A Hybrid Parallel Signature Matching Model for Network Security Applications Using SIMD GPU. - Chengkun Wu; Jianping Yin; Zhiping Cai; En Zhu; Jieren Cheng (APPT, 2009)

Detecting Distributed Denial of Service Attack Based on Multi-feature Fusion. - Jieren Cheng; Jianping Yin; Yun Liu; Zhiping Cai; Chengkun Wu (FGIT-SecTech, 2009)

An Efficient Pre-filtering Mechanism for Parallel Intrusion Detection Based on Many-Core GPU. - Chengkun Wu; Jianping Yin; Zhiping Cai; En Zhu; Jieren Cheng (FGIT-SecTech, 2009)

DDoS Attack Detection Method Based on Linear Prediction Model. - Jieren Cheng; Jianping Yin; Chengkun Wu; Boyun Zhang; Yun Liu (ICIC (1), 2009)

DDoS Attack Detection Using IP Address Feature Interaction. - Jieren Cheng; Jianping Yin; Yun Liu; Zhiping Cai; Chengkun Wu (INCoS, 2009)

A Parallel Fusion Method for Heterogeneous Multi-sensor Transportation Data. - Yingjie Xia; Chengkun Wu; Qing-Jie Kong; Zhenyu Shan; Li Kuang (MDAI, 2011)

PathNER: a tool for systematic identification of biological pathway mentions in the literature. - Chengkun Wu; Jean-Marc Schwartz; Goran Nenadic (BMC Syst. Biol., 2013)

Meeting report on YBPW 2014 (the 3rd Young Bioinformatics PIs Workshop). - Mengyi Sun; Bingyu Yan; Chengkun Wu; Xiaole Shirley Liu (Quant. Biol., 2014)

mAMBER: Accelerating Explicit Solvent Molecular Dynamic with Intel Xeon Phi Many-Integrated Core Coprocessors. - Xin Liu; Shaoliang Peng; Canqun Yang; Chengkun Wu; Haiqiang Wang; Qian Cheng; Weiliang Zhu; Jinan Wang (CCGRID, 2015)

The Challenge of Scaling Genome Big Data Analysis Software on TH-2 Supercomputer. - Shaoliang Peng; Xiangke Liao; Canqun Yang; Yutong Lu; Jie Liu 002; Yingbo Cui 001; Heng Wang; Chengkun Wu; Bingqiang Wang (CCGRID, 2015)

A Method to Accelerate GROMACS in Offload Mode on Tianhe-2 Supercomputer. - Haiqiang Wang; Shaoliang Peng; Xiaoqian Zhu; Chengkun Wu; Xin Liu; Qian Chen; Weiliang Zhu; Jinan Wang; Huaiyu Yang (CCGRID, 2015)

Large-Scale Neo-Heterogeneous Programming and Optimization of SNP Detection on Tianhe-2. - Yingbo Cui 001; Xiangke Liao; Shaoliang Peng; Yutong Lu; Canqun Yang; Bingqiang Wang; Chengkun Wu (ISC, 2015)

BWTCP: A Parallel Method for Constructing BWT in Large Collection of Genomic Reads. - Heng Wang; Shaoliang Peng; Yutong Lu; Chengkun Wu; Jiajun Wen 002; Jie Liu 002; Xiaoqian Zhu (ISC, 2015)

SupraBiology 2014: Promoting UK-China collaboration on Systems Biology and High Performance Computing. - Ettore Murabito; Riccardo Colombo; Chengkun Wu; Malkhey Verma; Samrina Rehman; Jacky L. Snoep; Shaoliang Peng; Naiyang Guan; Xiangke Liao; Hans V. Westerhoff (Quant. Biol., 2015)

Neo-hetergeneous Programming and Parallelized Optimization of a Human Genome Re-sequencing Analysis Software Pipeline on TH-2 Supercomputer. - Xiangke Liao; Shaoliang Peng; Yutong Lu; Yingbo Cui 001; Chengkun Wu; Heng Wang; Jiajun Wen 002 (Supercomput. Front. Innov., 2015)

Predicting Unknown Interactions Between Known Drugs and Targets via Matrix Completion. - Qing Liao 001; Naiyang Guan; Chengkun Wu; Qian Zhang 001 (PAKDD (1), 2016)

Automatic cytoplasm and nuclei segmentation for color cervical smear image using an efficient gap-search MRF. - Lili Zhao; Kuan Li; Mao Wang; Jianping Yin; En Zhu; Chengkun Wu; Siqi Wang 001; Chengzhang Zhu (Comput. Biol. Medicine, 2016)

High Performance Coordinate Descent Matrix Factorization for Recommender Systems. - Xi Yang 020; Jianbin Fang; Jing Chen 038; Chengkun Wu; Tao Tang 001; Kai Lu 001 (Conf. Computing Frontiers, 2017)

SVRG with adaptive epoch size. - Erxue Min; Yawei Zhao; Jun Long; Chengkun Wu; Kuan Li; Jianping Yin (IJCNN, 2017)

Dependency-based long short term memory network for drug-drug interaction extraction. - Wei Wang 130; Xi Yang 020; Canqun Yang; Xiaowei Guo; Xiang Zhang 008; Chengkun Wu (BMC Bioinform., 2017)

GTZ: a fast compression and cloud transmission tool optimized for FASTQ files. - Yuting Xing; Gen Li 007; Zhenguo Wang; Bolun Feng; Zhuo Song; Chengkun Wu (BMC Bioinform., 2017)

P-Hint-Hunt: a deep parallelized whole genome DNA methylation detection tool. - Shaoliang Peng; Shunyun Yang; Ming Gao; Xiangke Liao; Jie Liu 002; Canqun Yang; Chengkun Wu; Wenqiang Yu (BMC Genom., 2017)

Collaborative Subspace Graph Hashing for Cross-modal Retrieval. - Xiang Zhang 008; Guohua Dong; Yimo Du; Chengkun Wu; Zhigang Luo; Canqun Yang (ICMR, 2018)

Constructing a database for the relations between CNV and human genetic diseases via systematic text mining. - Xi Yang 020; Zhuo Song; Chengkun Wu; Wei Wang 130; Gen Li 007; Wei Zhang 027; Lingqian Wu; Kai Lu 001 (BMC Bioinform., 2018)

Distributed and asynchronous Stochastic Gradient Descent with variance reduction. - Yuewei Ming; Yawei Zhao; Chengkun Wu; Kuan Li; Jianping Yin (Neurocomputing, 2018)

mSNP: A Massively Parallel Algorithm for Large-Scale SNP Detection. - Yingbo Cui 001; Shaoliang Peng; Yutong Lu; Xiaoqian Zhu; Bingqiang Wang; Chengkun Wu; Xiangke Liao (IEEE Trans. Parallel Distributed Syst., 2018)

Parallel Computing for Large-Scale Author Name Disambiguation in MEDLINE. - Anyao Tang; Chengkun Wu; Jie Liu 002; Wei Wang 130; Xi Yang 020; Yuting Xing (HPCC/SmartCity/DSS, 2019)

CGINet: graph convolutional network-based model for identifying chemical-gene interaction in an integrated multi-relational graph. - Wei Wang; Xi Yang 020; Chengkun Wu; Canqun Yang (BMC Bioinform., 2020)

Drug-drug interaction extraction from biomedical texts based on multi-attention mechanism. - Chengkun Wu; Wei Wang; Xi Yang 020; Canqun Yang (ICBRA, 2021)

Efficient Distributed Stochastic Gradient Descent Through Gaussian Averaging. - Kaifan Hu; Chengkun Wu; En Zhu (ICAIS (1), 2021)

Joint motion context and clip augmentation for spatio-temporal action detection. - Xurui Ma; Xiang Zhang 008; Chengkun Wu; Chuanfu Xu; Jie Liu 002; Zhigang Luo (ICMV, 2021)

AA-LSTM: An Adversarial Autoencoder Joint Model for Prediction of Equipment Remaining Useful Life. - Dong Zhu; Chengkun Wu; Chuanfu Xu; Zhenghua Wang (PAKDD (1), 2021)

Learning to SMILES: BAN-based strategies to improve latent representation learning from molecules. - Chengkun Wu; Xiao-Chen Zhang; Zhi-Jiang Yang; Ai-Ping Lu; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2021)

MG-BERT: leveraging unsupervised atomic representation learning for molecular property prediction. - Xiao-Chen Zhang; Chengkun Wu; Zhi-Jiang Yang; Zhen-Xing Wu; Jiacai Yi; Chang-Yu Hsieh; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2021)

Mining microbe-disease interactions from literature via a transfer learning model. - Chengkun Wu; Xinyi Xiao; Canqun Yang; Jinxiang Chen; Jiacai Yi; Yanlong Qiu (BMC Bioinform., 2021)

Mining a stroke knowledge graph from literature. - Xi Yang 020; Chengkun Wu; Goran Nenadic; Wei Wang 169; Kai Lu 001 (BMC Bioinform., 2021)

Correction to: Mining a stroke knowledge graph from literature. - Xi Yang 020; Chengkun Wu; Goran Nenadic; Wei Wang 169; Kai Lu 001 (BMC Bioinform., 2021)

ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties. - Guo-Li Xiong; Zhenxing Wu; Jiacai Yi; Li Fu; Zhi-Jiang Yang; Chang-Yu Hsieh; Mingzhu Yin; Xiangxiang Zeng; Chengkun Wu; Ai-Ping Lu; Xiang Chen; Tingjun Hou; et al. (Nucleic Acids Res., 2021)

Deep Anomaly Discovery from Unlabeled Videos via Normality Advantage and Self-Paced Refinement. - Guang Yu; Siqi Wang 001; Zhiping Cai; Xinwang Liu 002; Chuanfu Xu; Chengkun Wu (CVPR, 2022)

Stgat-Mad : Spatial-Temporal Graph Attention Network For Multivariate Time Series Anomaly Detection. - Jun Zhan; Siqi Wang 001; Xiandong Ma; Chengkun Wu; Canqun Yang; Detian Zeng; Shilin Wang (ICASSP, 2022)

An Unsupervised Short- and Long-Term Mask Representation for Multivariate Time Series Anomaly Detection. - Qiucheng Miao; Chuanfu Xu; Jun Zhan; Dong Zhu; Chengkun Wu (ICONIP (6), 2022)

Effective Video Abnormal Event Detection by Learning A Consistency-Aware High-Level Feature Extractor. - Guang Yu; Siqi Wang 001; Zhiping Cai; Xinwang Liu 002; Chengkun Wu (ACM Multimedia, 2022)

BioNet: a large-scale and heterogeneous biological network model for interaction prediction with graph convolution. - Xi Yang 020; Wei Wang; Jing-Lun Ma; Yan-Long Qiu; Kai Lu 001; Dong-Sheng Cao 001; Chengkun Wu (Briefings Bioinform., 2022)

ABC-Net: a divide-and-conquer based deep learning architecture for SMILES recognition from molecular images. - Xiao-Chen Zhang; Jiacai Yi; Guo-Ping Yang; Chengkun Wu; Tingjun Hou; Dong-Sheng Cao 001 (Briefings Bioinform., 2022)

DeepKG: an end-to-end deep learning-based workflow for biomedical knowledge graph extraction, optimization and applications. - Zongren Li; Qin Zhong; Jing Yang; Yongjie Duan; Wenjun Wang; Chengkun Wu; Kunlun He (Bioinform., 2022)

MICER: a pre-trained encoder-decoder architecture for molecular image captioning. - Jiacai Yi; Chengkun Wu; Xiao-Chen Zhang; Xinyi Xiao; Yanlong Qiu; Wentao Zhao; Tingjun Hou; Dong-Sheng Cao 001 (Bioinform., 2022)

ParaCopasi: A package for parallel biochemical simulation and analysis. - Lihuan Yuan; Chengkun Wu; Xiaowei Guo; Canqun Yang (J. Comput. Chem., 2022)

Exploring the Binding Affinity and Mechanism between ACE2 and the Trimers of Delta and Omicron Spike Proteins by Molecular Dynamics Simulation and Bioassay. - Liping Zhou; Tingting Liu; Mengxia Mo; Yulong Shi; Leyun Wu; Yishui Li; Qiuping Qin; Weiliang Zhu; Chengkun Wu; Likun Gong; Zhijian Xu (J. Chem. Inf. Model., 2022)

DDInter: an online drug-drug interaction database towards improving clinical decision-making and patient safety. - Guo-Li Xiong; Zhi-Jiang Yang; Jiacai Yi; Ningning Wang; Lei Wang; Huimin Zhu; Chengkun Wu; Ai-Ping Lu; Xiang Chen; Shao Liu; Tingjun Hou; Dongsheng Cao 001 (Nucleic Acids Res., 2022)

A risk factor attention-based model for cardiovascular disease prediction. - Yan-Long Qiu; Wei Wang; Chengkun Wu; Zhichang Zhang (BMC Bioinform., 2022)

DrugProtKGE: Weakly Supervised Knowledge Graph Embedding for Highly-Effective Drug-Protein Interaction Representation. - Yanlong Qiu; Siqi Wang 001; Xi Yang 020; Xinyuan Qiu; Chengkun Wu; Yingbo Cui 001; Canqun Yang (BIBM, 2023)

BioNet+: A Comprehensive Interaction Model of Finding Therapeutics for Diseases with Graph Deep Learning. - Jing-Lun Ma; Yanlong Qiu; Canqun Yang; Chengkun Wu (HPCC/DSS/SmartCity/DependSys, 2023)

Free energy perturbation-based large-scale virtual screening for effective drug discovery against COVID-19. - Zhe Li 029; Chengkun Wu; Yishui Li; Runduo Liu; Kai Lu 001; Ruibo Wang; Jie Liu 002; Chunye Gong; Canqun Yang; Xin Wang 111; Chang-Guo Zhan; Hai-Bin Luo (Int. J. High Perform. Comput. Appl., 2023)

An Open Source Graph-Based Weighted Cycle Closure Method for Relative Binding Free Energy Calculations. - Yishui Li; Runduo Liu; Jie Liu 002; Haibin Luo; Chengkun Wu; Zhe Li 029 (J. Chem. Inf. Model., 2023)

Molecular dynamics study on the behavior and binding mechanism of target protein Transgelin-2 with its agonist TSG12 for anti-asthma drug discovery. - Leyun Wu; Guangpu Wang; Liping Zhou; Mengxia Mo; Yulong Shi; Bo Li; Leimiao Yin; Qiang Zhao; Yongqing Yang; Chengkun Wu; Zhijian Xu; Weiliang Zhu (Comput. Biol. Medicine, 2023)

Exploring Natural Language Processing Model Acceleration in Molecular Dynamics Simulation Using High-Performance Computing and Machine Learning. - Qi Du; Feng Wang; Hui Huang; Heng Wan; Xiaoyu Wu; Chengkun Wu (BIBM, 2024)

ChemMORT: an automatic ADMET optimization platform using deep learning and multi-objective particle swarm optimization. - Jiacai Yi; Zi-Yi Yang; Wen-Tao Zhao; Zhi-Jiang Yang; Xiao-Chen Zhang; Chengkun Wu; Ai-Ping Lu; Dong-Sheng Cao 001 (Briefings Bioinform., 2024)

Pre-training molecular representation model with spatial geometry for property prediction. - Yishui Li; Wei Wang 130; Jie Liu 002; Chengkun Wu (Comput. Biol. Chem., 2024)

HFN: Heterogeneous feature network for multivariate time series anomaly detection. - Jun Zhan; Chengkun Wu; Canqun Yang; Qiucheng Miao; Xiandong Ma (Inf. Sci., 2024)

Long-Tailed Recognition via Multi-sampling Classifier Fusion with Frozen CLIP. - Yilou Zhang; Yunjie Liu; Yuan Zhao; Chengkun Wu (ICIC (12), 2025)