publications

publications by categories in reversed chronological order. generated by jekyll-scholar.

* Equal contribution.

2026

2026

  1. Nature Comm
    Decoding the sequence determinants of locus-specific DNA methylation across human tissues
    Junru Jin*, Ding Wang*, Jianbo Qiao*, Wenjia Gao, Yuhang Liu, and 5 more authors
    Nature Communications, Aug 2026
  2. JCTC
    Relation-Aware Pretraining and Reaction Center Modeling for Chemical Reaction Graph Representation Learning
    Jianbo Qiao, Kefei Li, Junru Jin, Ding Wang, Wenjia Gao, and 3 more authors
    Journal of Chemical Theory and Computation, Aug 2026
  3. JCIM
    FGSGT-DDI: An LLM-Enhanced Functional Group Semantic Graph Transformer for Drug–Drug Interaction Prediction
    Kefei Li, Jianbo Qiao, Yuntao Yang, Hanjun Zhao, Ding Wang, and 3 more authors
    Journal of Chemical Information and Modeling, Aug 2026
  4. ACS Synth. Biol.
    An Explainable Deep Learning Framework Integrating DNA Sequence and Transcription Initiation Signals for Gene Expression Prediction
    Jianbo Qiao*, Wenjia Gao*, Ding Wang*, Junru Jin*, Siqi Chen, and 2 more authors
    ACS Synthetic Biology, Jul 2026
  5. bioRxiv
    Spatial-neighbour encoding enables fast RNA 3D structure search
    Ding Wang, Junru Jin, Jianbo Qiao, Leyi Wei, Shu Wu, and 1 more author
    bioRxiv, Jul 2026

2025

2025

  1. Nature Comm
    A self-conformation-aware pre-training framework for molecular property prediction with substructure interpretability
    Jianbo Qiao*, Junru Jin*, Ding Wang*, Saisai Teng, Junyu Zhang, and 6 more authors
    Nature Communications, Jul 2025
  2. Neural Networks
    Taco-DDI: accurate prediction of drug-drug interaction events using graph transformers and dynamic co-attention matrices
    Jianbo Qiao, Xu Guo, Junru Jin, Ding Wang, Kefei Li, and 5 more authors
    Neural Networks, Jul 2025
  3. arXiv
    Materials Generation in the Era of Artificial Intelligence: A Comprehensive Survey
    Zhixun Li*, Bin Cao*, Rui Jiao*, Liang Wang*, Ding Wang, and 8 more authors
    Jul 2025
  4. Sci China Inf Sci
    Molecular pretraining models towards molecular property prediction
    Jianbo Qiao, Wenjia Gao, Junru Jin, Ding Wang, Xu Guo, and 2 more authors
    SCIS, Jul 2025

2024

2024

  1. NeurIPS 2024
    Beyond efficiency: Molecular data pruning for enhanced generalization
    Dingshuo Chen, Zhixun Li, Yuyan Ni, Guibin Zhang, Ding Wang, and 4 more authors
    NeurIPS, Jul 2024
  2. ACL findings
    Enhancing Temporal Knowledge Graph Forecasting with Large Language Models via Chain-of-History Reasoning
    Yuwei Xia*, Ding Wang*, Qiang Liu, Liang Wang, Shu Wu, and 1 more author
    ACL Findings, Jul 2024
  3. ACL findings
    Logical Closed Loop: Uncovering Object Hallucinations in Large Vision-Language Models
    Junfei Wu, Qiang Liu, Ding Wang, Jinghao Zhang, Shu Wu, and 2 more authors
    ACL Findings, Jul 2024

2023

2023

  1. Bioinformatics
    StructuralDPPIV: a novel deep learning model based on atom-structure for predicting dipeptidyl peptidase-IV inhibitory peptides
    Ding Wang, Junru Jin, Zhongshen Li, Yu Wang, Mushuang Fan, and 3 more authors
    Bioinformatics, Jul 2023