Xiangxiang Zeng

261 papers A* 14A 1B 3C 1Journal 207Unranked 35

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	A deep adversarial network model for multi-task analysis of single-cell omics data. Briefings Bioinform. Junlin Xu, Cheng Guo, Yajie Meng, Shuting Jin, Changcheng Lu, Zilong Zhang, Feifei Cui, Xiangzheng Fu, Quan Zou, Tian Tian, Xiangxiang Zeng
2026	J	`jnl`	DyACE: Dynamic Algorithm Co-evolution for Online Automated Heuristic Design with Large Language Model. CoRR Guidong Lu, Yiping Liu, Xiangxiang Zeng
2026	A*	`conf`	Expert-Inspired Multi-Agent Coordination for Multi-Objective Molecular Optimization. AAAI Daojian Zeng, Tianle Li, Jiahao Yang, Jiacai Yi, Xieping Gao, Lincheng Jiang, Tengfei Ma, Xiangxiang Zeng
2026	J	`jnl`	FKSUDDAPre: A drug-disease association prediction framework based on F-TEST feature selection and AMDKSU resampling with interpretability analysis. PLoS Comput. Biol. Yun Zuo, Chenyi Zhang, Ge Hua, Qiao Ning, Xiangrong Liu, Xiangxiang Zeng, Zhaohong Deng
2026	J	`jnl`	ImageDDI: Image-enhanced molecular motif sequence representation for drug-drug interaction prediction. Inf. Fusion Yuqin He, Tengfei Ma, Chaoyi Li, Pengsen Ma, Hongxin Xiang, Jianmin Wang, Yiping Liu, Bosheng Song, Xiangxiang Zeng
2026	J	`jnl`	LatentChem: From Textual CoT to Latent Thinking in Chemical Reasoning. CoRR Xinwu Ye, Yicheng Mao, Jia Zhang, Yimeng Liu, Li Hao, Fang Wu, Zhiwei Li, Yuxuan Liao, Zehong Wang, Zhiyuan Liu, Zhenfei Yin, Li Yuan, Philip Torr, Huan Sun, Xiangxiang Zeng, Mengdi Wang, Le Cong, Shenghua Gao, Xiangru Tang
2026	J	`jnl`	Leveraging Adaptive Evolutionary Optimization for Drug Molecular Design Involving Many Properties. Big Data Min. Anal. Xin Xia, Xiangxiang Zeng, Xing-yi Zhang, Chunhou Zheng, Ya-Jie Zhang, Yansen Su
2026	J	`jnl`	Rethinking Genomic Modeling Through Optical Character Recognition. CoRR Hongxin Xiang, Pengsen Ma, Yunkang Cao, Di Yu, Haowen Chen, Xinyu Yang, Xiangxiang Zeng
2026	J	`jnl`	Sparse Task Vector Mixup with Hypernetworks for Efficient Knowledge Transfer in Whole-Slide Image Prognosis. CoRR Pei Liu, Xiangxiang Zeng, Tengfei Ma, Yucheng Xing, Xuanbai Ren, Yiping Liu
2026	J	`jnl`	Surface-based Molecular Design with Multi-modal Flow Matching. CoRR Fang Wu, Zhengyuan Zhou, Shuting Jin, Xiangxiang Zeng, Jure Leskovec, Jinbo Xu
2026	A*	`conf`	TRACE: Transformation-Aware Graph Refinement for Reaction Condition Prediction. AAAI Yujie Chen, Tengfei Ma, Yuansheng Liu, Leyi Wei, Shu Wu, Dongsheng Cao, Yiping Liu, Xiangxiang Zeng
2025	J	`jnl`	AJGM: joint learning of heterogeneous gene networks with adaptive graphical model. Bioinform. Shunqi Yang, Lingyi Hu, Pengzhou Chen, Xiangxiang Zeng, Shanjun Mao
2025	J	`jnl`	AdaptMol: Adaptive Fusion from Sequence String to Topological Structure for Few-shot Drug Discovery. CoRR Yifan Dai, Xuanbai Ren, Tengfei Ma, Qipeng Yan, Yiping Liu, Yuansheng Liu, Xiangxiang Zeng
2025	A*	`conf`	An All-Atom Generative Model for Designing Protein Complexes. ICML Ruizhe Chen, Dongyu Xue, Xiangxin Zhou, Zaixiang Zheng, Xiangxiang Zeng, Quanquan Gu
2025	J	`jnl`	An All-Atom Generative Model for Designing Protein Complexes. CoRR Ruizhe Chen, Dongyu Xue, Xiangxin Zhou, Zaixiang Zheng, Xiangxiang Zeng, Quanquan Gu
2025	J	`jnl`	CMOMO: a deep multi-objective optimization framework for constrained molecular multi-property optimization. Briefings Bioinform. Xin Xia, Yajie Zhang, Xiangxiang Zeng, Xing-yi Zhang, Chun-Hou Zheng, Yansen Su
2025	J	`jnl`	Deep Generative Models for Therapeutic Peptide Discovery: A Comprehensive Review. ACM Comput. Surv. Leshan Lai, Yuansheng Liu, Bosheng Song, Keqin Li, Xiangxiang Zeng
2025	J	`jnl`	DeepDR: an integrated deep-learning model web server for drug repositioning. CoRR Shuting Jin, Yi Jiang, Yimin Liu, Tengfei Ma, Dong-Sheng Cao, Leyi Wei, Xiangrong Liu, Xiangxiang Zeng
2025	J	`jnl`	DrugAssist: a large language model for molecule optimization. Briefings Bioinform. Geyan Ye, Xibao Cai, Houtim Lai, Xing Wang, Junhong Huang, Longyue Wang, Wei Liu, Xiangxiang Zeng
2025	J	`jnl`	EDBench: Large-Scale Electron Density Data for Molecular Modeling. CoRR Hongxin Xiang, Ke Li, Mingquan Liu, Zhixiang Cheng, Bin Yao, Wenjie Du, Jun Xia, Li Zeng, Xin Jin, Xiangxiang Zeng
2025	A*	`conf`	Electron Density-enhanced Molecular Geometry Learning. IJCAI Hongxin Xiang, Jun Xia, Xin Jin, Wenjie Du, Li Zeng, Xiangxiang Zeng
2025	A*	`conf`	Enhancing Chemical Reaction and Retrosynthesis Prediction with Large Language Model and Dual-task Learning. IJCAI Xuan Lin, Qingrui Liu, Hongxin Xiang, Daojian Zeng, Xiangxiang Zeng
2025	J	`jnl`	Enhancing Chemical Reaction and Retrosynthesis Prediction with Large Language Model and Dual-task Learning. CoRR Xuan Lin, Qingrui Liu, Hongxin Xiang, Daojian Zeng, Xiangxiang Zeng
2025	J	`jnl`	Enhancing Molecular Property Prediction with Knowledge from Large Language Models. CoRR Peng Zhou, Lai Hou Tim, Zhixiang Cheng, Kun Xie, Chaoyi Li, Wei Liu, Xiangxiang Zeng
2025	—	`conf`	From Knowledge to Treatment: Large Language Model Assisted Biomedical Concept Representation for Drug Repurposing. EMNLP (Findings) Chengrui Xiang, Tengfei Ma, Xiangzheng Fu, Yiping Liu, Bosheng Song, Xiangxiang Zeng
2025	J	`jnl`	From Knowledge to Treatment: Large Language Model Assisted Biomedical Concept Representation for Drug Repurposing. CoRR Chengrui Xiang, Tengfei Ma, Xiangzheng Fu, Yiping Liu, Bosheng Song, Xiangxiang Zeng
2025	J	`jnl`	HyperACP: A cutting-edge hybrid framework for anticancer peptide classification via scalable feature extraction and adaptive neighbor-based synthesis. PLoS Comput. Biol. Bangyi Zhang, Yun Zuo, Jun Wan, Jiayue Liu, Xiangrong Liu, Xiangxiang Zeng, Zhaohong Deng
2025	J	`jnl`	Image-based generation for molecule design with SketchMol. Nat. Mac. Intell. Zixu Wang, Yangyang Chen, Pengsen Ma, Zhou Yu, Jianmin Wang, Yuansheng Liu, Xiucai Ye, Tetsuya Sakurai, Xiangxiang Zeng
2025	J	`jnl`	ImageDDI: Image-enhanced Molecular Motif Sequence Representation for Drug-Drug Interaction Prediction. CoRR Yuqin He, Tengfei Ma, Chaoyi Li, Pengsen Ma, Hongxin Xiang, Jianmin Wang, Yiping Liu, Bosheng Song, Xiangxiang Zeng
2025	—	`conf`	Large Language and Protein Assistant for Protein-Protein Interactions Prediction. ACL (1) Peng Zhou, Pengsen Ma, Jianmin Wang, Xibao Cai, Haitao Huang, Wei Liu, Longyue Wang, Lai Hou Tim, Xiangxiang Zeng
2025	J	`jnl`	Leveraging Induced Transferable Binding Principles for Associative Prediction of Novel Drug-Target Interactions. CoRR Xiaoqing Lian, Jie Zhu, Tianxu Lv, Shiyun Nie, Hang Fan, Guosheng Wu, Yunjun Ge, Lihua Li, Xiangxiang Zeng, Xiang Pan
2025	J	`jnl`	MOFormer: navigating the antimicrobial peptide design space with Pareto-based multi-objective transformer. Briefings Bioinform. Li Wang, Xiangzheng Fu, Jiahao Yang, Xinyi Zhang, Xiucai Ye, Tetsuya Sakurai, Xiangxiang Zeng, Yiping Liu
2025	J	`jnl`	MlyPredCSED: based on extreme point deviation compensated clustering combined with cross-scale convolutional neural networks to predict multiple lysine sites in human. Briefings Bioinform. Yun Zuo, Xingze Fang, Jiankang Chen, Jiayi Ji, Yuwen Li, Zeyu Wu, Xiangrong Liu, Xiangxiang Zeng, Zhaohong Deng, Hongwei Yin, Anjing Zhao
2025	J	`jnl`	Molecular Dynamics-Powered Hierarchical Geometric Deep Learning Framework for Protein-Ligand Interaction. IEEE Trans. Comput. Biol. Bioinform. Mingquan Liu, Shuting Jin, Houtim Lai, Longyue Wang, Jianmin Wang, Zhixiang Cheng, Xiangxiang Zeng
2025	J	`jnl`	Multi-Modal Deep Representation Learning Accurately Identifies and Interprets Drug-Target Interactions. IEEE J. Biomed. Health Informatics Jiayue Hu, Yuhang Liu, Xiangxiang Zeng, Quan Zou, Ran Su, Leyi Wei
2025	A*	`conf`	Multi-Objective Molecular Design Through Learning Latent Pareto Set. AAAI Yiping Liu, Jiahao Yang, Xuanbai Ren, Xinyi Zhang, Yuansheng Liu, Bosheng Song, Xiangxiang Zeng, Hisao Ishibuchi
2025	J	`jnl`	Multiview Deep Learning-Based Molecule Design and Structural Optimization Accelerates Inhibitor Discover. IEEE Trans. Neural Networks Learn. Syst. Chao Pang, Yu Wang, Yi Jiang, Ruheng Wang, Xiaojun Yao, Quan Zou, Xiangxiang Zeng, Ran Su, Leyi Wei
2025	J	`jnl`	PKAN: Leveraging Kolmogorov-Arnold Networks and Multi-Modal Learning for Peptide Prediction With Advanced Language Models. IEEE J. Biomed. Health Informatics Li Wang, Xiangzheng Fu, Xiucai Ye, Tetsuya Sakurai, Xiangxiang Zeng, Yiping Liu
2025	J	`jnl`	PreAIS: Prediction of A-to-I editing sites based on DNN-CNN deep learning models. Comput. Biol. Chem. Xingze Fang, Yun Zuo, Youxu Tan, Xiangrong Liu, Xiangxiang Zeng, Zhaohong Deng
2025	J	`jnl`	Predicting Drug-Drug Interaction via Dual-Drug Visual Representation. J. Chem. Inf. Model. Lingxuan Xie, Tengfei Ma, Yuqin He, Yiping Liu, Xiangxiang Zeng
2025	J	`jnl`	Pretraining graph transformer for molecular representation with fusion of multimodal information. Inf. Fusion Ruizhe Chen, Chunyan Li, Longyue Wang, Mingquan Liu, Shugao Chen, Jiahao Yang, Xiangxiang Zeng
2025	J	`jnl`	Quality Scores Compression of Genomic Sequencing Data: A Comprehensive Review and Performance Evaluation. IEEE Trans. Comput. Biol. Bioinform. Yuansheng Liu, Tao Tang, Zexuan Zhu, Xiangxiang Zeng, Quan Zou, Keqin Li
2025	J	`jnl`	SQ-DiffuPep: A multimodal information-guided quantitative latent diffusion model for antimicrobial peptide discovery. Inf. Fusion Luoda Tan, Li Wang, Xuanbai Ren, Quan Zou, Xiaojun Yao, Xiangxiang Zeng, Xiangzheng Fu
2025	J	`jnl`	Self-supervised learning in drug discovery. Sci. China Inf. Sci. Yangyang Chen, Zixu Wang, Jianmin Wang, Yanyi Chu, Qingpeng Zhang, Zhong Alan Li, Xiangxiang Zeng
2025	—	`conf`	Surface-based Molecular Design with Multi-modal Flow Matching. KDD (2) Fang Wu, Zhengyuan Zhou, Shuting Jin, Xiangxiang Zeng, Jure Leskovec, Jinbo Xu
2025	A*	`conf`	S²DN: Learning to Denoise Unconvincing Knowledge for Inductive Knowledge Graph Completion. AAAI Tengfei Ma, Yujie Chen, Liang Wang, Xuan Lin, Bosheng Song, Xiangxiang Zeng
2025	J	`jnl`	The computational properties of P systems with mutative membrane structures. Inf. Comput. Bosheng Song, Chuanlong Hu, David Orellana-Martín, Antonio Ramírez-de-Arellano, Mario J. Pérez-Jiménez, Xiangxiang Zeng
2025	A*	`conf`	Towards Synergistic Path-based Explanations for Knowledge Graph Completion: Exploration and Evaluation. ICLR Tengfei Ma, Xiang Song, Wen Tao, Mufei Li, Jiani Zhang, Xiaoqin Pan, Yijun Wang, Bosheng Song, Xiangxiang Zeng
2025	J	`jnl`	Towards Understanding and Harnessing the Transferability of Prognostic Knowledge in Computational Pathology. CoRR Pei Liu, Luping Ji, Jiaxiang Gou, Xiangxiang Zeng
2025	—	`conf`	VQH-AM: Vector Quantization-Augmented Heterogeneous Graph Learning for Antibody Affinity Maturation Prediction. BIBM Zhuowen Zhen, Tengfei Ma, Jiaxuan Li, Dashun Zheng, Patrick Cheong-Iao Pang, Yiping Liu, Xiangxiang Zeng
2025	J	`jnl`	Wireless spiking neural P systems. J. Membr. Comput. David Orellana-Martín, Francis George C. Cabarle, Prithwineel Paul, Xiangxiang Zeng, Rudolf Freund
2025	J	`jnl`	ZeroGEN: leveraging language models for zero-shot ligand design from protein sequences. Bioinform. Yangyang Chen, Zixu Wang, Pengyong Li, Li Zeng, Xiangxiang Zeng, Lei Xu
2024	J	`jnl`	A deep learning approach for rational ligand generation with toxicity control via reactive building blocks. Nat. Comput. Sci. Pengyong Li, Kaihao Zhang, Tianxiao Liu, Ruiqiang Lu, Yangyang Chen, Xiaojun Yao, Lin Gao, Xiangxiang Zeng
2024	J	`jnl`	AMGDTI: drug-target interaction prediction based on adaptive meta-graph learning in heterogeneous network. Briefings Bioinform. Yansen Su, Zhiyang Hu, Fei Wang, Yannan Bin, Chun-Hou Zheng, Haitao Li, Haowen Chen, Xiangxiang Zeng
2024	A*	`conf`	An Image-enhanced Molecular Graph Representation Learning Framework. IJCAI Hongxin Xiang, Shuting Jin, Jun Xia, Man Zhou, Jianmin Wang, Li Zeng, Xiangxiang Zeng
2024	J	`jnl`	Anti-symmetric framework for balanced learning of protein-protein interactions. Bioinform. Tao Tang, Tianyang Li, Weizhuo Li, Xiaofeng Cao, Yuansheng Liu, Xiangxiang Zeng
2024	J	`jnl`	Attribute-guided prototype network for few-shot molecular property prediction. Briefings Bioinform. Linlin Hou, Hongxin Xiang, Xiangxiang Zeng, Dongsheng Cao, Li Zeng, Bosheng Song
2024	J	`jnl`	Balancing property optimization and constraint satisfaction for constrained multi-property molecular optimization. CoRR Xin Xia, Ya-Jie Zhang, Xiangxiang Zeng, Xingyi Zhang, Chun-Hou Zheng, Yansen Su
2024	—	`conf`	CSCL-DTI: predicting drug-target interaction through cross-view and self-supervised contrastive learning. BIBM Xuan Lin, Xi Zhang, Zu-Guo Yu, Yahui Long, Xiangxiang Zeng, Philip S. Yu
2024	—	`conf`	Compound-Protein Interaction Prediction with Sparse Perturbation-Aware Attention. ICIC (LNBI 2) Qiwen Wang, Chen Lin, Wei Su, Liang Xiao, Xiangxiang Zeng
2024	J	`jnl`	Deep Generative Models in J. Chem. Inf. Model. Chao Pang, Jianbo Qiao, Xiangxiang Zeng, Quan Zou, Leyi Wei
2024	J	`jnl`	DrugAssist: A Large Language Model for Molecule Optimization. CoRR Geyan Ye, Xibao Cai, Houtim Lai, Xing Wang, Junhong Huang, Longyue Wang, Wei Liu, Xiangxiang Zeng
2024	J	`jnl`	Dual-View Learning Based on Images and Sequences for Molecular Property Prediction. IEEE J. Biomed. Health Informatics Xiang Zhang, Hongxin Xiang, Xixi Yang, Jingxin Dong, Xiangzheng Fu, Xiangxiang Zeng, Haowen Chen, Keqin Li
2024	J	`jnl`	DualSyn: A dual-level feature interaction method to predict synergistic drug combinations. Expert Syst. Appl. Zehui Chen, Zimeng Li, Xiangzhen Shen, Yuansheng Liu, Xuan Lin, Daojian Zeng, Xiangxiang Zeng
2024	J	`jnl`	Dynamic threshold spiking neural P systems with weights and multiple channels. Theor. Comput. Sci. Yanyan Li, Bosheng Song, Yuansheng Liu, Xiangxiang Zeng, Shengye Huang
2024	J	`jnl`	ECD-CDGI: An efficient energy-constrained diffusion model for cancer driver gene identification. PLoS Comput. Biol. Tao Wang, Linlin Zhuo, Yifan Chen, Xiangzheng Fu, Xiangxiang Zeng, Quan Zou
2024	J	`jnl`	Effective drug-target affinity prediction via generative active learning. Inf. Sci. Yuansheng Liu, Zhenran Zhou, Xiaofeng Cao, Dongsheng Cao, Xiangxiang Zeng
2024	J	`jnl`	Evolutionary Multimodal Multiobjective Optimization for Traveling Salesman Problems. IEEE Trans. Evol. Comput. Yiping Liu, Liting Xu, Yuyan Han, Xiangxiang Zeng, Gary G. Yen, Hisao Ishibuchi
2024	J	`jnl`	Evolutionary Multiobjective Molecule Optimization in an Implicit Chemical Space. J. Chem. Inf. Model. Xin Xia, Yiping Liu, Chunhou Zheng, Xingyi Zhang, Qingwen Wu, Xin Gao, Xiangxiang Zeng, Yansen Su
2024	J	`jnl`	Evolutionary multimodal multiobjective optimization guided by growing neural gas. Swarm Evol. Comput. Yiping Liu, Ling Zhang, Xiangxiang Zeng, Yuyan Han
2024	J	`jnl`	GenoM7GNet: An Efficient N IEEE ACM Trans. Comput. Biol. Bioinform. Chuang Li, Heshi Wang, Yanhua Wen, Rui Yin, Xiangxiang Zeng, Keqin Li
2024	J	`jnl`	Geometric deep learning for drug discovery. Expert Syst. Appl. Mingquan Liu, Chunyan Li, Ruizhe Chen, Dongsheng Cao, Xiangxiang Zeng
2024	J	`jnl`	Geometry-Based Molecular Generation With Deep Constrained Variational Autoencoder. IEEE Trans. Neural Networks Learn. Syst. Chunyan Li, Junfeng Yao, Wei Wei, Zhangming Niu, Xiangxiang Zeng, Jin Li, Jianmin Wang
2024	J	`jnl`	Glypred: Lysine Glycation Site Prediction via CCU-LightGBM-BiLSTM Framework with Multi-Head Attention Mechanism. J. Chem. Inf. Model. Yun Zuo, Bangyi Zhang, Yinkang Dong, Wenying He, Yue Bi, Xiangrong Liu, Xiangxiang Zeng, Zhaohong Deng
2024	J	`jnl`	HMAMP: Hypervolume-Driven Multi-Objective Antimicrobial Peptides Design. CoRR Li Wang, Yiping Li, Xiangzheng Fu, Xiucai Ye, Junfeng Shi, Gary G. Yen, Xiangxiang Zeng
2024	J	`jnl`	Instruction Multi-Constraint Molecular Generation Using a Teacher-Student Large Language Model. CoRR Peng Zhou, Jianmin Wang, Chunyan Li, Zixu Wang, Yiping Liu, Siqi Sun, Jianxin Lin, Longyue Wang, Xiangxiang Zeng
2024	J	`jnl`	Interface-aware molecular generative framework for protein-protein interaction modulators. J. Cheminformatics Jianmin Wang, Jiashun Mao, Chunyan Li, Hongxin Xiang, Xun Wang, Shuang Wang, Zixu Wang, Yangyang Chen, Yuquan Li, Kyoung Tai No, Tao Song, Xiangxiang Zeng
2024	J	`jnl`	KGExplainer: Towards Exploring Connected Subgraph Explanations for Knowledge Graph Completion. CoRR Tengfei Ma, Xiang Song, Wen Tao, Mufei Li, Jiani Zhang, Xiaoqin Pan, Jianxin Lin, Bosheng Song, Xiangxiang Zeng
2024	J	`jnl`	Learning to Denoise Biomedical Knowledge Graph for Robust Molecular Interaction Prediction. IEEE Trans. Knowl. Data Eng. Tengfei Ma, Yujie Chen, Wen Tao, Dashun Zheng, Xuan Lin, Patrick Cheong-Iao Pang, Yiping Liu, Yijun Wang, Longyue Wang, Bosheng Song, Xiangxiang Zeng, Philip S. Yu
2024	J	`jnl`	MSlocPRED: deep transfer learning-based identification of multi-label mRNA subcellular localization. Briefings Bioinform. Yun Zuo, Bangyi Zhang, Wenying He, Yue Bi, Xiangrong Liu, Xiangxiang Zeng, Zhaohong Deng
2024	J	`jnl`	MaskMol: Knowledge-guided Molecular Image Pre-Training Framework for Activity Cliffs. CoRR Zhixiang Cheng, Hongxin Xiang, Pengsen Ma, Li Zeng, Xin Jin, Xixi Yang, Jianxin Lin, Yang Deng, Bosheng Song, Xinxin Feng, Changhui Deng, Xiangxiang Zeng
2024	J	`jnl`	Memristive Circuit Implementation of Caenorhabditis Elegans Mechanism for Neuromorphic Computing. IEEE Trans. Neural Networks Learn. Syst. Hegan Chen, Qinghui Hong, Zhongrui Wang, Chunhua Wang, Xiangxiang Zeng, Jiliang Zhang
2024	J	`jnl`	MoFormer: Multi-objective Antimicrobial Peptide Generation Based on Conditional Transformer Joint Multi-modal Fusion Descriptor. CoRR Li Wang, Xiangzheng Fu, Jiahao Yang, Xinyi Zhang, Xiucai Ye, Yiping Liu, Tetsuya Sakurai, Xiangxiang Zeng
2024	B	`conf`	Multi-Objective Molecular Design in Constrained Latent Space. IJCNN Yiwei Liu, Yiping Liu, Jiahao Yang, Xinyi Zhang, Li Wang, Xiangxiang Zeng
2024	J	`jnl`	On the migrativity properties between uni-nullnorms and overlap (grouping) functions. Soft Comput. Xiangxiang Zeng, Kuanyun Zhu
2024	J	`jnl`	PEB-DDI: A Task-Specific Dual-View Substructural Learning Framework for Drug-Drug Interaction Prediction. IEEE J. Biomed. Health Informatics Xiangzhen Shen, Zimeng Li, Yuansheng Liu, Bosheng Song, Xiangxiang Zeng
2024	J	`jnl`	PreMLS: The undersampling technique based on ClusterCentroids to predict multiple lysine sites. PLoS Comput. Biol. Yun Zuo, Xingze Fang, Jiayong Wan, Wenying He, Xiangrong Liu, Xiangxiang Zeng, Zhaohong Deng
2024	J	`jnl`	Property Enhanced Instruction Tuning for Multi-task Molecule Generation with Large Language Models. CoRR Xuan Lin, Long Chen, Yile Wang, Xiangxiang Zeng, Philip S. Yu
2024	J	`jnl`	S CoRR Tengfei Ma, Yujie Chen, Liang Wang, Xuan Lin, Bosheng Song, Xiangxiang Zeng
2024	J	`jnl`	SSR-DTA: Substructure-aware multi-layer graph neural networks for drug-target binding affinity prediction. Artif. Intell. Medicine Yuansheng Liu, Xinyan Xia, Yongshun Gong, Bosheng Song, Xiangxiang Zeng
2024	J	`jnl`	SiSGC: A Drug Repositioning Prediction Model Based on Heterogeneous Simplifying Graph Convolution. J. Chem. Inf. Model. Zhong-Hao Ren, Chang-Qing Yu, Li-Ping Li, Zhu-Hong You, Zheng-Wei Li, Shanwen Zhang, Xiangxiang Zeng, Yi-Fan Shang
2024	J	`jnl`	WalkGAN: Network Representation Learning With Sequence-Based Generative Adversarial Networks. IEEE Trans. Neural Networks Learn. Syst. Taisong Jin, Xixi Yang, Zhengtao Yu, Han Luo, Yongmei Zhang, Feiran Jie, Xiangxiang Zeng, Min Jiang
2024	J	`jnl`	Y-Mol: A Multiscale Biomedical Knowledge-Guided Large Language Model for Drug Development. CoRR Tengfei Ma, Xuan Lin, Tianle Li, Chaoyi Li, Long Chen, Peng Zhou, Xibao Cai, Xinyu Yang, Daojian Zeng, Dong-Sheng Cao, Xiangxiang Zeng
2024	J	`jnl`	scCAN: Clustering With Adaptive Neighbor-Based Imputation Method for Single-Cell RNA-Seq Data. IEEE ACM Trans. Comput. Biol. Bioinform. Shujie Dong, Yuansheng Liu, Yongshun Gong, Xiangjun Dong, Xiangxiang Zeng
2023	J	`jnl`	A Multi-Population Multi-Objective Evolutionary Algorithm Based on the Contribution of Decision Variables to Objectives for Large-Scale Multi/Many-Objective Optimization. IEEE Trans. Cybern. Ying Xu, Chong Xu, Huan Zhang, Lei Huang, Yiping Liu, Yusuke Nojima, Xiangxiang Zeng
2023	J	`jnl`	A general hypergraph learning algorithm for drug multi-task predictions in micro-to-macro biomedical networks. PLoS Comput. Biol. Shuting Jin, Yue Hong, Li Zeng, Yinghui Jiang, Yuan Lin, Leyi Wei, Zhuohang Yu, Xiangxiang Zeng, Xiangrong Liu
2023	A*	`conf`	Adaptive Compositional Continual Meta-Learning. ICML Bin Wu, Jinyuan Fang, Xiangxiang Zeng, Shangsong Liang, Qiang Zhang
2023	J	`jnl`	Chemical structure-aware molecular image representation learning. Briefings Bioinform. Hongxin Xiang, Shuting Jin, Xiangrong Liu, Xiangxiang Zeng, Li Zeng
2023	J	`jnl`	Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction. Briefings Bioinform. Xuan Lin, Lichang Dai, Yafang Zhou, Zu-Guo Yu, Wen Zhang, Jian-Yu Shi, Dong-Sheng Cao, Li Zeng, Haowen Chen, Bosheng Song, Philip S. Yu, Xiangxiang Zeng
2023	J	`jnl`	Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction. CoRR Xuan Lin, Lichang Dai, Yafang Zhou, Zu-Guo Yu, Wen Zhang, Jian-Yu Shi, Dong-Sheng Cao, Li Zeng, Haowen Chen, Bosheng Song, Philip S. Yu, Xiangxiang Zeng
2023	J	`jnl`	DSN-DDI: an accurate and generalized framework for drug-drug interaction prediction by dual-view representation learning. Briefings Bioinform. Zimeng Li, Shichao Zhu, Bin Shao, Xiangxiang Zeng, Tong Wang, Tie-Yan Liu
2023	J	`jnl`	Deep generative model for drug design from protein target sequence. J. Cheminformatics Yangyang Chen, Zixu Wang, Lei Wang, Jianmin Wang, Pengyong Li, Dongsheng Cao, Xiangxiang Zeng, Xiucai Ye, Tetsuya Sakurai
2023	J	`jnl`	DiffColor: Toward High Fidelity Text-Guided Image Colorization with Diffusion Models. CoRR Jianxin Lin, Peng Xiao, Yijun Wang, Rongju Zhang, Xiangxiang Zeng
2023	J	`jnl`	Dimensionality reduction and visualization of single-cell RNA-seq data with an improved deep variational autoencoder. Briefings Bioinform. Jing Jiang, Junlin Xu, Yuansheng Liu, Bosheng Song, Xiulan Guo, Xiangxiang Zeng, Quan Zou
2023	J	`jnl`	Effectively Identifying Compound-Protein Interaction Using Graph Neural Representation. IEEE ACM Trans. Comput. Biol. Bioinform. Xuan Lin, Zhe Quan, Zhi-Jie Wang, Yan Guo, Xiangxiang Zeng, Philip S. Yu
2023	J	`jnl`	Evolutionary Multi-Objective Optimization in Searching for Various Antimicrobial Peptides [Feature]. IEEE Comput. Intell. Mag. Yiping Liu, Xinyi Zhang, Yuansheng Liu, Yansen Su, Xiangxiang Zeng, Gary G. Yen
2023	A*	`conf`	GPMO: Gradient Perturbation-Based Contrastive Learning for Molecule Optimization. IJCAI Xixi Yang, Li Fu, Yafeng Deng, Yuansheng Liu, Dongsheng Cao, Xiangxiang Zeng
2023	—	`conf`	ImmRegInformer: an interpretable Transformer-based method for prioritizing immune-regulatory cancer drivers. BIBM Liwen Xu, Boya Ji, Yijun Peng, Wending Pi, Xiangxiang Zeng, Peng Zhao, Shaoliang Peng
2023	—	`conf`	Interpretable multi-view attention network for drug-drug interaction prediction. BIBM Xuan Lin, Qi Wen, Sijie Yang, Zu-Guo Yu, Yahui Long, Xiangxiang Zeng
2023	J	`jnl`	KG-MTL: Knowledge Graph Enhanced Multi-Task Learning for Molecular Interaction. IEEE Trans. Knowl. Data Eng. Tengfei Ma, Xuan Lin, Bosheng Song, Philip S. Yu, Xiangxiang Zeng
2023	A*	`conf`	LagNet: Deep Lagrangian Mechanics for Plug-and-Play Molecular Representation Learning. AAAI Chunyan Li, Junfeng Yao, Jinsong Su, Zhaoyang Liu, Xiangxiang Zeng, Chenxi Huang
2023	J	`jnl`	Learning to Denoise Unreliable Interactions for Link Prediction on Biomedical Knowledge Graph. CoRR Tengfei Ma, Yujie Chen, Wen Tao, Dashun Zheng, Xuan Lin, Patrick Cheong-Iao Pang, Yiping Liu, Yijun Wang, Bosheng Song, Xiangxiang Zeng
2023	J	`jnl`	Machine learning on protein-protein interaction prediction: models, challenges and trends. Briefings Bioinform. Tao Tang, Xiaocai Zhang, Yuansheng Liu, Hui Peng, Binshuang Zheng, Yanlin Yin, Xiangxiang Zeng
2023	J	`jnl`	Modality-DTA: Multimodality Fusion Strategy for Drug-Target Affinity Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. Xixi Yang, Zhangming Niu, Yuansheng Liu, Bosheng Song, Weiqiang Lu, Li Zeng, Xiangxiang Zeng
2023	J	`jnl`	Monodirectional evolutional symport tissue P systems with channel states and cell division. Sci. China Inf. Sci. Bosheng Song, Kenli Li, Xiangxiang Zeng, Mario J. Pérez-Jiménez, Claudio Zandron
2023	—	`conf`	PACS: Prediction and analysis of cancer subtypes from multi-omics data based on a multi-head attention mechanism model. BIBM Liangrui Pan, Pinle Qin, Pengfei Rong, Xiangxiang Zeng, Dazheng Liu, Shaoliang Peng
2023	J	`jnl`	PointDE: Protein Docking Evaluation Using 3D Point Cloud Neural Network. IEEE ACM Trans. Comput. Biol. Bioinform. Zihao Chen, Nan Liu, Yang Huang, Xiaoping Min, Xiangxiang Zeng, Shengxiang Ge, Jun Zhang, Ning-Shao Xia
2023	J	`jnl`	Prediction of multi-relational drug-gene interaction via Dynamic hyperGraph Contrastive Learning. Briefings Bioinform. Wen Tao, Yuansheng Liu, Xuan Lin, Bosheng Song, Xiangxiang Zeng
2023	J	`jnl`	Reducing false positive rate of docking-based virtual screening by active learning. Briefings Bioinform. Lei Wang, Shao-Hua Shi, Hui Li, Xiangxiang Zeng, Su-You Liu, Zhao-Qian Liu, Yafeng Deng, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
2023	J	`jnl`	Sequence Alignment/Map format: a comprehensive review of approaches and applications. Briefings Bioinform. Yuansheng Liu, Xiangzhen Shen, Yongshun Gong, Yiping Liu, Bosheng Song, Xiangxiang Zeng
2023	J	`jnl`	Spiking neural P systems with weights and delays on synapses. Theor. Comput. Sci. Yanyan Li, Bosheng Song, Xiangxiang Zeng
2023	J	`jnl`	Tissue P Systems With States in Cells. IEEE Trans. Computers Bosheng Song, Kenli Li, David Orellana-Martín, Xiangxiang Zeng, Mario J. Pérez-Jiménez
2023	A*	`conf`	Totally Dynamic Hypergraph Neural Networks. IJCAI Peng Zhou, Zongqian Wu, Xiangxiang Zeng, Guoqiu Wen, Junbo Ma, Xiaofeng Zhu
2022	J	`jnl`	3DMol-Net: Learn 3D Molecular Representation Using Adaptive Graph Convolutional Network Based on Rotation Invariance. IEEE J. Biomed. Health Informatics Chunyan Li, Wei Wei, Jin Li, Junfeng Yao, Xiangxiang Zeng, Zhihan Lv
2022	J	`jnl`	A Robust Algorithm Based on Link Label Propagation for Identifying Functional Modules From Protein-Protein Interaction Networks. IEEE ACM Trans. Comput. Biol. Bioinform. Hao Jiang, Fei Zhan, Congtao Wang, Jianfeng Qiu, Yansen Su, Chunhou Zheng, Xingyi Zhang, Xiangxiang Zeng
2022	—	`conf`	A heterogeneous graph cross-omics attention model for single-cell representation learning. BIBM Yue Liu, Junfeng Zhang, Shulin Wang, Wei Zhang, Xiangxiang Zeng, Chee Keong Kwoh
2022	J	`jnl`	A weighted bilinear neural collaborative filtering approach for drug repositioning. Briefings Bioinform. Yajie Meng, Changcheng Lu, Min Jin, Junlin Xu, Xiangxiang Zeng, Jialiang Yang
2022	J	`jnl`	Accurate prediction of molecular properties and drug targets using a self-supervised image representation learning framework. Nat. Mac. Intell. Xiangxiang Zeng, Hongxin Xiang, Linhui Yu, Jianmin Wang, Kenli Li, Ruth Nussinov, Feixiong Cheng
2022	J	`jnl`	An adaptive convergence enhanced evolutionary algorithm for many-objective optimization problems. Swarm Evol. Comput. Ying Xu, Huan Zhang, Xiangxiang Zeng, Yusuke Nojima
2022	J	`jnl`	Are dropout imputation methods for scRNA-seq effective for scATAC-seq data? Briefings Bioinform. Yue Liu, Junfeng Zhang, Shu-Lin Wang, Xiangxiang Zeng, Wei Zhang
2022	J	`jnl`	Deep learning for drug repurposing: methods, databases, and applications. CoRR Xiaoqin Pan, Xuan Lin, Dongsheng Cao, Xiangxiang Zeng, Philip S. Yu, Lifang He, Ruth Nussinov, Feixiong Cheng
2022	J	`jnl`	Deep learning in retrosynthesis planning: datasets, models and tools. Briefings Bioinform. Jingxin Dong, Mingyi Zhao, Yuansheng Liu, Yansen Su, Xiangxiang Zeng
2022	J	`jnl`	Deep learning joint models for extracting entities and relations in biomedical: a survey and comparison. Briefings Bioinform. Yansen Su, Minglu Wang, Pengpeng Wang, Chunhou Zheng, Yuansheng Liu, Xiangxiang Zeng
2022	J	`jnl`	Learning spatial structures of proteins improves protein-protein interaction prediction. Briefings Bioinform. Bosheng Song, Xiaoyan Luo, Xiaoli Luo, Yuansheng Liu, Zhangming Niu, Xiangxiang Zeng
2022	J	`jnl`	MLysPRED: graph-based multi-view clustering and multi-dimensional normal distribution resampling techniques to predict multiple lysine sites. Briefings Bioinform. Yun Zuo, Yue Hong, Xiangxiang Zeng, Qiang Zhang, Xiangrong Liu
2022	J	`jnl`	Molecule optimization via multi-objective evolutionary in implicit chemical space. CoRR Xin Xia, Yansen Su, Chunhou Zheng, Xiangxiang Zeng
2022	J	`jnl`	Monodirectional Evolutional Symport Tissue P Systems With Promoters and Cell Division. IEEE Trans. Parallel Distributed Syst. Bosheng Song, Kenli Li, Xiangxiang Zeng
2022	J	`jnl`	Multi-View Substructure Learning for Drug-Drug Interaction Prediction. CoRR Zimeng Li, Shichao Zhu, Bin Shao, Tie-Yan Liu, Xiangxiang Zeng, Tong Wang
2022	J	`jnl`	Normal forms for spiking neural P systems and some of its variants. Inf. Sci. Ivan Cedric H. Macababayao, Francis George C. Cabarle, Ren Tristan A. de la Cruz, Xiangxiang Zeng
2022	J	`jnl`	On the cross-migrativity between uninorms and overlap (grouping) functions. Fuzzy Sets Syst. Kuanyun Zhu, Xiangxiang Zeng, Junsheng Qiao
2022	J	`jnl`	Rule synchronization for monodirectional tissue-like P systems with channel states. Inf. Comput. Yanyan Li, Bosheng Song, Xiangxiang Zeng
2022	J	`jnl`	preMLI: a pre-trained method to uncover microRNA-lncRNA potential interactions. Briefings Bioinform. Xinyu Yu, Likun Jiang, Shuting Jin, Xiangxiang Zeng, Xiangrong Liu
2021	J	`jnl`	A Framework for Evolving Spiking Neural P Systems. Int. J. Unconv. Comput. Lovely Joy P. Casauay, Francis George C. Cabarle, Ivan Cedric H. Macababayao, Ren Tristan A. de la Cruz, Henry N. Adorna, Xiangxiang Zeng, Miguel Ángel Martínez-del-Amor
2021	J	`jnl`	A Polar-Metric-Based Evolutionary Algorithm. IEEE Trans. Cybern. Hang Xu, Wenhua Zeng, Xiangxiang Zeng, Gary G. Yen
2021	J	`jnl`	A novel antibacterial peptide recognition algorithm based on BERT. Briefings Bioinform. Yue Zhang, Jianyuan Lin, Lianmin Zhao, Xiangxiang Zeng, Xiangrong Liu
2021	J	`jnl`	A spatial-temporal gated attention module for molecular property prediction based on molecular geometry. Briefings Bioinform. Chunyan Li, Jianmin Wang, Zhangming Niu, Junfeng Yao, Xiangxiang Zeng
2021	J	`jnl`	ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties. Nucleic Acids Res. Guo-Li Xiong, Zhenxing Wu, Jiacai Yi, Li Fu, Zhi-Jiang Yang, Chang-Yu Hsieh, Mingzhu Yin, Xiangxiang Zeng, Chengkun Wu, Aiping Lu, Xiang Chen, Tingjun Hou, Dong-Sheng Cao
2021	J	`jnl`	Application of deep learning methods in biological networks. Briefings Bioinform. Shuting Jin, Xiangxiang Zeng, Feng Xia, Wei Huang, Xiangrong Liu
2021	J	`jnl`	Artificial-Intelligence-Enabled Reagent-Free Imaging Hematology Analyzer. Adv. Intell. Syst. Xin Shu, Sameera Sansare, Di Jin, Xiangxiang Zeng, Kai-Yu Tong, Rishikesh Pandey, Renjie Zhou
2021	J	`jnl`	Artificial-Intelligence-Enabled Reagent-Free Imaging Hematology Analyzer. Adv. Intell. Syst. Xin Shu, Sameera Sansare, Di Jin, Xiangxiang Zeng, Kai-Yu Tong, Rishikesh Pandey, Renjie Zhou
2021	J	`jnl`	CarSite-II: an integrated classification algorithm for identifying carbonylated sites based on K-means similarity-based undersampling and synthetic minority oversampling techniques. BMC Bioinform. Yun Zuo, Jianyuan Lin, Xiangxiang Zeng, Quan Zou, Xiangrong Liu
2021	J	`jnl`	De novo generation of dual-target ligands using adversarial training and reinforcement learning. Briefings Bioinform. Fengqing Lu, Mufei Li, Xiaoping Min, Chunyan Li, Xiangxiang Zeng
2021	J	`jnl`	Deep learning methods for biomedical named entity recognition: a survey and qualitative comparison. Briefings Bioinform. Bosheng Song, Fen Li, Yuansheng Liu, Xiangxiang Zeng
2021	J	`jnl`	Drug repositioning based on the heterogeneous information fusion graph convolutional network. Briefings Bioinform. Lijun Cai, Changcheng Lu, Junlin Xu, Yajie Meng, Peng Wang, Xiangzheng Fu, Xiangxiang Zeng, Yansen Su
2021	A	`conf`	Fast k-NN Graph Construction by GPU based NN-Descent. CIKM Hui Wang, Wan-Lei Zhao, Xiangxiang Zeng, Jianye Yang
2021	J	`jnl`	HeTDR: Drug repositioning based on heterogeneous networks and text mining. Patterns Shuting Jin, Zhangming Niu, Changzhi Jiang, Wei Huang, Feng Xia, Xurui Jin, Xiangrong Liu, Xiangxiang Zeng
2021	J	`jnl`	Heterogeneous network-based drug repurposing for COVID-19. CoRR Shuting Jin, Xiangxiang Zeng, Wei Huang, Feng Xia, Changzhi Jiang, Xiangrong Liu, Shaoliang Peng
2021	J	`jnl`	Homogeneous spiking neural P systems with structural plasticity. J. Membr. Comput. Ren Tristan A. de la Cruz, Francis George C. Cabarle, Ivan Cedric H. Macababayao, Henry N. Adorna, Xiangxiang Zeng
2021	J	`jnl`	ITP-Pred: an interpretable method for predicting, therapeutic peptides with fused features low-dimension representation. Briefings Bioinform. Lijun Cai, Li Wang, Xiangzheng Fu, Chenxing Xia, Xiangxiang Zeng, Quan Zou
2021	—	`conf`	LADstackING: Stacking Ensemble Learning-based Computational Model for Predicting Potential LncRNA-disease Associations. BIBM Jiechen Li, Xiangxiang Zeng, Yong Dou, Fei Xia, Shaoliang Peng
2021	J	`jnl`	Large-Scale Approximate k-NN Graph Construction on GPU. CoRR Hui Wang, Wan-Lei Zhao, Xiangxiang Zeng
2021	J	`jnl`	MUFFIN: multi-scale feature fusion for drug-drug interaction prediction. Bioinform. Yujie Chen, Tengfei Ma, Xixi Yang, Jianmin Wang, Bosheng Song, Xiangxiang Zeng
2021	J	`jnl`	Minirmd: accurate and fast duplicate removal tool for short reads via multiple minimizers. Bioinform. Yuansheng Liu, Xiaocai Zhang, Quan Zou, Xiangxiang Zeng
2021	J	`jnl`	Mobility Based Trust Evaluation for Heterogeneous Electric Vehicles Network in Smart Cities. IEEE Trans. Intell. Transp. Syst. Tian Wang, Hao Luo, Xiangxiang Zeng, Zhiyong Yu, Anfeng Liu, Arun Kumar Sangaiah
2021	J	`jnl`	Monodirectional Tissue P Systems With Promoters. IEEE Trans. Cybern. Bosheng Song, Xiangxiang Zeng, Min Jiang, Mario J. Pérez-Jiménez
2021	J	`jnl`	Monodirectional tissue P systems with channel states. Inf. Sci. Bosheng Song, Xiangxiang Zeng, Alfonso Rodríguez-Patón
2021	J	`jnl`	Neural-like P systems with plasmids. Inf. Comput. Francis George C. Cabarle, Xiangxiang Zeng, Niall Murphy, Tao Song, Alfonso Rodríguez-Patón, Xiangrong Liu
2021	—	`conf`	Pm BIBM Yun Zuo, Xiangrong Liu, Xiangxiang Zeng
2021	J	`jnl`	Predicting enhancer-promoter interactions by deep learning and matching heuristic. Briefings Bioinform. Xiaoping Min, Congmin Ye, Xiangrong Liu, Xiangxiang Zeng
2021	J	`jnl`	Solving a PSPACE-complete problem by symport/antiport P systems with promoters and membrane division. J. Membr. Comput. Bosheng Song, Xiangxiang Zeng
2021	J	`jnl`	The computational power of monodirectional tissue P systems with symport rules. Inf. Comput. Bosheng Song, Shengye Huang, Xiangxiang Zeng
2021	J	`jnl`	iEnhancer-XG: interpretable sequence-based enhancers and their strength predictor. Bioinform. Lijun Cai, Xuanbai Ren, Xiangzheng Fu, Li Peng, Mingyu Gao, Xiangxiang Zeng
2020	J	`jnl`	A Consensus Community-Based Particle Swarm Optimization for Dynamic Community Detection. IEEE Trans. Cybern. Xiangxiang Zeng, Wen Wang, Cong Chen, Gary G. Yen
2020	J	`jnl`	A Network Reduction-Based Multiobjective Evolutionary Algorithm for Community Detection in Large-Scale Complex Networks. IEEE Trans. Cybern. Xingyi Zhang, Kefei Zhou, Hebin Pan, Lei Zhang, Xiangxiang Zeng, Yaochu Jin
2020	C	`conf`	A drug information embedding method based on graph convolution neural network. HealthCom Xiaoyi Feng, Shaoliang Peng, Fei Li, Ying Xu, Xiangxiang Zeng, Dong-Qing Wei, Yunhao Liu
2020	—	`conf`	A multi-task learning method for analyzing microbiota as cancer immunotherapy signal. BIBM Changzhi Jiang, Yousi Fu, Shuting Jin, Xiangrong Liu, Baishan Fang, Xiangxiang Zeng
2020	J	`jnl`	A novel molecular representation with BiGRU neural networks for learning atom. Briefings Bioinform. Xuan Lin, Zhe Quan, Zhi-Jie Wang, Huang Huang, Xiangxiang Zeng
2020	J	`jnl`	Computational methods for identifying the critical nodes in biological networks. Briefings Bioinform. Xiangrong Liu, Zengyan Hong, Juan Liu, Yuan Lin, Alfonso Rodríguez-Patón, Quan Zou, Xiangxiang Zeng
2020	J	`jnl`	Deep Collaborative Filtering for Prediction of Disease Genes. IEEE ACM Trans. Comput. Biol. Bioinform. Xiangxiang Zeng, Yinglai Lin, Yuying He, Linyuan Lü, Xiaoping Min, Alfonso Rodríguez-Patón
2020	J	`jnl`	Identifying enhancer-promoter interactions with neural network based on pre-trained DNA vectors and attention mechanism. Bioinform. Zengyan Hong, Xiangxiang Zeng, Leyi Wei, Xiangrong Liu
2020	A*	`conf`	KGNN: Knowledge Graph Neural Network for Drug-Drug Interaction Prediction. IJCAI Xuan Lin, Zhe Quan, Zhi-Jie Wang, Tengfei Ma, Xiangxiang Zeng
2020	J	`jnl`	Multiobjective Particle Swarm Optimization Based on Network Embedding for Complex Network Community Detection. IEEE Trans. Comput. Soc. Syst. Xiangrong Liu, Yanzi Du, Min Jiang, Xiangxiang Zeng
2020	J	`jnl`	Network-based prediction of drug-target interactions using an arbitrary-order proximity embedded deep forest. Bioinform. Xiangxiang Zeng, Siyi Zhu, Yuan Hou, Pengyue Zhang, Lang Li, Jing Li, L. Frank Huang, Stephen J. Lewis, Ruth Nussinov, Feixiong Cheng
2020	J	`jnl`	On the Computational Power of Asynchronous Axon Membrane Systems. IEEE Trans. Emerg. Top. Comput. Intell. Tao Song, Pan Zheng, M. L. Dennis Wong, Min Jiang, Xiangxiang Zeng
2020	J	`jnl`	Predicting disease-associated circular RNAs using deep forests combined with positive-unlabeled learning methods. Briefings Bioinform. Xiangxiang Zeng, Yue Zhong, Wei Lin, Quan Zou
2020	J	`jnl`	Repurpose Open Data to Discover Therapeutics for COVID-19 using Deep Learning. CoRR Xiangxiang Zeng, Xiang Song, Tengfei Ma, Xiaoqin Pan, Yadi Zhou, Yuan Hou, Zheng Zhang, George Karypis, Feixiong Cheng
2020	J	`jnl`	Sequence clustering in bioinformatics: an empirical study. Briefings Bioinform. Quan Zou, Gang Lin, Xingpeng Jiang, Xiangrong Liu, Xiangxiang Zeng
2020	J	`jnl`	StackCPPred: a stacking and pairwise energy content-based prediction of cell-penetrating peptides and their uptake efficiency. Bioinform. Xiangzheng Fu, Lijun Cai, Xiangxiang Zeng, Quan Zou
2020	J	`jnl`	The computational power of cell-like P systems with one protein on membrane. J. Membr. Comput. Bosheng Song, Xiaoyan Luo, Luis Valencia-Cabrera, Xiangxiang Zeng
2019	—	`conf`	A Deep Neural Network for Antimicrobial Peptide Recognition. BIBM Jianyuan Lin, Xiangxiang Zeng, Yun Zuo, Ying Ju, Xiangrong Liu
2019	J	`jnl`	A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications. PLoS Comput. Biol. He Peng, Xiangxiang Zeng, Yadi Zhou, Defu Zhang, Ruth Nussinov, Feixiong Cheng
2019	J	`jnl`	An Evolutionary Algorithm Based on Minkowski Distance for Many-Objective Optimization. IEEE Trans. Cybern. Hang Xu, Wenhua Zeng, Xiangxiang Zeng, Gary G. Yen
2019	J	`jnl`	Details in the evaluation of circular RNA detection tools: Reply to Chen and Chuang. PLoS Comput. Biol. Xiangxiang Zeng, Wei Lin, Maozu Guo, Quan Zou
2019	—	`conf`	Drug Target Interaction Prediction using Multi-task Learning and Co-attention. BIBM Yuyou Weng, Chen Lin, Xiangxiang Zeng, Yun Liang
2019	—	`conf`	GraphCPI: Graph Neural Representation Learning for Compound-Protein Interaction. BIBM Zhe Quan, Yan Guo, Xuan Lin, Zhi-Jie Wang, Xiangxiang Zeng
2019	J	`jnl`	MOEA/HD: A Multiobjective Evolutionary Algorithm Based on Hierarchical Decomposition. IEEE Trans. Cybern. Hang Xu, Wenhua Zeng, Defu Zhang, Xiangxiang Zeng
2019	J	`jnl`	Matrix representation and simulation algorithm of spiking neural P systems with structural plasticity. J. Membr. Comput. Zechariah B. Jimenez, Francis George C. Cabarle, Ren Tristan A. de la Cruz, Kelvin C. Buño, Henry N. Adorna, Nestine Hope S. Hernandez, Xiangxiang Zeng
2019	J	`jnl`	Meta-Path Methods for Prioritizing Candidate Disease miRNAs. IEEE ACM Trans. Comput. Biol. Bioinform. Xuan Zhang, Quan Zou, Alfonso Rodríguez-Patón, Xiangxiang Zeng
2019	J	`jnl`	On solutions and representations of spiking neural P systems with rules on synapses. Inf. Sci. Francis George C. Cabarle, Ren Tristan A. de la Cruz, Dionne Peter P. Cailipan, Defu Zhang, Xiangrong Liu, Xiangxiang Zeng
2019	J	`jnl`	deepDR: a network-based deep learning approach to in silico drug repositioning. Bioinform. Xiangxiang Zeng, Siyi Zhu, Xiangrong Liu, Yadi Zhou, Ruth Nussinov, Feixiong Cheng
2018	—	`conf`	An Implementation of Elementary Arithmetic with Virus Machine. Enjoying Natural Computing Xiaoshan Yan, Xiangrong Liu, Xiangxiang Zeng, Alfonso Rodríguez-Patón
2018	—	`conf`	Drug Target Interaction Prediction with Non-random Missing Labels. BIBM Sheng Ni, Chen Lin, Xiangxiang Zeng, Yun Liang
2018	—	`conf`	LncRNA-disease association prediction based on neighborhood information aggregation in neural network. BIBM Hongjie Chen, Xun Wang, Xuan Zhang, Xiangxiang Zeng, Tao Song, Alfonso Rodríguez-Patón
2018	J	`jnl`	Prediction of potential disease-associated microRNAs using structural perturbation method. Bioinform. Xiangxiang Zeng, Li Liu, Linyuan Lü, Quan Zou
2018	—	`conf`	Small Spiking Neural P Systems with Structural Plasticity. Enjoying Natural Computing Francis George C. Cabarle, Ren Tristan A. de la Cruz, Henry N. Adorna, Ma. Daiela Dimaano, Faith Therese Peña, Xiangxiang Zeng
2018	J	`jnl`	Spiking Neural P Systems With Colored Spikes. IEEE Trans. Cogn. Dev. Syst. Tao Song, Alfonso Rodríguez-Patón, Pan Zheng, Xiangxiang Zeng
2018	J	`jnl`	Structural Hole Spanner in HumanNet Identifies Disease Gene and Drug targets. IEEE Access Xiangxiang Zeng, Jiawei Lin, Chen Lin, Xiangrong Liu, Alfonso Rodríguez-Patón
2017	J	`jnl`	A comprehensive overview and evaluation of circular RNA detection tools. PLoS Comput. Biol. Xiangxiang Zeng, Wei Lin, Maozu Guo, Quan Zou
2017	J	`jnl`	Inferring MicroRNA-Disease Associations by Random Walk on a Heterogeneous Network with Multiple Data Sources. IEEE ACM Trans. Comput. Biol. Bioinform. Yuansheng Liu, Xiangxiang Zeng, Zengyou He, Quan Zou
2017	—	`conf`	Iteratively collective prediction of disease-gene associations through the incomplete network. BIBM Xiangyi Meng, Quan Zou, Alfonso Rodríguez-Patón, Xiangxiang Zeng
2017	—	`conf`	Motion generation of multi-legged robot in complex terrains by using estimation of distribution algorithm. SSCI Min Jiang, Zhongqiang Huang, Guiying Jiang, Minghui Shi, Xiangxiang Zeng
2017	J	`jnl`	Prediction and Validation of Disease Genes Using HeteSim Scores. IEEE ACM Trans. Comput. Biol. Bioinform. Xiangxiang Zeng, Yuanlu Liao, Yuansheng Liu, Quan Zou
2017	J	`jnl`	Pretata: predicting TATA binding proteins with novel features and dimensionality reduction strategy. CoRR Quan Zou, Shixiang Wan, Ying Ju, Jijun Tang, Xiangxiang Zeng
2017	J	`jnl`	Reconstructing evolutionary trees in parallel for massive sequences. BMC Syst. Biol. Quan Zou, Shixiang Wan, Xiangxiang Zeng, Zhanshan (Sam) Ma
2017	J	`jnl`	Theory and Application of Bio-inspired Intelligence and Methods. J. Univers. Comput. Sci. Xingyi Zhang, Alfonso Rodríguez-Patón Aradas, Xiangxiang Zeng, Tao Song
2016	J	`jnl`	Computing with viruses. Theor. Comput. Sci. Xu Chen, Mario J. Pérez-Jiménez, Luis Valencia-Cabrera, Beizhan Wang, Xiangxiang Zeng
2016	J	`jnl`	Embedded Based Miniaturized Universal Electrochemical Sensing Platform. J. Sensors Jiamin Chen, Yihuang Lin, Rui Gong, Jiming Guo, Xiangxiang Zeng, Juan Liu
2016	—	`conf`	HPTree: Reconstructing phylogenetic trees for ultra-large unaligned DNA sequences via NJ model and Hadoop. BIBM Quan Zou, Shixiang Wan, Xiangxiang Zeng
2016	J	`jnl`	Integrative approaches for predicting microRNA function and prioritizing disease-related microRNA using biological interaction networks. Briefings Bioinform. Xiangxiang Zeng, Xuan Zhang, Quan Zou
2016	J	`jnl`	Investment behavior prediction in heterogeneous information network. Neurocomputing Xiangxiang Zeng, You Li, Stephen C. H. Leung, Ziyu Lin, Xiangrong Liu
2016	—	`conf`	Latent factor model with heterogeneous similarity regularization for predicting gene-disease associations. BIBM Xiangxiang Zeng, Ningxiang Ding, Quan Zou
2016	J	`jnl`	Pretata: predicting TATA binding proteins with novel features and dimensionality reduction strategy. BMC Syst. Biol. Quan Zou, Shixiang Wan, Ying Ju, Jijun Tang, Xiangxiang Zeng
2015	B	`conf`	A Stable Matching-Based Selection and Memory Enhanced MOEA/D for Evolutionary Dynamic Multiobjective Optimization. ICTAI Xiaofeng Chen, Defu Zhang, Xiangxiang Zeng
2015	J	`jnl`	A decision-making framework for precision marketing. Expert Syst. Appl. Zhen You, Yain-Whar Si, Defu Zhang, Xiangxiang Zeng, Stephen C. H. Leung, Tao Li
2015	J	`jnl`	Asynchronous Spiking Neural P Systems with Anti-Spikes. Neural Process. Lett. Tao Song, Xiangrong Liu, Xiangxiang Zeng
2015	J	`jnl`	Asynchronous spiking neural P systems with rules on synapses. Neurocomputing Tao Song, Quan Zou, Xiangrong Liu, Xiangxiang Zeng
2015	J	`jnl`	Identification of cytokine via an improved genetic algorithm. Frontiers Comput. Sci. Xiangxiang Zeng, Sisi Yuan, Xianxian Huang, Quan Zou
2015	—	`conf`	MOEA/D for Energy-Aware Scheduling on Heterogeneous Computing Systems. BIC-TA Gaoshan Deng, Ziming Li, Yuming Zhao, Xiangxiang Zeng
2015	B	`conf`	Short-term optimal hydrothermal scheduling problem considering power flow constraint. CEC Jingrui Zhang, Shuang Lin, Xiangxiang Zeng, Qinghui Tang
2015	J	`jnl`	The power of time-free tissue P systems: Attacking NP-complete problems. Neurocomputing Xiangrong Liu, Juan Suo, Stephen C. H. Leung, Juan Liu, Xiangxiang Zeng
2014	—	`conf`	A New Graphical Representation of Protein Sequences Based on Dual-Vector Model. BIC-TA Zhujin Zhang, Xiangxiang Zeng, Zhihua Chen, Eric Ke Wang
2014	J	`jnl`	A hybrid heuristic algorithm for the 2D variable-sized bin packing problem. Eur. J. Oper. Res. Shaohui Hong, Defu Zhang, Hoong Chuin Lau, Xiangxiang Zeng, Yain-Whar Si
2014	J	`jnl`	Decision Tree Classification Model for Popularity Forecast of Chinese Colleges. J. Appl. Math. Xiangxiang Zeng, Sisi Yuan, You Li, Quan Zou
2014	J	`jnl`	On Some Classes of Sequential Spiking Neural P Systems. Neural Comput. Xingyi Zhang, Xiangxiang Zeng, Bin Luo, Linqiang Pan
2014	J	`jnl`	On languages generated by spiking neural P systems with weights. Inf. Sci. Xiangxiang Zeng, Lei Xu, Xiangrong Liu, Linqiang Pan
2014	J	`jnl`	Small universal simple spiking neural P systems with weights. Sci. China Inf. Sci. Xiangxiang Zeng, Linqiang Pan, Mario J. Pérez-Jiménez
2014	J	`jnl`	Solving Multidimensional 0-1 Knapsack Problem with Time-Free Tissue P Systems. J. Appl. Math. Xiangrong Liu, Ziming Li, Juan Suo, Ying Ju, Juan Liu, Xiangxiang Zeng
2014	J	`jnl`	Spiking Neural P Systems with Thresholds. Neural Comput. Xiangxiang Zeng, Xingyi Zhang, Tao Song, Linqiang Pan
2014	—	`conf`	Time-Free Tissue P Systems for Solving the Hamilton Path Problem. BIC-TA Xiangxiang Zeng, Ningxiang Ding, Fei Xing, Xiangrong Liu
2014	J	`jnl`	Weighted Spiking Neural P Systems with Rules on Synapses. Fundam. Informaticae Xingyi Zhang, Xiangxiang Zeng, Linqiang Pan
2014	J	`jnl`	nDNA-prot: identification of DNA-binding proteins based on unbalanced classification. BMC Bioinform. Li Song, Dapeng Li, Xiangxiang Zeng, Yunfeng Wu, Li Guo, Quan Zou
2013	—	`conf`	A Bayesian Investment Model for Online P2P Lending. ICoC Xubo Wang, Defu Zhang, Xiangxiang Zeng, Xiaoying Wu
2013	J	`jnl`	A Polynomial-Time Solution to Constraint Satisfaction Problems by Neural-like P Systems. Int. J. Unconv. Comput. Lei Xu, Xiangxiang Zeng, Peter Jeavons
2013	J	`jnl`	Spiking neural P systems with anti-spikes and without annihilating priority working in a 'flip-flop' way. Int. J. Comput. Sci. Math. Gangjun Tan, Tao Song, Zhihua Chen, Xiangxiang Zeng
2013	—	`conf`	Stock Price Forecast Using Tree Augmented Naïve (TAN) Bayes. BIC-TA Yuanlu Liao, Xiangxiang Zeng, Tao Song, Lianfeng Zhang
2012	J	`jnl`	A uniform solution to the independent set problem through tissue P systems with cell separation. Frontiers Comput. Sci. Xingyi Zhang, Xiangxiang Zeng, Bin Luo, Zheng Zhang
2012	J	`jnl`	Spiking Neural P Systems with Weighted Synapses. Neural Process. Lett. Linqiang Pan, Xiangxiang Zeng, Xingyi Zhang, Yun Jiang
2011	—	`conf`	A Modified Estimation of Distribution Algorithm for Numeric Optimization. BIC-TA Yuquan Li, Gexiang Zhang, Xiangxiang Zeng, Jixiang Cheng, Marian Gheorghe, Susan Elias
2011	J	`jnl`	A Novel Membrane Algorithm Based on Differential Evolution for Numerical Optimization. Int. J. Unconv. Comput. Jixiang Cheng, Gexiang Zhang, Xiangxiang Zeng
2011	—	`conf`	P Systems with 2D Picture Grammars. BIC-TA Tao Song, Xiangxiang Zeng
2011	—	`conf`	Spiking Neural P Systems for Arithmetic Operations. BIC-TA Xiangxiang Zeng, Tao Song, Linqiang Pan, Xingyi Zhang
2011	J	`jnl`	Time-Free Spiking Neural P Systems. Neural Comput. Linqiang Pan, Xiangxiang Zeng, Xingyi Zhang
2010	J	`jnl`	A weakly universal spiking neural P system. Math. Comput. Model. Xiangxiang Zeng, Chun Lu, Linqiang Pan
2010	J	`jnl`	Deterministic solutions to QSAT and Q3SAT by spiking neural P systems with pre-computed resources. Theor. Comput. Sci. Tseren-Onolt Ishdorj, Alberto Leporati, Linqiang Pan, Xiangxiang Zeng, Xingyi Zhang
2010	—	`conf`	Matrix Representation of Spiking Neural P Systems. Int. Conf. on Membrane Computing Xiangxiang Zeng, Henry N. Adorna, Miguel A. Martínez-del-Amor, Linqiang Pan, Mario J. Pérez-Jiménez
2010	—	`conf`	Small universal asynchronous spiking neural P systems. BIC-TA Linqiang Pan, Xiangxiang Zeng, Xingyi Zhang
2009	—	`conf`	A Note on Small Universal Spiking Neural P Systems. Workshop on Membrane Computing Linqiang Pan, Xiangxiang Zeng
2009	J	`jnl`	Homogeneous Spiking Neural P Systems. Fundam. Informaticae Xiangxiang Zeng, Xingyi Zhang, Linqiang Pan
2009	J	`jnl`	On languages generated by asynchronous spiking neural P systems. Theor. Comput. Sci. Xingyi Zhang, Xiangxiang Zeng, Linqiang Pan
2008	J	`jnl`	On string languages generated by spiking neural P systems with exhaustive use of rules. Nat. Comput. Xingyi Zhang, Xiangxiang Zeng, Linqiang Pan
2008	J	`jnl`	Smaller Universal Spiking Neural P Systems. Fundam. Informaticae Xingyi Zhang, Xiangxiang Zeng, Linqiang Pan