Papers by Wanli Li
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. |
ResearchBench: Benchmarking LLMs in Scientific Discovery via Inspiration-Based Task Decomposition (2026.findings-acl)
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Yujie Liu, Zonglin Yang, Tong Xie, Jinjie Ni, Ben Gao, Yuqiang Li, Shixiang Tang, Wanli Ouyang, Erik Cambria, Dongzhan Zhou
| Challenge: | Large language models have shown potential in assisting scientific research, yet their ability to discover high-quality research hypotheses remains unexamined due to the lack of a dedicated benchmark. |
| Approach: | They propose a benchmark for evaluating large language models on a sufficient set of scientific discovery sub-tasks. |
| Outcome: | The proposed framework extracts critical components from papers across 12 disciplines with expert validation confirming its accuracy. |
Graph-based Model Generation for Few-Shot Relation Extraction (2022.emnlp-main)
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| Challenge: | Existing models follow a 'one-for-all' scheme where one general large model performs all individual N-way-K-shot tasks, which prevents the model from achieving the optimal point on each task. |
| Approach: | They propose a model generation framework that consists of one general model for all tasks and many tiny task-specific models for each individual task. |
| Outcome: | The proposed framework achieves state-of-the-art performance on two public datasets. |
META-LORA: Memory-Efficient Sample Reweighting for Fine-Tuning Large Language Models (2025.coling-main)
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| Challenge: | Supervised fine-tuning (SFT) is widely adopted for tailoring large language models (LLMs) to specific downstream tasks. |
| Approach: | They propose a memory-efficient method for automatic sample reweighting that learns to re-weight fine-tuning samples by minimizing the loss on a small, high-quality validation set. |
| Outcome: | Meta-LoRA learns to reweight fine-tuning samples by minimizing the loss on a small, high-quality validation set through an end-to-end bi-level optimization framework based on meta-learning. |
LLaMA-Berry: Pairwise Optimization for Olympiad-level Mathematical Reasoning via O1-like Monte Carlo Tree Search (2025.naacl-long)
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Di Zhang, Jianbo Wu, Jingdi Lei, Tong Che, Jiatong Li, Tong Xie, Xiaoshui Huang, Shufei Zhang, Marco Pavone, Yuqiang Li, Wanli Ouyang, Dongzhan Zhou
| Challenge: | LLaMA-Berry is an advanced mathematical reasoning framework to enhance the problem-solving ability of large language models (LLMs). |
| Approach: | They propose a Monte Carlo Tree Search and Self-Refine framework to optimize reasoning paths and a pairwise reward model to evaluate different paths globally. |
| Outcome: | The proposed framework overcomes inefficiencies and limitations of step-wise and greedy search algorithms, enabling more efficient exploration of solution spaces. |
GraphReader: Building Graph-based Agent to Enhance Long-Context Abilities of Large Language Models (2024.findings-emnlp)
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Shilong Li, Yancheng He, Hangyu Guo, Xingyuan Bu, Ge Bai, Jie Liu, Jiaheng Liu, Xingwei Qu, Yangguang Li, Wanli Ouyang, Wenbo Su, Bo Zheng
| Challenge: | Existing models for long contexts struggle to handle long inputs due to limited context window and memory usage. |
| Approach: | They propose a graph-based agent system that analyzes long texts into a graphical graph . GraphReader consistently outperforms GPT-4-128k across context lengths from 16k to 256k . |
| Outcome: | The proposed model outperforms existing models on four challenging benchmarks. |