publications

2026

1. NeurIPS

   

   Can Agents Price a Reaction? Evaluating LLMs on Chemical Cost Reasoning

   Yuyang Wu, Yue Huang, Shuaike Shen, Xujian Wang, Shuhao Zhang, Qiyao Xue, Weichen Liu, Runtian Gao, Jian Ma, Xiangliang Zhang, and Olexandr Isayev

   In Advances in Neural Information Processing Systems (NeurIPS), 2026

   arXiv Bib Code

   @inproceedings{wu2026chemcost,
     title = {Can Agents Price a Reaction? Evaluating LLMs on Chemical Cost Reasoning},
     author = {Wu, Yuyang and Huang, Yue and Shen, Shuaike and Wang, Xujian and Zhang, Shuhao and Xue, Qiyao and Liu, Weichen and Gao, Runtian and Ma, Jian and Zhang, Xiangliang and Isayev, Olexandr},
     booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
     year = {2026},
   }

2. ECCV

   

   Reasoning Path and Latent State Analysis for Multi-view Visual Spatial Reasoning: A Cognitive Science Perspective

   Qiyao Xue, Weichen Liu, Shiqi Wang, Haoming Wang, Yuyang Wu, and Wei Gao

   In European Conference on Computer Vision (ECCV), 2026

   arXiv Bib Code

   @inproceedings{xue2026reasoning,
     title = {Reasoning Path and Latent State Analysis for Multi-view Visual Spatial Reasoning: A Cognitive Science Perspective},
     author = {Xue, Qiyao and Liu, Weichen and Wang, Shiqi and Wang, Haoming and Wu, Yuyang and Gao, Wei},
     booktitle = {European Conference on Computer Vision (ECCV)},
     year = {2026},
   }

3. BioNLP

   

   KGRxn-LLM: Knowledge Graph Enhanced Large Language Models for Molecular Reaction Reasoning

   Weichen Liu, Qiyao Xue, Yuyang Wu, Olexandr Isayev, and Natasa Miskov-Zivanov

   In Proceedings of the BioNLP Workshop (ACL), 2026

   DOI Bib HTML Code

   @inproceedings{liu2026kgrxnllm,
     title = {KGRxn-LLM: Knowledge Graph Enhanced Large Language Models for Molecular Reaction Reasoning},
     author = {Liu, Weichen and Xue, Qiyao and Wu, Yuyang and Isayev, Olexandr and Miskov-Zivanov, Natasa},
     booktitle = {Proceedings of the BioNLP Workshop (ACL)},
     pages = {268--281},
     year = {2026},
     publisher = {Association for Computational Linguistics},
     doi = {10.18653/v1/2026.bionlp-1.22},
   }

4. VIS

   

   VeriLLMed: Interactive Visual Debugging of Medical Large Language Models with Knowledge Graphs

   Yurui Xiang, Xingyi Mao, Rui Sheng, Zixin Chen, Zelin Zang, Yuyang Wu, Haipeng Zeng, Huamin Qu, Yushi Sun, and Yanna Lin

   In IEEE Visualization Conference (VIS), 2026

   arXiv Bib

   @inproceedings{xiang2026verillmed,
     title = {VeriLLMed: Interactive Visual Debugging of Medical Large Language Models with Knowledge Graphs},
     author = {Xiang, Yurui and Mao, Xingyi and Sheng, Rui and Chen, Zixin and Zang, Zelin and Wu, Yuyang and Zeng, Haipeng and Qu, Huamin and Sun, Yushi and Lin, Yanna},
     booktitle = {IEEE Visualization Conference (VIS)},
     year = {2026},
   }

5. UIST

   

   MolecularCanvas: LLM-assisted Small-Molecule Drug Discovery via Structure-Guided Constraints

   Haoyu Dong, Rui Sheng, Shuhao Zhang, Yushi Sun, Dingyang Wu, Hanxiang Chao, Olexandr Isayev, Huamin Qu, Yuyang Wu^†, and Yanna Lin

   In ACM Symposium on User Interface Software and Technology (UIST), 2026

   arXiv Bib

   @inproceedings{dong2026molecularcanvas,
     title = {MolecularCanvas: LLM-assisted Small-Molecule Drug Discovery via Structure-Guided Constraints},
     author = {Dong, Haoyu and Sheng, Rui and Zhang, Shuhao and Sun, Yushi and Wu, Dingyang and Chao, Hanxiang and Isayev, Olexandr and Qu, Huamin and Wu, Yuyang and Lin, Yanna},
     booktitle = {ACM Symposium on User Interface Software and Technology (UIST)},
     year = {2026},
   }

6. bioRxiv

   

   High-throughput physics-based enzyme engineering

   Xujian Wang, Xiang Qiu, Yuyang Wu, Taoyu Niu, Shuhao Zhang, Runtian Gao, Ilkwon Cho, Haocheng Tang, Kangdelong Hu, Xiaoguang Lei, Olexandr Isayev, and Junmei Wang

   bioRxiv preprint (under review), 2026

   DOI Bib

   @article{wang2026enzyme,
     title = {High-throughput physics-based enzyme engineering},
     author = {Wang, Xujian and Qiu, Xiang and Wu, Yuyang and Niu, Taoyu and Zhang, Shuhao and Gao, Runtian and Cho, Ilkwon and Tang, Haocheng and Hu, Kangdelong and Lei, Xiaoguang and Isayev, Olexandr and Wang, Junmei},
     journal = {bioRxiv preprint (under review)},
     year = {2026},
     doi = {10.64898/2026.09.15.751901},
   }

7. arXiv

   

   KARA: Efficient Reasoning LLM Serving via Sliding-Window KV Cache Compression

   Shen Han^*, Yuyang Wu^*, Junpu Yu, and Olexandr Isayev

   arXiv preprint arXiv:2607.01237, 2026

   arXiv Bib

   @article{han2026kara,
     title = {KARA: Efficient Reasoning LLM Serving via Sliding-Window KV Cache Compression},
     author = {Han, Shen and Wu, Yuyang and Yu, Junpu and Isayev, Olexandr},
     journal = {arXiv preprint arXiv:2607.01237},
     year = {2026},
   }

8. arXiv

   

   CLORE: Content-Level Optimization for Reasoning Efficiency

   Yuyang Wu, Qiyao Xue, Guanxing Lu, Weichen Liu, Zihan Wang, Manling Li, and Olexandr Isayev

   arXiv preprint arXiv:2605.22211, 2026

   arXiv Bib Code

   @article{wu2026clore,
     title = {CLORE: Content-Level Optimization for Reasoning Efficiency},
     author = {Wu, Yuyang and Xue, Qiyao and Lu, Guanxing and Liu, Weichen and Wang, Zihan and Li, Manling and Isayev, Olexandr},
     journal = {arXiv preprint arXiv:2605.22211},
     year = {2026},
   }

2025

1. EMNLP

   

   MolErr2Fix: Benchmarking LLM Trustworthiness in Chemistry via Modular Error Detection, Localization, Explanation, and Revision

   Yuyang Wu, Jinhui Ye, Shuhao Zhang, Lu Dai, Yonatan Bisk, and Olexandr Isayev

   In Proceedings of the Conference on Empirical Methods in Natural Language Processing (EMNLP) Oral Presentation , 2025

   Bib HTML PDF Code

   @inproceedings{wu2025molerr2fix,
     title = {MolErr2Fix: Benchmarking LLM Trustworthiness in Chemistry via Modular Error Detection, Localization, Explanation, and Revision},
     author = {Wu, Yuyang and Ye, Jinhui and Zhang, Shuhao and Dai, Lu and Bisk, Yonatan and Isayev, Olexandr},
     booktitle = {Proceedings of the Conference on Empirical Methods in Natural Language Processing (EMNLP)},
     year = {2025},
     publisher = {Association for Computational Linguistics},
   }

2024

1. BIB

   

   Multiview representation learning for identification of novel cancer genes and their causative biological mechanisms

   Jianye Yang, Haitao Fu, Feiyang Xue, Menglu Li, Yuyang Wu, Zhanhui Yu, Haohui Luo, Jing Gong, Xiaohui Niu, and Wen Zhang

   Briefings in Bioinformatics, 2024

   DOI Bib Code

   @article{yang2024multiview,
     title = {Multiview representation learning for identification of novel cancer genes and their causative biological mechanisms},
     author = {Yang, Jianye and Fu, Haitao and Xue, Feiyang and Li, Menglu and Wu, Yuyang and Yu, Zhanhui and Luo, Haohui and Gong, Jing and Niu, Xiaohui and Zhang, Wen},
     journal = {Briefings in Bioinformatics},
     volume = {25},
     number = {5},
     pages = {bbae418},
     year = {2024},
     publisher = {Oxford Academic},
     doi = {10.1093/bib/bbae418},
   }

2023

1. BIB

   

   HimGNN: a novel hierarchical molecular graph representation learning framework for property prediction

   Shen Han, Haitao Fu, Yuyang Wu, Ganglan Zhao, Zhenyu Song, Feng Huang, Zhongfei Zhang, Shichao Liu, and Wen Zhang

   Briefings in Bioinformatics, 2023

   DOI Bib Code

   @article{han2023himgnn,
     title = {HimGNN: a novel hierarchical molecular graph representation learning framework for property prediction},
     author = {Han, Shen and Fu, Haitao and Wu, Yuyang and Zhao, Ganglan and Song, Zhenyu and Huang, Feng and Zhang, Zhongfei and Liu, Shichao and Zhang, Wen},
     journal = {Briefings in Bioinformatics},
     volume = {24},
     number = {5},
     pages = {bbad305},
     year = {2023},
     publisher = {Oxford Academic},
     doi = {10.1093/bib/bbad305},
   }