Publication
My research topics can be broadly classified into two primary categories.
The first category is AI-empowered interdisciplinary research, such as AI for science, AI for medicine, and AI for engineering.
The second category is fundemental AI research, such as machine learning, computer vision, and natural language processing.
# denotes Equal Contribution.
† denotes Corresponding Author(s).
‡ denotes Project Lead.
Journal Papers
The research topics are listed in alphabetical order.
AI for Engineering
Scalable Multi-Agent Reinforcement Learning for Residential Load Scheduling under Data Governance
Zhaoming Qin#, Nanqing Dong†, Di Liu†, Zhefan Wang, Junwei Cao†.
IEEE Transactions on Industrial Cyber-Physical Systems (TICPS), 2024. [Link]A Demand Side Joint Electricity and Carbon Trading Mechanism
Haochen Hua, Xingying Chen, Lei Gan, Jiaxiang Sun, Nanqing Dong, Di Liu†, Zhaoming Qin, Mingjia Yin, Kang Li.
IEEE Transactions on Industrial Cyber-Physical Systems (TICPS), 2023. [Link]Data-driven Dynamical Control for Bottom-up Energy Internet System
Haochen Hua, Zhaoming Qin, Nanqing Dong, Yuchao Qin, Maojiao Ye, Zidong Wang, Xingying Chen, Junwei Cao†.
IEEE Transactions on Sustainable Energy (TSTE), 2021. [Link]
AI for Medicine
An Exploratory Study of Self-Supervised Pre-Training on Partially Supervised Multi-Label Classification on Chest X-Ray Images
Nanqing Dong†, Michael Kampffmeyer†, Haoyang Su, Eric Xing.
Applied Soft Computing, 2024. [Link]Smoke Veil Prior Regularized Surgical Field Desmoking without Paired In-vivo Data
Congcong Wang, Yuru Song, Meng Zhao†, Nanqing Dong, Zohaib Amjad Khan, Xintong Zhao, Faouzi Alaya Cheikh, Azeddine Beghdadi, Shengyong Chen.
Computers in Biology and Medicine, 2023. [Link]Federated Partially Supervised Learning with Limited Decentralized Medical Images
Nanqing Dong†, Michael Kampffmeyer, Irina Voiculescu, Eric Xing.
IEEE Transactions on Medical Imaging (TMI), 2022. [Link]Towards Robust Partially Supervised Multi-Structure Medical Image Segmentation on Small-Scale Data
Nanqing Dong, Michael Kampffmeyer†, Xiaodan Liang, Min Xu, Irina Voiculescu, Eric Xing.
Applied Soft Computing, 2021. [Link][arXiv]
AI for Science
SeedLLM·Rice: A Large Language Model Integrated with Rice Biological Knowledge Graph
Fan Yang#†, Huanjun Kong, Jie Ying, Zihong Chen, Tao Luo, Wanli Jiang, Zhonghang Yuan, Zhefan Wang, Zhaona Ma, Shikuan Wang, Wanfeng Ma, Xiaoyi Wang, Xiaoying Li, Zhengyin Hu, Xiaodong Ma, Minguo Liu, Xiqing Wang†, Fan Chen, Nanqing Dong#†.
Molecular Plant, 2025. [Link][MPlant植物科学] [2024 IF 24.1]Deep Generative Model for Protein Subcellular Localization Prediction
Guohua Yuan#, Jinzhe Li#, Zejun Yang#, Yaoqi Chen#, Zhonghang Yuan, Tao Chen, Wanli Ouyang, Nanqing Dong†, Li Yang†
Briefings in Bioinformatics, 2025. [Link][bioRxiv]Structure-Informed Insights into Catalytic Mechanism and Multi-Domain Collaboration in α-Agarase CmAga
Yuxian You, Bee Koon Gan, Min Luo, Xinzhe Zheng, Nanqing Dong, Yixiong Tian, Caiming Li, Haocun Kong, Zhengbiao Gu, Daiwen Yang†, Zhaofeng Li†
Journal of Agricultural and Food Chemistry, 2025. [Link]π-PrimeNovo: An Accurate and Efficient Non-Autoregressive Deep Learning Model for De Novo Peptide Sequencing
Xiang Zhang#, Tianze Ling#, Zhi Jin#, Sheng Xu#, Zhiqiang Gao, Boyan Sun, Zijie Qiu, Jiaqi Wei, Nanqing Dong, Guangshuai Wang, Guibin Wang, Leyuan Li, Muhammad Abdul-Mageed, Laks V.S. Lakshmanan, Fuchu He, Wanli Ouyang†, Cheng Chang†, Siqi Sun†.
Nature Communications, 2025. [Link]
Computer Vision
Label-Efficient Object Detection via Region Proposal Network Pre-Training
Nanqing Dong#†, Linus Ericsson#, Yongxin Yang, Ales Leonardis, Steven McDonagh†.
Neurocomputing, 2024. [Link][arXiv]ConnNet: A Long-Range Relation-Aware Pixel-Connectivity Network for Salient Segmentation
Michael Kampffmeyer#, Nanqing Dong#, Xiaodan Liang†, Yujia Zhang, Eric Xing.
IEEE Transactions on Image Processing (TIP), 2018. [Link][arXiv]
Finance
- Improving Equity Fund Alpha Estimates with a Second Size Factor
Nanqing Dong, Luka Jankovic, Anne Stewart, Scott Stewart†.
Journal of Portfolio Management, 2022. [Link]
Federated Learning
zkFL: Zero-Knowledge Proof-based Gradient Aggregation for Federated Learning
Zhipeng Wang, Nanqing Dong†, Jiahao Sun, William Knottenbelt, Yike Guo
IEEE Transactions on Big Data (TBD), 2024. [Link][arXiv]Defending Against Poisoning Attacks in Federated Learning with Blockchain
Nanqing Dong#†, Zhipeng Wang#, Jiahao Sun, Michhael Kampffmeyer, William Knottenbelt, Eric Xing.
IEEE Transactions on Artificial Intelligence (TAI), 2024. [Link][arXiv] [机器之心]Edge Computing with Artificial Intelligence: A Machine Learning Perspective
Haochen Hua, Yutong Li, Tonghe Wang, Nanqing Dong, Wei Li, Xingying Chen, Junwei Cao†.
ACM Computing Surveys, 2023. [Link]
Machine Learning
- Negational Symmetry of Quantum Neural Networks for Binary Pattern Classification
Nanqing Dong†, Michael Kampffmeyer, Irina Voiculescu, Eric Xing.
Pattern Recognition, 2022. [Link]
Conference Papers
The research topics are listed in alphabetical order.
AI for Engineering
- Towards Efficient and Intelligent Laser Weeding: Method and Dataset for Weed Stem Detection
Dingning Liu#，Jinzhe Li#，Haoyang Su#，Bei Cui†, Zhihui Wang, Qingbo Yuan, Wanli Ouyang, Nanqing Dong†
AAAI Conference on Artificial Intelligence (AAAI), 2025. [Link]
AI for Medicine
Learning Underrepresented Classes from Decentralized Partially Labeled Medical Images
Nanqing Dong†, Michael Kampffmeyer, Irina Voiculescu.
International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2022. [Link][arXiv]Federated Contrastive Learning for Decentralized Unlabeled Medical Images
Nanqing Dong†, Irina Voiculescu.
International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2021. [Link][arXiv]Self-Supervised Multi-Task Representation Learning for Sequential Medical Images
Nanqing Dong†, Michael Kampffmeyer, Irina Voiculescu.
European Conference on Machine Learning (ECML), 2021. [Link]Neural Architecture Search for Adversarial Medical Image Segmentation
Nanqing Dong†, Min Xu, Xiaodan Liang, Yiliang Jiang, Wei Dai, Eric Xing.
International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2019. [Link][RG][Data]Unsupervised Domain Adaptation for Automatic Estimation of Cardiothoracic Ratio
Nanqing Dong†, Michael Kampffmeyer, Xiaodan Liang, Zeya Wang, Wei Dai, Eric Xing.
International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2018. [Link][arXiv][Data]
AI for Science
Many Heads Are Better Than One: Improved Scientific Idea Generation by A LLM-Based Multi-Agent System
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†‡.
Annual Meeting of the Association for Computational Linguistics (ACL), 2025. [Link][arXiv][GitHub][ScienceAI][新智元]SeedBench: A Multi-task Benchmark for Evaluating Large Language Models in Seed Science
Jie Ying#, Zihong Chen#, Zhefan Wang#, Wanli Jiang, Chenyang Wang, Zhonghang Yuan, Haoyang Su, Huanjun Kong, Fan Yang, Nanqing Dong†.
Annual Meeting of the Association for Computational Linguistics (ACL), 2025. [Link][arXiv][GitHub][ScienceAI]Curriculum Learning for Biological Sequence Prediction: The Case of De Novo Peptide Sequencing
Xiang Zhang, Jiaqi Wei, Sheng Xu, Zijie Qiu, Nanqing Dong, Zhiqiang Gao, Siqi Sun.
International Conference on Machine Learning (ICML), 2025.Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing
Zijie Qiu, Jiaqi Wei, Xiang Zhang, Sheng Xu, Kai Zou, Zhi Jin, Zhiqiang Gao, Nanqing Dong, Siqi Sun.
International Conference on Machine Learning (ICML), 2025.Empowering and Assessing the Utility of Large Language Models in Crop Science
Hang Zhang#, Jiawei Sun#, Renqi Chen#, Wei Liu, Zhonghang Yuan, Xinzhe Zheng, Zhefan Wang, Zhiyuan Yang, Hang Yan, HanSen Zhong, Xiqing Wang, Wanli Ouyang, Fan Yang†, Nanqing Dong†.
Annual Conference on Neural Information Processing Systems (NeuIPS), 2024. [Link]Model Decides How to Tokenize: Adaptive DNA Sequence Tokenization with MxDNA
Lifeng Qiao, Peng Ye, Yuchen Ren, Weiqiang Bai, Chaoqi Liang, Xinzhu Ma, Nanqing Dong, Wanli Ouyang.
Annual Conference on Neural Information Processing Systems (NeuIPS), 2024Benchmarking Fish Dataset and Evaluation Metric in Keypoint Detection - Towards Precise Fish Morphological Assessment in Aquaculture Breeding
Weizhen Liu, Jiayu Tan, Guangyu Lan, Ao Li, Dongye Li, Le Zhao, Xiaohui Yuan†, Nanqing Dong†.
International Joint Conference on Artificial Intelligence (IJCAI), 2024. [Oral][Link]An Embarrassingly Simple Approach to Enhance Transformer Performance in Genomic Selection for Crop Breeding
Renqi Chen#, Wenwei Han#, Haohao Zhang#, Haoyang Su, Zhefan Wang, Xiaolei Liu, Hao Jiang, Wanli Ouyang, Nanqing Dong†.
International Joint Conference on Artificial Intelligence (IJCAI), 2024. [Oral][Link]Revealing Hierarchical Structure of Leaf Venations in Plant Science via Label-Efficient Segmentation: Dataset and Method
Weizhen Liu, Ao Li, Ze Wu, Yue Li, Baobin Ge, Guangyu Lan, Shilin Chen, Minghe Li, Yunfei Liu, Xiaohui Yuan†, Nanqing Dong†.
International Joint Conference on Artificial Intelligence (IJCAI), 2024. [Oral][Link]ContraNovo: A Contrastive Learning Approach to Enhance De Novo Peptide Sequencing
Zhi Jin#, Sheng Xu#, Xiang Zhang#, Tianze Ling, Nanqing Dong, Wanli Ouyang†, Zhiqiang Gao†, Cheng Chang†, Siqi Sun†.
AAAI Conference on Artificial Intelligence (AAAI), 2024. [Link][arXiv]
Computer Vision
- Few-Shot Semantic Segmentation with Prototype Learning
Nanqing Dong†, Eric Xing.
British Machine Vision Conference (BMVC), 2018. [Link]
Machine Learning
Residual Contrastive Learning for Image Reconstruction: Learning Transferable Representations from Noisy Images
Nanqing Dong†, Matteo Maggioni, Yongxin Yang, Eduardo Pérez-Pellitero, Ales Leonardis, Steven McDonagh†.
International Joint Conference on Artificial Intelligence (IJCAI), 2022. [Oral][Link][arXiv]Adversarial Domain Adaptation Being Aware of Class Relationships
Zeya Wang†, Baoyu Jing, Yang Ni, Nanqing Dong, Pengtao Xie, Eric Xing.
European Conference on Aritifical Inteligence (ECAI), 2020. [Oral][arXiv]Toward Understanding the Impact of Staleness in Distributed Machine Learning
Wei Dai†, Yi Zhou, Nanqing Dong, Hao Zhang, Eric Xing.
International Conference on Learning Representations (ICLR), 2019. [Link][arXiv]Domain Adaption in One-Shot Learning
Nanqing Dong†, Eric Xing.
European Conference on Machine Learning (ECML), 2018. [Oral][Link][RG]