Xiangxiang Zeng

发表

Decision Tree Classification Model for Popularity Forecast of Chinese Colleges

Xiangxiang Zeng, You Li, Quan Zou, 2014, J. Appl. Math..

MOEA/HD: A Multiobjective Evolutionary Algorithm Based on Hierarchical Decomposition

Xiangxiang Zeng, Hang Xu, Wenhua Zeng, 2019, IEEE Transactions on Cybernetics.

Spiking Neural P Systems With Scheduled Synapses

Xiangxiang Zeng, H. Adorna, F. Cabarle, 2017, IEEE Transactions on NanoBioscience.

StackCPPred: a stacking and pairwise energy content-based prediction of cell-penetrating peptides and their uptake efficiency

Xiangxiang Zeng, Quan Zou, Lijun Cai, 2020, Bioinform..

Q. Zou, Xiangxiang Zeng, Guohua Wang, 2015, Briefings in functional genomics.

Identification and Analysis of Rice Yield-Related Candidate Genes by Walking on the Functional Network

Xiangxiang Zeng, Chun-yu Wang, Jingyi Jiang, 2018, Front. Plant Sci..

RicyerDB: A Database For Collecting Rice Yield-related Genes with Biological Analysis

Q. Zou, Xiangxiang Zeng, Jingyi Jiang, 2018, International journal of biological sciences.

Approaches for Recognizing Disease Genes Based on Network

Q. Zou, Xiangxiang Zeng, Chun-yu Wang, 2014, BioMed research international.

Accurate prediction of molecular targets using a self-supervised image representation learning framework

R. Nussinov, F. Cheng, Xiangxiang Zeng, 2022, Research square.

Predict the Relationship between Gene and Large Yellow Croaker’s Economic Traits

Xiangxiang Zeng, Xiangrong Liu, Kunhuang Han, 2017, Molecules.

Integrative approaches for predicting microRNA function and prioritizing disease-related microRNA using biological interaction networks

Q. Zou, Xiangxiang Zeng, Xuan Zhang, 2016, Briefings Bioinform..

MLysPRED: graph-based multi-view clustering and multi-dimensional normal distribution resampling techniques to predict multiple lysine sites

Q. Zhang, Xiangxiang Zeng, Xiangrong Liu, 2022, Briefings Bioinform..

KG-MTL: Knowledge Graph Enhanced Multi-Task Learning for Molecular Interaction

Xiangxiang Zeng, Tengfei Ma, Xuan Lin, 2023, IEEE Transactions on Knowledge and Data Engineering.

Deep generative molecular design reshapes drug discovery

R. Nussinov, F. Cheng, W. Cornell, 2022, Cell reports. Medicine.

Cooperative Membrane Damage as a Mechanism for Pentamidine-Antibiotic Mutual Sensitization.

Xiangxiang Zeng, Cailing Zhou, Wei Huang, 2022, ACS chemical biology.

Accurate prediction of molecular properties and drug targets using a self-supervised image representation learning framework

R. Nussinov, F. Cheng, Xiangxiang Zeng, 2022, Nature Machine Intelligence.

A novel antibacterial peptide recognition algorithm based on BERT

Xiangxiang Zeng, Xiangrong Liu, Lianming Zhao, 2021, Briefings Bioinform..

3DMol-Net: Learn 3D Molecular Representation Using Adaptive Graph Convolutional Network Based on Rotation Invariance

Xiangxiang Zeng, Zhihan Lv, Wei Wei, 2021, IEEE Journal of Biomedical and Health Informatics.

Improving tRNAscan‐SE Annotation Results via Ensemble Classifiers

Ying Ju, Xiangxiang Zeng, Zhiling Hong, 2015, Molecular informatics.

Repurpose Open Data to Discover Therapeutics for COVID-19 Using Deep Learning

George Karypis, Yadi Zhou, Feixiong Cheng, 2020, Journal of proteome research.

ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties

Aiping Lu, Xiangxiang Zeng, Tingjun Hou, 2021, Nucleic Acids Res..

Target identification among known drugs by deep learning from heterogeneous networks

Xiangxiang Zeng, Ruth Nussinov, Feixiong Cheng, 2020, Chemical science.

Sc-ncDNAPred: A Sequence-Based Predictor for Identifying Non-coding DNA in Saccharomyces cerevisiae

Xiangrong Liu, Xiangxiang Zeng, Wenying He, 2018, Front. Microbiol..

Complex Network Clustering by a Multi-objective Evolutionary Algorithm Based on Decomposition and Membrane Structure

Ying Ju, Songming Zhang, Xiangxiang Zeng, 2016, Scientific Reports.

Multiobjective Particle Swarm Optimization Based on Network Embedding for Complex Network Community Detection

Xiangxiang Zeng, Min Jiang, Xiangrong Liu, 2020, IEEE Transactions on Computational Social Systems.

A Parallel Workflow Pattern Modeling Using Spiking Neural P Systems With Colored Spikes

Xiangxiang Zeng, Pan Zheng, Alfonso Rodríguez-Patón, 2018, IEEE Transactions on NanoBioscience.

Drug repositioning based on the heterogeneous information fusion graph convolutional network

Xiangxiang Zeng, Xiangzheng Fu, Lijun Cai, 2021, Briefings Bioinform..

Graph embedding and Gaussian mixture variational autoencoder network for end-to-end analysis of single-cell RNA sequencing data

R. Nussinov, F. Cheng, Xiangxiang Zeng, 2023, Cell reports methods.

A heterogeneous graph cross-omics attention model for single-cell representation learning

Yue Liu, Junfeng Zhang, Wei Zhang, 2022, 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

scIMC: a platform for benchmarking comparison and visualization analysis of scRNA-seq data imputation methods

K. Nakai, Q. Zou, Xiangxiang Zeng, 2022, Nucleic acids research.

Deep learning for drug repurposing: Methods, databases, and applications

Philip S. Yu, R. Nussinov, F. Cheng, 2022, WIREs Computational Molecular Science.

Review of unsupervised pretraining strategies for molecules representation.

Xiangxiang Zeng, Yuansheng Liu, Yansen Su, 2021, Briefings in functional genomics.

Inferring MicroRNA-Disease Associations by Random Walk on a Heterogeneous Network with Multiple Data Sources

Xiangxiang Zeng, Yuansheng Liu, Quan Zou, 2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Prediction and validation of association between microRNAs and diseases by multipath methods.

Xiangxiang Zeng, Linqiang Pan, Yuanlu Liao, 2016, Biochimica et biophysica acta.

Prediction of MicroRNA-disease Associations by Matrix Completion

Ying Ju, Xiangxiang Zeng, Alfonso Rodríguez-Patón, 2016 .

A network-based approach to uncover microRNA-mediated disease comorbidities and potential pathobiological implications

Xiangxiang Zeng, Feixiong Cheng, Shuting Jin, 2019, npj Systems Biology and Applications.

Prediction of Potential Disease-Associated MicroRNAs by Using Neural Networks

Xiangxiang Zeng, Wen Wang, Quan Zou, 2019, Molecular therapy. Nucleic acids.

Meta-Path Methods for Prioritizing Candidate Disease miRNAs

Alfonso Rodríguez-Patón, Xuan Zhang, Quan Zou, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Computational methods for identifying the critical nodes in biological networks

Xiangrong Liu, Xiangxiang Zeng, Juan Liu, 2019, Briefings Bioinform..

A multi-task learning method for analyzing microbiota as cancer immunotherapy signal

Xiangxiang Zeng, Shuting Jin, Xiangrong Liu, 2020, 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

A comprehensive overview and evaluation of circular RNA detection tools

Wei Lin, Xiangxiang Zeng, Maozu Guo, 2017, PLoS Comput. Biol..

A weighted bilinear neural collaborative filtering approach for drug repositioning

Xiangxiang Zeng, Jialiang Yang, Yajie Meng, 2022, Briefings Bioinform..

Probability-based collaborative filtering model for predicting gene–disease associations

Q. Zou, Xiangxiang Zeng, Alfonso Rodríguez-Patón, 2017, BMC Medical Genomics.

Latent factor model with heterogeneous similarity regularization for predicting gene-disease associations

Xiangxiang Zeng, Quan Zou, Ningxiang Ding, 2016, 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Learning spatial structures of proteins improves protein-protein interaction prediction

Xiangxiang Zeng, Yuansheng Liu, Zhangming Niu, 2022, Briefings Bioinform..

deepDR: a network-based deep learning approach to in silico drug repositioning

Xiangrong Liu, Xiangxiang Zeng, Ruth Nussinov, 2019, Bioinform..

Application of deep learning methods in biological networks

Xiangxiang Zeng, Feng Xia, Wei Huang, 2020, Briefings Bioinform..

Deep Collaborative Filtering for Prediction of Disease Genes

Xiangxiang Zeng, Alfonso Rodríguez-Patón, Yinglai Lin, 2020, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Deep learning methods for biomedical named entity recognition: a survey and qualitative comparison

Xiangxiang Zeng, Yuansheng Liu, Bosheng Song, 2021, Briefings Bioinform..

Structural Hole Spanner in HumanNet Identifies Disease Gene and Drug targets

Xiangrong Liu, Xiangxiang Zeng, Alfonso Rodríguez-Patón, 2018, IEEE Access.

Identifying enhancer-promoter interactions with neural network based on pre-trained DNA vectors and attention mechanism

Xiangrong Liu, Xiangxiang Zeng, Leyi Wei, 2019, Bioinform..

MUFFIN: multi-scale feature fusion for drug-drug interaction prediction

Xiangxiang Zeng, Tengfei Ma, Bosheng Song, 2021, Bioinform..

iEnhancer-CLA: Self-attention-based interpretable model for enhancers and their strength prediction

Xiangxiang Zeng, Xiangzheng Fu, Lijun Cai, 2021, bioRxiv.

KGNN: Knowledge Graph Neural Network for Drug-Drug Interaction Prediction

Xiangxiang Zeng, Zhi-Jie Wang, Tengfei Ma, 2020, IJCAI.

Sequence clustering in bioinformatics: an empirical study.

Xingpeng Jiang, Xiangrong Liu, Xiangxiang Zeng, 2018, Briefings in bioinformatics.

Prediction of potential disease-associated microRNAs using structural perturbation method

Xiangxiang Zeng, Linyuan Lu, Li Liu, 2017, bioRxiv.

Drug Target Interaction Prediction using Multi-task Learning and Co-attention

Xiangxiang Zeng, Yun Liang, Chen Lin, 2019, 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Learning to Predict Drug Target Interaction From Missing Not at Random Labels

Chen Lin, Xiangrong Liu, Xiangxiang Zeng, 2019, IEEE Transactions on NanoBioscience.

Drug Target Interaction Prediction with Non-random Missing Labels

Chen Lin, Xiangxiang Zeng, Yun Liang, 2018, 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Predicting disease-associated circular RNAs using deep forests combined with positive-unlabeled learning methods

Xiangxiang Zeng, Wei Lin, Quan Zou, 2020, Briefings Bioinform..

Network-based prediction of drug-target interactions using an arbitrary-order proximity embedded deep forest

Xiangxiang Zeng, Jing Li, Ruth Nussinov, 2020, Bioinform..

Prediction of Drug–Gene Interaction by Using Metapath2vec

Xiangxiang Zeng, Chen Lin, Xiaoping Min, 2018, Front. Genet..

Machine learning on protein-protein interaction prediction: models, challenges and trends

Xiangxiang Zeng, Binshuang Zheng, Yuansheng Liu, 2023, Briefings Bioinform..

Deep learning in retrosynthesis planning: datasets, models and tools

Xiangxiang Zeng, Yuansheng Liu, Yansen Su, 2021, Briefings Bioinform..

Reducing false positive rate of docking-based virtual screening by active learning

Lei Wang, Aiping Lu, Xiangxiang Zeng, 2023, Briefings Bioinform..

Modality-DTA: Multimodality Fusion Strategy for Drug–Target Affinity Prediction

Xiangxiang Zeng, Yuansheng Liu, Weiqiang Lu, 2022, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Toward better drug discovery with knowledge graph.

Xiangxiang Zeng, Yuansheng Liu, Xiangzheng Fu, 2021, Current opinion in structural biology.

Identification of cytokine via an improved genetic algorithm

Xiangxiang Zeng, Quan Zou, Sisi Yuan, 2014, Frontiers of Computer Science.

HPTree: Reconstructing phylogenetic trees for ultra-large unaligned DNA sequences via NJ model and Hadoop

Xiangxiang Zeng, Quan Zou, Shixiang Wan, 2016, 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Details in the evaluation of circular RNA detection tools: Reply to Chen and Chuang

Xiangxiang Zeng, Wei Lin, Maozu Guo, 2019, PLoS Comput. Biol..

Motion generation of multi-legged robot in complex terrains by using estimation of distribution algorithm

Xiangxiang Zeng, Min Jiang, Zhongqiang Huang, 2017, 2017 IEEE Symposium Series on Computational Intelligence (SSCI).

Investigation and development of maize fused network analysis with multi-omics.

Xiangxiang Zeng, Quan Zou, Jing Jiang, 2019, Plant physiology and biochemistry : PPB.

DSN-DDI: an accurate and generalized framework for drug-drug interaction prediction by dual-view representation learning

Xiangxiang Zeng, Bin Shao, Tie-Yan Liu, 2023, Briefings Bioinform..

Multi-View Substructure Learning for Drug-Drug Interaction Prediction

Xiangxiang Zeng, Bin Shao, Tie-Yan Liu, 2022, ArXiv.

A novel molecular representation with BiGRU neural networks for learning atom

Xiangxiang Zeng, Zhe Quan, Xuan Lin, 2019, Briefings Bioinform..

Deep generative model for drug design from protein target sequence

Xiangxiang Zeng, Zixu Wang, Xiucai Ye, 2023, Journal of Cheminformatics.

Embedded Based Miniaturized Universal Electrochemical Sensing Platform

Xiangxiang Zeng, Jiming Guo, Jiamin Chen, 2016, J. Sensors.

Molecular language models: RNNs or transformer?

Xiangxiang Zeng, Zixu Wang, Xiucai Ye, 2023, Briefings in functional genomics.

preMLI: a pre-trained method to uncover microRNA-lncRNA potential interactions

Xiangxiang Zeng, Xiangrong Liu, Likun Jiang, 2021, Briefings Bioinform..

Investment behavior prediction in heterogeneous information network

Xiangxiang Zeng, You Li, Stephen C. H. Leung, 2016, Neurocomputing.

De novo generation of dual-target ligands using adversarial training and reinforcement learning

Xiangxiang Zeng, Mufei Li, Xiaoping Min, 2021, Briefings Bioinform..

iEnhancer-XG: interpretable sequence-based enhancers and their strength predictor

Xiangxiang Zeng, Lijun Cai, Xiangzheng Fu, 2020, Bioinform..

ITP-Pred: an interpretable method for predicting, therapeutic peptides with fused features low-dimension representation

Xiangxiang Zeng, Quan Zou, Li Wang, 2020, Briefings Bioinform..

Prediction of potential disease-associated microRNAs using structural perturbation method

Xiangxiang Zeng, Li Liu, Quan Zou, 2017, bioRxiv.

Dimensionality reduction and visualization of single-cell RNA-seq data with an improved deep variational autoencoder

Q. Zou, Xiangxiang Zeng, Yuansheng Liu, 2023, Briefings Bioinform..

Minirmd: accurate and fast duplicate removal tool for short reads via multiple minimizers

Xiangxiang Zeng, Quan Zou, Xiaocai Zhang, 2020, Bioinform..

A spatial-temporal gated attention module for molecular property prediction based on molecular geometry

Xiangxiang Zeng, Jianmin Wang, Junfeng Yao, 2021, Briefings Bioinform..

Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction

Philip S. Yu, Xiangxiang Zeng, Jian-Yu Shi, 2023, Briefings Bioinform..

Deep learning joint models for extracting entities and relations in biomedical: a survey and comparison

Xiangxiang Zeng, Yuansheng Liu, Chunhou Zheng, 2022, Briefings Bioinform..

nDNA-prot: identification of DNA-binding proteins based on unbalanced classification

Q. Zou, Xiangxiang Zeng, Yunfeng Wu, 2014, BMC Bioinformatics.

Pretata: predicting TATA binding proteins with novel features and dimensionality reduction strategy

Ying Ju, Xiangxiang Zeng, Jijun Tang, 2016, BMC Systems Biology.

HeTDR: Drug repositioning based on heterogeneous networks and text mining

Zhangming Niu, Xiangrong Liu, Wei Huang, 2021, Patterns.

Predicting enhancer-promoter interactions by deep learning and matching heuristic

Xiangxiang Zeng, Xiangrong Liu, Xiaoping Min, 2020, Briefings Bioinform..

KGNN: Knowledge Graph Neural Network for Drug-Drug Interaction Prediction

Xiangxiang Zeng, Tengfei Ma, Zhi-Jie Wang, 2020, IJCAI.

Review of Protein Subcellular Localization Prediction

Ying Ju, Xiangxiang Zeng, Quan Zou, 2014 .

Effectively Identifying Compound-Protein Interaction Using Graph Neural Representation

Philip S. Yu, Xiangxiang Zeng, Zhi-Jie Wang, 2022, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

GraphCPI: Graph Neural Representation Learning for Compound-Protein Interaction

Yan Guo, Xiangxiang Zeng, Zhe Quan, 2019, 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Prediction and Validation of Disease Genes Using HeteSim Scores

Xiangxiang Zeng, Yuansheng Liu, Quan Zou, 2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Active Semisupervised Model for Improving the Identification of Anticancer Peptides

Lijun Cai, Li Wang, Xiangzheng Fu, 2021, ACS omega.

Computing with viruses

Xiangxiang Zeng, Beizhan Wang, Mario J. Pérez-Jiménez, 2016, Theor. Comput. Sci..

DiffColor: Toward High Fidelity Text-Guided Image Colorization with Diffusion Models

Xiangxiang Zeng, Rongsheng Zhang, Yijun Wang, 2023, ArXiv.

A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications

Xiangxiang Zeng, Ruth Nussinov, Yadi Zhou, 2019, PLoS Comput. Biol..

Reconstructing evolutionary trees in parallel for massive sequences

Xiangxiang Zeng, Zhanshan Ma, Quan Zou, 2017, BMC Systems Biology.

Investigating Maize Yield-Related Genes in Multiple Omics Interaction Network Data

Xiangxiang Zeng, Quan Zou, Q. Zou, 2020, IEEE Transactions on NanoBioscience.

Probability-based collaborative filtering model for predicting gene–disease associations

Xiangxiang Zeng, Alfonso Rodríguez-Patón, Quan Zou, 2017, BMC Medical Genomics.

Iteratively collective prediction of disease-gene associations through the incomplete network

Xiangxiang Zeng, Alfonso Rodríguez-Patón, Xiangyi Meng, 2017, 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Pharmacophoric-constrained heterogeneous graph transformer model for molecular property prediction

Xiangxiang Zeng, Xiangrong Liu, Guang Yang, 2023, Communications Chemistry.

A drug information embedding method based on graph convolution neural network

Fei Li, Xiangxiang Zeng, Dongqing Wei, 2021, 2020 IEEE International Conference on E-health Networking, Application & Services (HEALTHCOM).

Using MOEA with Redistribution and Consensus Branches to Infer Phylogenies

Xiangrong Liu, Xiangxiang Zeng, Xiaoping Min, 2017, International journal of molecular sciences.

Target identi ﬁ cation among known drugs by deep learning from heterogeneous networks †

R. Nussinov, F. Cheng, Yadi Zhou, 2020 .

Molecular logic computation with debugging method

Yan Gao, Xiangrong Liu, Xiangxiang Zeng, 2015 .

Only Relevant Information Matters: Filtering Out Noisy Samples To Boost RL

Xiangxiang Zeng, Tengfei Ma, Zhi-Jie Wang, 2019, IJCAI.

Improving tRNAscan‐SE Annotation Results via Ensemble Classifiers

Q. Zou, Xiangxiang Zeng, Y. Ju, 2015, Molecular informatics.

WalkGAN: Network Representation Learning With Sequence-Based Generative Adversarial Networks

Xiangxiang Zeng, Taisong Jin, Min Jiang, 2022, IEEE Transactions on Neural Networks and Learning Systems.

Geometry-Based Molecular Generation With Deep Constrained Variational Autoencoder

Xiangxiang Zeng, Zhangming Niu, Wei Wei, 2022, IEEE Transactions on Neural Networks and Learning Systems.

PointDE: Protein Docking Evaluation Using 3D Point Cloud Neural Network

Xiangxiang Zeng, Xiaoping Min, Jun Zhang, 2023, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Integrative approaches for predicting microRNA function and prioritizing disease-related microRNA using biological interaction networks

Xiangxiang Zeng, Xuan Zhang, Quan Zou, 2016, Briefings Bioinform..

LagNet: Deep Lagrangian Mechanics for Plug-and-Play Molecular Representation Learning

Jinsong Su, Xiangxiang Zeng, Junfeng Yao, 2023, AAAI.

Asynchronous spiking neural P systems with rules on synapses

Xiangrong Liu, Xiangxiang Zeng, Tao Song, 2015, Neurocomputing.

Totally Dynamic Hypergraph Neural Networks

Xiangxiang Zeng, Guoqiu Wen, Junbo Ma, 2023, IJCAI.