Publications

Peer-reviewed research on AI for drug discovery, ADMET prediction, and bioinformatics.

2026

  1. DeepCYP: an integrated deep learning web server for the holistic “pathway–site–product” prediction of CYP450 metabolism

    Yiling Zhou, Sen Yang, Xiaoli Wang, Yuanhang He, Yao Tian, Jiacai Yi, Yikun Wang, Youchao Deng, Dejun Jiang, Dongsheng Cao

    Nucleic Acids Res. PDF
  2. Expert-Inspired Multi-Agent Coordination for Multi-Objective Molecular Optimization

    Daojian Zeng, Tianle Li, Jiahao Yang, Jiacai Yi, Xieping Gao, Lincheng Jiang, Tengfei Ma, Xiangxiang Zeng

    AAAI PDF

2025

  1. Machine learning prediction of pediatric adverse drug reactions using consensus-derived scarce data

    Yao Tian, Jiacai Yi, Kun Li, Jinfu Peng, Youchao Deng, Dejun Jiang, Dongsheng Cao

    Commun. Chem. PDF
  2. A fused deep learning approach to transform drug repositioning

    Kun Li, Jiacai Yi, Qing Ye, Xixi Yang, Long Yu, YouChao Deng, Chengkun Wu, Tingjun Hou, Dejun Jiang, Dongsheng Cao

    Commun. Chem. PDF
  3. Decoding the limits of deep learning in molecular docking for drug discovery

    Yue Li, Jiacai Yi, Hui Li, Kun Li, Fenghua Kang, Youchao Deng, Chengkun Wu, Xiangzheng Fu, Dejun Jiang, Dongsheng Cao · Co-first author

    Chem. Sci. PDF
  4. DeepMetab: a comprehensive and mechanistically informed graph learning framework for end-to-end drug metabolism prediction

    Yiling Zhou, Dejun Jiang, Xiao Wei, Jiacai Yi, Yikun Wang, Youchao Deng, Dongsheng Cao

    Chem. Sci. PDF
  5. Pushing the boundaries of few-shot learning for low-data drug discovery with a Bayesian meta-learning hypernetwork framework

    Jiacai Yi, Dejun Jiang, Chengkun Wu, Xiaochen Zhang, Weixing He, Wentao Zhao, Dongsheng Cao · First author

    Brief. Bioinform. PDF
  6. DDInter 2.0: an enhanced drug interaction resource with expanded data coverage, new interaction types, and improved user interface

    Yao Tian, Jiacai Yi, Ningning Wang, Chengkun Wu, Jinfu Peng, Shao Liu, Guoping Yang, Dongsheng Cao · Co-first author

    Nucleic Acids Res. PDF

2024

  1. ADMETlab 3.0: an updated comprehensive online ADMET prediction platform enhanced with broader coverage, improved performance, API functionality and decision support

    Li Fu, Shaohua Shi, Jiacai Yi, Ningning Wang, Yuanhang He, Zhenxing Wu, Jinfu Peng, Youchao Deng, Wenxuan Wang, Chengkun Wu, Aiping Lyu, Xiangxiang Zeng, Wentao Zhao, Tingjun Hou, Dongsheng Cao · Co-first author

    Nucleic Acids Res. PDF
  2. ChemFH: an integrated tool for screening frequent false positives in chemical biology and drug discovery

    Shaohua Shi, Li Fu, Jiacai Yi, Ziyi Yang, Xiaochen Zhang, Youchao Deng, Wenxuan Wang, Chengkun Wu, Wentao Zhao, Tingjun Hou, Xiangxiang Zeng, Aiping Lyu, Dongsheng Cao · Co-first author

    Nucleic Acids Res. PDF
  3. ISTransbase: an online database for inhibitor and substrate of drug transporters

    Jinfu Peng, Jiacai Yi, Guoping Yang, Zhijun Huang, Dongsheng Cao

    Database PDF
  4. OptADMET: a web-based tool for substructure modifications to improve ADMET properties of lead compounds

    Jiacai Yi, Shaohua Shi, Li Fu, Ziyi Yang, Pengfei Nie, Aiping Lu, Chengkun Wu, Yafeng Deng, Changyu Hsieh, Xiangxiang Zeng, Tingjun Hou, Dongsheng Cao · First author

    Nat. Protoc. PDF
  5. ChemMORT: an automatic ADMET optimization platform using deep learning and multi-objective particle swarm optimization

    Jiacai Yi, Ziyi Yang, Wentao Zhao, Zhijiang Yang, Xiaochen Zhang, Chengkun Wu, Aiping Lu, Dongsheng Cao · First author

    Brief. Bioinform. PDF

2023

  1. Situational awareness ontology modeling for threat from space cyber operations

    Bin Liu, Jiacai Yi, Li Yao, Yanjuan Wang, Zhaoyun Ding, Xianqiang Zhu

    Syst. Eng. Electron. PDF

2022

  1. MICER: a pre-trained encoder-decoder architecture for molecular image captioning

    Jiacai Yi, Chengkun Wu, Xiaochen Zhang, Xinyi Xiao, Yanlong Qiu, Wentao Zhao, Tingjun Hou, Dongsheng Cao · First author

    Bioinformatics PDF
  2. Satellite cyber situational understanding based on knowledge reasoning

    Jiacai Yi, Bin Liu, Li Yao, Wentao Zhao

    Syst. Eng. Electron. PDF
  3. ABC-Net: a divide-and-conquer based deep learning architecture for SMILES recognition from molecular images

    Xiaochen Zhang, Jiacai Yi, Guoping Yang, Chengkun Wu, Tingjun Hou, Dongsheng Cao

    Brief. Bioinform. PDF
  4. DDInter: an online drug-drug interaction database towards improving clinical decision-making and patient safety

    Guoli Xiong, Zhijiang Yang, Jiacai Yi, Ningning Wang, Lei Wang, Huimin Zhu, Chengkun Wu, Aiping Lu, Xiang Chen, Shao Liu, Tingjun Hou, Dongsheng Cao · Co-first author

    Nucleic Acids Res. PDF
  5. Pushing the Boundaries of Molecular Property Prediction for Drug Discovery with Multitask Learning BERT Enhanced by SMILES Enumeration

    Xiaochen Zhang, Chengkun Wu, Jiacai Yi, Xiangxiang Zeng, Canqun Yang, Aiping Lyu, Tingjun Hou, Dongsheng Cao

    Research PDF

2021

  1. Mining microbe-disease interactions from literature via a transfer learning model

    Chengkun Wu, Xinyi Xiao, Canqun Yang, Jinxiang Chen, Jiacai Yi, Yanlong Qiu

    BMC Bioinformatics PDF
  2. ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties

    Guoli Xiong, Zhenxing Wu, Jiacai Yi, Li Fu, Zhijiang Yang, Changyu Hsieh, Mingzhu Yin, Xiangxiang Zeng, Chengkun Wu, Aiping Lu, Xiang Chen, Tingjun Hou, Dongsheng Cao · Co-first author

    Nucleic Acids Res. PDF
  3. MG-BERT: leveraging unsupervised atomic representation learning for molecular property prediction

    Xiaochen Zhang, Chengkun Wu, Zhijiang Yang, Zhenhua Wu, Jiacai Yi, Chang-Yu Hsieh, Tingjun Hou, Dongsheng Cao

    Brief. Bioinform. PDF