Papers by Shufei Zhang
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. |
AOT*: Efficient Synthesis Planning via LLM-Empowered AND-OR Tree Search (2026.findings-acl)
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| Challenge: | Experimental evaluation shows that AOT* achieves competitive solve rates using 3-5 fewer iterations than existing LLM-based approaches. |
| Approach: | They propose a framework that integrates LLM-generated chemical synthesis pathways with systematic AND-OR tree search. |
| Outcome: | Experimental results show that AOT* improves search efficiency and solves faster than existing approaches. |
Nature-Inspired Population-Based Evolution of Large Language Models (2026.acl-long)
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| Challenge: | a new framework for population-based evolution of large language models is emerging . a population-driven evolution of LLMs is a key component of evolution, authors say . |
| Approach: | They propose a framework that allows for population-based evolution of large language models . they start with a population of parent LLMs and allow this population to evolve . |
| Outcome: | The proposed framework outperforms existing methods on 12 datasets. |
ReKG-MCTS: Reinforcing LLM Reasoning on Knowledge Graphs via Training-Free Monte Carlo Tree Search (2025.findings-acl)
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| Challenge: | Existing approaches to combining knowledge graphs with large language models face limitations in path exploration strategies or excessive computational overhead. |
| Approach: | They propose a training-free framework that synergizes Monte Carlo Tree Search with LLM capabilities to enable dynamic reasoning over KGs. |
| Outcome: | The proposed framework outperforms existing training-free methods and achieves competitive performance compared to fine-tuned baselines. |
FlowSearch: Advancing Deep Research with Dynamic Structured Knowledge Flow (2026.acl-long)
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Yusong Hu, Runmin Ma, Yue Fan, Jinxin Shi, Zongsheng Cao, Yuhao Zhou, Jiakang Yuan, Shuaiyu Zhang, Shiyang Feng, Xiangchao Yan, Shufei Zhang, Wenlong Zhang, Lei Bai, Bo Zhang
| Challenge: | FlowSearch is a multi-agent framework that actively constructs and evolves a dynamic structured knowledge flow to drive subtask execution and reasoning. |
| Approach: | They propose a multi-agent framework that actively constructs and evolves a dynamic structured knowledge flow to drive subtask execution and reasoning. |
| Outcome: | The proposed framework achieves competitive performance on GAIA, HLE, GPQA and TRQA benchmarks and is available to download. |
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. |
Step-GRPO: Internalizing Dynamic Early Exit for Efficient Reasoning (2026.acl-long)
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| Challenge: | Large reasoning models that use long chain-of-thought excel at problem-solving but waste computational resources. |
| Approach: | They propose a framework that internalizes dynamic early-exit capabilities directly into the model. |
| Outcome: | The proposed framework reduces token consumption by 32.0% on a Qwen3-8B model compared to the vanilla model . |