Papers by Dongzhan Zhou
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. |
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. |
LOCR: Location-Guided Transformer for Optical Character Recognition (2024.findings-emnlp)
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| Challenge: | Academic documents are packed with texts, equations, tables, and figures, posing challenges for accurate OCR results. |
| Approach: | They propose a model that integrates location guiding into the transformer architecture during autoregression. |
| Outcome: | The proposed model outperforms existing methods on an original large-scale dataset comprising 53M text-location pairs from 89K academic document pages. |
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. |