Papers by Nanqing 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. |
Many Heads Are Better Than One: Improved Scientific Idea Generation by A LLM-Based Multi-Agent System (2025.acl-long)
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Haoyang Su, Renqi Chen, Shixiang Tang, Zhenfei Yin, Xinzhe Zheng, Jinzhe Li, Biqing Qi, Qi Wu, Hui Li, Wanli Ouyang, Philip Torr, Bowen Zhou, Nanqing Dong
| Challenge: | Recent AI methods have shown promise in tasks such as hypothesis generation and experimental design, but they fail to replicate the collaborative nature of real-world scientific practices. |
| Approach: | They propose a virtual scientific system that mimics the collaborative nature of scientific research by organizing a team of agents to generate, evaluate, and refine research ideas. |
| Outcome: | The proposed system outperforms the state-of-the-art method in producing new scientific ideas and offers valuable insights to guide future research. |
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. |
ROGRAG: A Robustly Optimized GraphRAG Framework (2025.acl-demo)
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| Challenge: | Existing pipelines for large language models struggle with specialized or emerging topics which are rarely seen in the training corpus. |
| Approach: | They propose a multi-stage retrieval mechanism that integrates dual-level with logic form retrieval methods to improve retrieval robustness without increasing computational cost. |
| Outcome: | The proposed framework outperforms Qwen2.5-7B-Instruct and outperformed mainstream methods on seedbench and significantly improves the performance of each component. |
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. |