publications

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

2026

2026

  1. 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
    * Equal contribution
  2. 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. bioRxiv
    Melody: 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
    bioRxiv, Jul 2025
  2. 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
  3. 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
  4. 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
  5. 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