and real-world seed science problems . |
| Outcome: | The new seed benchmark highlights the gap between the power of large language models and real-world seed science problems. |
FinChart-Bench: Benchmarking Financial Chart Comprehension in Vision-Language Models (2026.acl-long)
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| Challenge: | FinChart-Bench is the first benchmark specifically focused on real-world financial charts. |
| Approach: | They propose a benchmark specifically focused on real-world financial charts. |
| Outcome: | The proposed benchmark evaluates 26 state-of-the-art LVLMs on FinChart-Bench. |
Exploring Dual Encoder Architectures for Question Answering (2022.emnlp-main)
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| Challenge: | Dual encoders have been used for question-answering and information retrieval tasks with good results. |
| Approach: | They propose to use two different versions of dual encoders for QA retrieval tasks . they propose to share parameters in projection layers between two encoder towers . |
| Outcome: | The proposed architectures outperform SDE and ADE on QA retrieval tasks. |
Unleashing Low-Bit Inference on Ascend NPUs: A Comprehensive Evaluation of HiFloat Formats (2026.acl-industry)
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Pengxiang Zhao, Hui-Ling Zhen, Xing Li, Han Bao, Weizhe Lin, Zhiyuan Yang, Yu Zi Wei, Xin Wang, Mingxuan Yuan, Xianzhi Yu, Zhenhua Dong
| Challenge: | Low-bit floating-point formats like MXFP and NVFP4 offer new opportunities for precision and efficiency. |
| Approach: | They evaluate HiFloat (HiF8 and HiF4), a family of floating-point formats tailored for Ascend NPUs. |
| Outcome: | The proposed formats excel with high-variance data and are compatible with state-of-the-art quantization frameworks. |