Publications | HLiuLab

Chenpeng Yu, Xing Fang, Shiye Tian, Hui Liu*

A unified cross-attention model for predicting antigen binding specificity to both HLA and TCR molecules

Nature Machine Intelligence, 2025

PDF | Code | Server

Hui Liu*, Shikai Jin

Learning Cross-Domain Representations for Transferable Drug Perturbations on Single-Cell Transcriptional Responses

AAAI Conference on Artificial Intelligence (AAAI-25), 2025

PDF | Code

Kaishuan Huang, Hui Liu*

Identifying drug-resistant individual cells within tumors by semi-supervised transfer learning from bulk to single-cell transcriptome

Communications Biology, 2025

PDF | Code

Hui Liu, Wei Duan, Judong Luo.

Predicting Single-Cell Drug Sensitivity Utilizing Adaptive Weighted Features for Multi-Source Domain Adaptation

Journal of Biomedical and Health Informatics (JBHI), 2025

PDF | Code

Hui Liu, Yinpu Bai, Zhidong Wang, Shi Yin*, Cheng Gong*, Bin Wang*

Multimodal deep learning for predicting PD-L1 biomarker and clinical immunotherapy outcomes of esophageal cancer

Front. Immunol. , 11 March 2025

PDF | Code

Jia Zhai, Hui Liu*

Cross-domain feature disentanglement for interpretable modeling of tumor microenvironment impact on drug response

IEEE Journal of Biomedical and Health Informatics, 28(7):10.1109/JBHI.2024.3387930.2024.

PDF | Code

Wei Huang, Hui Liu*

Predicting single-cell cellular responses to perturbations using cycle consistency learning

Bioinformatics (ISMB2024) , 40, i462-i470. 2024

PDF | Code

Guobang Yu, Yi Zuo, Bin Wang*, Hui Liu*

Prediction of Tumor-Associated Macrophages and Immunotherapy Benefits Using Weakly Supervised Contrastive Learning in Breast Cancer Pathology Images

Journal of Imaging Informatics in Medicine. 37(6): 10.1007/s10278-024-01166-y.2024

PDF | Code

Hui Liu*, Xiaodong Xie , Bin Wang*

Deep learning infers clinically relevant protein levels and drug response in breast cancer from unannotated pathology images

npj breast cancer. 10:18. 10.1038/s41523-024-00620-y, 2024

PDF | Code

Judong Luo, Qianman Gao, Meihua Wang, Hui Liu*, Hong Zhu*

Single-cell and spatial transcriptome characterize coinhibitory cell-cell communications during histological progression of lung adenocarcinoma

Front. Immunol. 15-2024, 2024

PDF | Code

Fengfeng Cai, YuanYuan Li, Hui Liu*, Judong Luo*

Single-cell and Spatial Transcriptomic Analyses Implicate Formation of the Immunosuppressive Microenvironment during Breast Tumor Progression

The Journal of Immunolog, 2024, 213(9):1392-1401

PDF | Code

Hui Liu, Yang Zhang, Judong Luo*

Contrastive learning-based histopathological features infer molecular subtypes and clinical outcomes of breast cancer from unannotated whole slide images

Computers in Biology and Medicine. 170:10.1016/j.compbiomed.2024

PDF | Code

Lei Deng, Ziyu Fan, Xiaojun Xiao, Hui Liu*, Jiaxuan Zhang

Dual-Channel Heterogeneous Graph Neural Network for Predicting microRNA-Mediated Drug Sensitivity

Journal of Chemical Information and Modeling, 2022

PDF | Code

Yiming Fang, Xuejun Liu, Hui Liu*

Attention-aware contrastive learning for predicting T cell receptor-antigen binding specificity

Briefings in Bioinformatics, 2022

PDF | Code

Hui Liu, Yibiao Huang, Xuejun Liu*, Lei Deng*

Attention-wise masked graph contrastive learning for predicting molecular property

Briefings in Bioinformatics, 2022

PDF | Code

Haojie Huang, Gongming Zhou, Xuejun Liu, Lei Deng, Chen Wu, Dachuan Zhang, Hui Liu*

Contrastive learning-based computational histopathology predict differential expression of cancer driver genes

Briefings in Bioinformatics, 2022

PDF | Code

Mengxue Jiao, Hui Liu*, Xuejun Liu*

Transcriptional patterns reveal tumor histologic heterogeneity and immunotherapy response in lung adenocarcinoma

Frontiers in Immunology, 2022

PDF | Code

Yinfang Li, Ling Zou, Xuejun Liu, Judong Luo*, Hui Liu*

Identification of immune-related genes for establishment of prognostic index in hepatocellular carcinoma

Frontiers in Cell and Developmental Biology, 2021

PDF | Code

Jinxian Wang, Xuejun Liu, Siyuan Shen, Lei Deng, Hui Liu*

DeepDDS: deep graph neural network with attention mechanism to predict synergistic drug combinations

Briefings in Bioinformatics, 2022

PDF | Code

Lei Deng, Yibiao Huang, Xuejun Liu, Hui Liu*

Graph2MDA: a multi-modal variational graph embedding model for predicting microbe–drug associations

Bioinformatics, 2022

PDF | Code

Lei Deng, Hui Wu, Xuejun Liu,Hui Liu*

DeepD2V: A Novel Deep Learning-Based Framework for Predicting Transcription Factor Binding Sites from Combined DNA Sequence

International Journal of Molecular Sciences, 2021

PDF | Code

Hui Liu, Wenhao Zhang, Bo Zou, Jinxian Wang, Yuanyuan Deng, Lei Deng*

DrugCombDB: a comprehensive database of drug combinations toward the discovery of combinatorial therapy

Nucleic Acids Research, 2020

PDF | Code

Hui Liu, Wenhao Zhang, Yinglong Song, Lei Deng*, Shuigeng Zhou*

HNet-DNN: inferring new drug-disease associations with deep neural network based on heterogeneous network features

Journal of Chemical Information and Modeling, 2020

PDF | Code

Hui Liu, Wenhao Zhang, Lixia Nie, Xiancheng Ding, Judong Luo*, Ling Zou*

Predicting effective drug combinations using gradient tree boosting based on features extracted from drug-protein heterogeneous network

BMC Bioinformatics, 2019

PDF | Code

Hui Liu, Zhanzhan Cheng, Jianjiang Sun, Jihong Guan, Jie Zheng*, Shuigeng Zhou*

Sparse linear modeling kinase inhibition network for predicting combinatorial drug sensitivity in cancer cells

Current Bioinformatics, 2018

PDF | Code

Hui Liu, Wai Lam, Jihong Guan, Shuigeng Zhou*

A New Hybrid Method for Learning Bayesian Networks: Separation and Reunion

Knowledge-Based Systems, 2017

PDF | Code

Hui Liu, Fan Zhang, Shital Kumar Mishra, Shuigeng Zhou and Jie Zheng*

Knowledge-guided fuzzy logic modeling to infer cellular signaling networks from proteomic data

Scientific Reports, 2016

PDF | Code

Hui Liu, Mengmeng Guo, Ting Xue, Jihong Guan, Libo Luo, Ziheng Zhuang*

Screening lifespan-extending drugs in Caenorhabditis elegans via label propagation on drugprotein networks

BMC System Biology, 2016

PDF | Code

Hui Liu, Yinglong Song, Jihong Guan, Libo Luo, Ziheng Zhuang*

Inferring new indications for approved drugs via random walk on drug-disease heterogenous networks

BMC Bioinformatics, 2016

PDF | Code

Hui Liu, Jianjiang Sun, Jihong Guan, Jie Zheng and Shuigeng Zhou*

Improving compound protein interaction prediction by building up highly credible negative samples

Bioinformatics (ISMB/ECCB 2015), 2015

PDF | Code

Hui Liu, Ruichang Zhang, Wei Xiong, Jihong Guan, Ziheng Zhuang, Shuigeng Zhou*

A comparative evaluation on prediction methods of nucleosome positioning

Briefings in Bioinformatics, 2014

PDF | Code

Guo Jing, Hui Liu*, Zheng Jie*

SynLethDB: synthetic lethality database towards discovery of selective and sensitive anticancer drug targets

Nucleic Acids Research, 2016

PDF | Code

Si Cheng, Zhe Li, Wenhao Zhang, Zhiqiang Sun, Zhigang Fan, Judong Luo*, Hui Liu*

Identification of IL10RA by weighted correlation network analysis and in vitro validation of its association with prognosis of metastatic melanoma

Frontiers in Cell and Developmental Biology, 2020

PDF | Code

Lei Deng, Youzhi Liu, Yechuan Shi, Wenhao Zhang, Chun Yang, Hui Liu*

Deep neural networks for inferring binding sites of RNA-binding proteins by using distributed representations of RNA primary sequence and secondary structure

BMC Genomics, 2020

PDF | Code

@InProceedings{minghao24a,
                                                  author       = "Minghao Chen and Iro Laina and Andrea Vedaldi",
                                                  title        = "Training-Free Layout Control with Cross-Attention Guidance",
                                                  booktitle    = "Winter Conference on Applications of Computer Vision (WACV)",
                                                  year         = "2024",
                                                }

Yideng Cai, Wenhao Zhang, Wenyi Yang, Bo Gao, and Hui Liu*

Pathway-Guided Deep Neural Network toward Interpretable and Predictive Modeling of Drug Sensitivity

Journal of Chemical Information and Modeling, 2020

PDF | Code

Lei Deng, Guolun Zhong, Chenzhe Liu, Judong Luo, Hui Liu*

MADOKA: an ultrafast approach for large-scale protein structure similarity searching

BMC Bioinformatics, 2019

PDF | Code

Lei Deng, Wenyi Yang, Hui Liu*

PredPRBA: Prediction of Protein-RNA Binding Affinity Using Gradient Boosted Regression Trees

Frontiers in Genetics, 2019

PDF | Code

Lei Deng, Juan Pan, Xiaojie Xu, Wenyi Yang, Chuyao Liu and Hui Liu*

PDRLGB: precise DNA-binding residue prediction using a light gradient boosting machine

BMC Bioinformatics, 2018

PDF | Code

Lei Deng, Junqiang Wang, Yun Xiao, Zixiang Wang, Hui Liu*

Accurate prediction of protein-lncRNA interactions by diffusion and HeteSim features across heterogeneous network

BMC Bioinformatics, 2018

PDF | Code

Lei Deng, Xiaojie Xu, Hui Liu*

PredCSO: an ensemble method for prediction of S-sulfenylation sites in proteins

Molecular BioSystems, 2018

PDF | Code

Lei Deng, Hui Wu, Hui Liu*

D2VCB: A Hybrid Deep Neural Network for the Prediction of in-vivo Protein-DNA Binding from Combined DNA Sequence

Proceeding of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM2019), 2019

PDF | Code