Papers by Ziyang 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. |
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. |
Calibrating Inference Time Alignment with Sequence-level Risk Accumulation (2026.acl-long)
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| Challenge: | Existing approaches to decode large language models (LLMs) often over-reject benign information, limiting their generalizability in real-world scenarios where harmful and benign information coexist. |
| Approach: | They propose a framework to regulate decoding alignments for Large Language Models (LLMs) they employ a reward-guided branch decoding paradigm to incorporate safety awareness during generation. |
| Outcome: | The proposed framework achieves superior performance on four attack benchmarks and two neutral datasets. |