Xiangxiang Zeng

Orcid: 0000-0003-1081-7658

According to our database1, Xiangxiang Zeng authored at least 167 papers between 2008 and 2024.

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Bibliography

2024
Dual-View Learning Based on Images and Sequences for Molecular Property Prediction.
IEEE J. Biomed. Health Informatics, March, 2024

PEB-DDI: A Task-Specific Dual-View Substructural Learning Framework for Drug-Drug Interaction Prediction.
IEEE J. Biomed. Health Informatics, January, 2024

SiSGC: A Drug Repositioning Prediction Model Based on Heterogeneous Simplifying Graph Convolution.
J. Chem. Inf. Model., January, 2024

scCAN: Clustering With Adaptive Neighbor-Based Imputation Method for Single-Cell RNA-Seq Data.
IEEE ACM Trans. Comput. Biol. Bioinform., 2024

DrugAssist: A Large Language Model for Molecule Optimization.
CoRR, 2024

2023
Deep generative model for drug design from protein target sequence.
J. Cheminformatics, December, 2023

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., November, 2023

A general hypergraph learning algorithm for drug multi-task predictions in micro-to-macro biomedical networks.
PLoS Comput. Biol., November, 2023

Tissue P Systems With States in Cells.
IEEE Trans. Computers, September, 2023

Sequence Alignment/Map format: a comprehensive review of approaches and applications.
Briefings Bioinform., September, 2023

Spiking neural P systems with weights and delays on synapses.
Theor. Comput. Sci., August, 2023

KG-MTL: Knowledge Graph Enhanced Multi-Task Learning for Molecular Interaction.
IEEE Trans. Knowl. Data Eng., July, 2023

Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction.
Briefings Bioinform., July, 2023

Evolutionary Multi-Objective Optimization in Searching for Various Antimicrobial Peptides [Feature].
IEEE Comput. Intell. Mag., May, 2023

Dimensionality reduction and visualization of single-cell RNA-seq data with an improved deep variational autoencoder.
Briefings Bioinform., May, 2023

Monodirectional evolutional symport tissue P systems with channel states and cell division.
Sci. China Inf. Sci., March, 2023

Machine learning on protein-protein interaction prediction: models, challenges and trends.
Briefings Bioinform., March, 2023

Reducing false positive rate of docking-based virtual screening by active learning.
Briefings Bioinform., January, 2023

DSN-DDI: an accurate and generalized framework for drug-drug interaction prediction by dual-view representation learning.
Briefings Bioinform., January, 2023

Modality-DTA: Multimodality Fusion Strategy for Drug-Target Affinity Prediction.
IEEE ACM Trans. Comput. Biol. Bioinform., 2023

Effectively Identifying Compound-Protein Interaction Using Graph Neural Representation.
IEEE ACM Trans. Comput. Biol. Bioinform., 2023

PointDE: Protein Docking Evaluation Using 3D Point Cloud Neural Network.
IEEE ACM Trans. Comput. Biol. Bioinform., 2023

Learning to Denoise Unreliable Interactions for Link Prediction on Biomedical Knowledge Graph.
CoRR, 2023

DiffColor: Toward High Fidelity Text-Guided Image Colorization with Diffusion Models.
CoRR, 2023

Totally Dynamic Hypergraph Neural Networks.
Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence, 2023

GPMO: Gradient Perturbation-Based Contrastive Learning for Molecule Optimization.
Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence, 2023

Adaptive Compositional Continual Meta-Learning.
Proceedings of the International Conference on Machine Learning, 2023

ImmRegInformer: an interpretable Transformer-based method for prioritizing immune-regulatory cancer drivers.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

PACS: Prediction and analysis of cancer subtypes from multi-omics data based on a multi-head attention mechanism model.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

Interpretable multi-view attention network for drug-drug interaction prediction.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

LagNet: Deep Lagrangian Mechanics for Plug-and-Play Molecular Representation Learning.
Proceedings of the Thirty-Seventh AAAI Conference on Artificial Intelligence, 2023

2022
Accurate prediction of molecular properties and drug targets using a self-supervised image representation learning framework.
Nat. Mac. Intell., November, 2022

Monodirectional Evolutional Symport Tissue P Systems With Promoters and Cell Division.
IEEE Trans. Parallel Distributed Syst., 2022

3DMol-Net: Learn 3D Molecular Representation Using Adaptive Graph Convolutional Network Based on Rotation Invariance.
IEEE J. Biomed. Health Informatics, 2022

A Robust Algorithm Based on Link Label Propagation for Identifying Functional Modules From Protein-Protein Interaction Networks.
IEEE ACM Trans. Comput. Biol. Bioinform., 2022

An adaptive convergence enhanced evolutionary algorithm for many-objective optimization problems.
Swarm Evol. Comput., 2022

Normal forms for spiking neural P systems and some of its variants.
Inf. Sci., 2022

Rule synchronization for monodirectional tissue-like P systems with channel states.
Inf. Comput., 2022

On the cross-migrativity between uninorms and overlap (grouping) functions.
Fuzzy Sets Syst., 2022

Molecule optimization via multi-objective evolutionary in implicit chemical space.
CoRR, 2022

Multi-View Substructure Learning for Drug-Drug Interaction Prediction.
CoRR, 2022

Deep learning for drug repurposing: methods, databases, and applications.
CoRR, 2022

MLysPRED: graph-based multi-view clustering and multi-dimensional normal distribution resampling techniques to predict multiple lysine sites.
Briefings Bioinform., 2022

preMLI: a pre-trained method to uncover microRNA-lncRNA potential interactions.
Briefings Bioinform., 2022

Deep learning joint models for extracting entities and relations in biomedical: a survey and comparison.
Briefings Bioinform., 2022

Learning spatial structures of proteins improves protein-protein interaction prediction.
Briefings Bioinform., 2022

A weighted bilinear neural collaborative filtering approach for drug repositioning.
Briefings Bioinform., 2022

Are dropout imputation methods for scRNA-seq effective for scATAC-seq data?
Briefings Bioinform., 2022

Deep learning in retrosynthesis planning: datasets, models and tools.
Briefings Bioinform., 2022

A heterogeneous graph cross-omics attention model for single-cell representation learning.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

2021
ITP-Pred: an interpretable method for predicting, therapeutic peptides with fused features low-dimension representation.
Briefings Bioinform., July, 2021

Mobility Based Trust Evaluation for Heterogeneous Electric Vehicles Network in Smart Cities.
IEEE Trans. Intell. Transp. Syst., 2021

A Polar-Metric-Based Evolutionary Algorithm.
IEEE Trans. Cybern., 2021

Monodirectional Tissue P Systems With Promoters.
IEEE Trans. Cybern., 2021

HeTDR: Drug repositioning based on heterogeneous networks and text mining.
Patterns, 2021

ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties.
Nucleic Acids Res., 2021

Solving a PSPACE-complete problem by symport/antiport P systems with promoters and membrane division.
J. Membr. Comput., 2021

Homogeneous spiking neural P systems with structural plasticity.
J. Membr. Comput., 2021

Monodirectional tissue P systems with channel states.
Inf. Sci., 2021

A Framework for Evolving Spiking Neural P Systems.
Int. J. Unconv. Comput., 2021

The computational power of monodirectional tissue P systems with symport rules.
Inf. Comput., 2021

Neural-like P systems with plasmids.
Inf. Comput., 2021

Heterogeneous network-based drug repurposing for COVID-19.
CoRR, 2021

Large-Scale Approximate k-NN Graph Construction on GPU.
CoRR, 2021

CarSite-II: an integrated classification algorithm for identifying carbonylated sites based on K-means similarity-based undersampling and synthetic minority oversampling techniques.
BMC Bioinform., 2021

Minirmd: accurate and fast duplicate removal tool for short reads via multiple minimizers.
Bioinform., 2021

MUFFIN: multi-scale feature fusion for drug-drug interaction prediction.
Bioinform., 2021

iEnhancer-XG: interpretable sequence-based enhancers and their strength predictor.
Bioinform., 2021

A novel antibacterial peptide recognition algorithm based on BERT.
Briefings Bioinform., 2021

Deep learning methods for biomedical named entity recognition: a survey and qualitative comparison.
Briefings Bioinform., 2021

Predicting enhancer-promoter interactions by deep learning and matching heuristic.
Briefings Bioinform., 2021

De novo generation of dual-target ligands using adversarial training and reinforcement learning.
Briefings Bioinform., 2021

A spatial-temporal gated attention module for molecular property prediction based on molecular geometry.
Briefings Bioinform., 2021

Application of deep learning methods in biological networks.
Briefings Bioinform., 2021

Drug repositioning based on the heterogeneous information fusion graph convolutional network.
Briefings Bioinform., 2021

Artificial-Intelligence-Enabled Reagent-Free Imaging Hematology Analyzer.
Adv. Intell. Syst., 2021

Fast k-NN Graph Construction by GPU based NN-Descent.
Proceedings of the CIKM '21: The 30th ACM International Conference on Information and Knowledge Management, Virtual Event, Queensland, Australia, November 1, 2021

Pm<sup>6</sup> A: an Integrated Classification Algorithm for 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Identifying m<sup>6</sup> A Sites.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

LADstackING: Stacking Ensemble Learning-based Computational Model for Predicting Potential LncRNA-disease Associations.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

2020
On the Computational Power of Asynchronous Axon Membrane Systems.
IEEE Trans. Emerg. Top. Comput. Intell., 2020

A Network Reduction-Based Multiobjective Evolutionary Algorithm for Community Detection in Large-Scale Complex Networks.
IEEE Trans. Cybern., 2020

A Consensus Community-Based Particle Swarm Optimization for Dynamic Community Detection.
IEEE Trans. Cybern., 2020

Multiobjective Particle Swarm Optimization Based on Network Embedding for Complex Network Community Detection.
IEEE Trans. Comput. Soc. Syst., 2020

Deep Collaborative Filtering for Prediction of Disease Genes.
IEEE ACM Trans. Comput. Biol. Bioinform., 2020

The computational power of cell-like P systems with one protein on membrane.
J. Membr. Comput., 2020

Repurpose Open Data to Discover Therapeutics for COVID-19 using Deep Learning.
CoRR, 2020

Network-based prediction of drug-target interactions using an arbitrary-order proximity embedded deep forest.
Bioinform., 2020

Identifying enhancer-promoter interactions with neural network based on pre-trained DNA vectors and attention mechanism.
Bioinform., 2020

StackCPPred: a stacking and pairwise energy content-based prediction of cell-penetrating peptides and their uptake efficiency.
Bioinform., 2020

Sequence clustering in bioinformatics: an empirical study.
Briefings Bioinform., 2020

Predicting disease-associated circular RNAs using deep forests combined with positive-unlabeled learning methods.
Briefings Bioinform., 2020

Computational methods for identifying the critical nodes in biological networks.
Briefings Bioinform., 2020

A novel molecular representation with BiGRU neural networks for learning atom.
Briefings Bioinform., 2020

KGNN: Knowledge Graph Neural Network for Drug-Drug Interaction Prediction.
Proceedings of the Twenty-Ninth International Joint Conference on Artificial Intelligence, 2020

A drug information embedding method based on graph convolution neural network.
Proceedings of the 22nd IEEE International Conference on E-health Networking, 2020

A multi-task learning method for analyzing microbiota as cancer immunotherapy signal.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020

2019
MOEA/HD: A Multiobjective Evolutionary Algorithm Based on Hierarchical Decomposition.
IEEE Trans. Cybern., 2019

An Evolutionary Algorithm Based on Minkowski Distance for Many-Objective Optimization.
IEEE Trans. Cybern., 2019

Meta-Path Methods for Prioritizing Candidate Disease miRNAs.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Details in the evaluation of circular RNA detection tools: Reply to Chen and Chuang.
PLoS Comput. Biol., 2019

A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications.
PLoS Comput. Biol., 2019

Matrix representation and simulation algorithm of spiking neural P systems with structural plasticity.
J. Membr. Comput., 2019

On solutions and representations of spiking neural P systems with rules on synapses.
Inf. Sci., 2019

deepDR: a network-based deep learning approach to in silico drug repositioning.
Bioinform., 2019

Drug Target Interaction Prediction using Multi-task Learning and Co-attention.
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

GraphCPI: Graph Neural Representation Learning for Compound-Protein Interaction.
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

A Deep Neural Network for Antimicrobial Peptide Recognition.
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

2018
Spiking Neural P Systems With Colored Spikes.
IEEE Trans. Cogn. Dev. Syst., 2018

Prediction of potential disease-associated microRNAs using structural perturbation method.
Bioinform., 2018

Structural Hole Spanner in HumanNet Identifies Disease Gene and Drug targets.
IEEE Access, 2018

An Implementation of Elementary Arithmetic with Virus Machine.
Proceedings of the Enjoying Natural Computing, 2018

Small Spiking Neural P Systems with Structural Plasticity.
Proceedings of the Enjoying Natural Computing, 2018

Drug Target Interaction Prediction with Non-random Missing Labels.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

LncRNA-disease association prediction based on neighborhood information aggregation in neural network.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

2017
Prediction and Validation of Disease Genes Using HeteSim Scores.
IEEE ACM Trans. Comput. Biol. Bioinform., 2017

Inferring MicroRNA-Disease Associations by Random Walk on a Heterogeneous Network with Multiple Data Sources.
IEEE ACM Trans. Comput. Biol. Bioinform., 2017

A comprehensive overview and evaluation of circular RNA detection tools.
PLoS Comput. Biol., 2017

Theory and Application of Bio-inspired Intelligence and Methods.
J. Univers. Comput. Sci., 2017

Reconstructing evolutionary trees in parallel for massive sequences.
BMC Syst. Biol., 2017

Motion generation of multi-legged robot in complex terrains by using estimation of distribution algorithm.
Proceedings of the 2017 IEEE Symposium Series on Computational Intelligence, 2017

Iteratively collective prediction of disease-gene associations through the incomplete network.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

2016
Computing with viruses.
Theor. Comput. Sci., 2016

Embedded Based Miniaturized Universal Electrochemical Sensing Platform.
J. Sensors, 2016

Investment behavior prediction in heterogeneous information network.
Neurocomputing, 2016

Pretata: predicting TATA binding proteins with novel features and dimensionality reduction strategy.
BMC Syst. Biol., 2016

Integrative approaches for predicting microRNA function and prioritizing disease-related microRNA using biological interaction networks.
Briefings Bioinform., 2016

HPTree: Reconstructing phylogenetic trees for ultra-large unaligned DNA sequences via NJ model and Hadoop.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

Latent factor model with heterogeneous similarity regularization for predicting gene-disease associations.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015
Asynchronous Spiking Neural P Systems with Anti-Spikes.
Neural Process. Lett., 2015

Asynchronous spiking neural P systems with rules on synapses.
Neurocomputing, 2015

The power of time-free tissue P systems: Attacking NP-complete problems.
Neurocomputing, 2015

Identification of cytokine via an improved genetic algorithm.
Frontiers Comput. Sci., 2015

A decision-making framework for precision marketing.
Expert Syst. Appl., 2015

A Stable Matching-Based Selection and Memory Enhanced MOEA/D for Evolutionary Dynamic Multiobjective Optimization.
Proceedings of the 27th IEEE International Conference on Tools with Artificial Intelligence, 2015

Short-term optimal hydrothermal scheduling problem considering power flow constraint.
Proceedings of the IEEE Congress on Evolutionary Computation, 2015

MOEA/D for Energy-Aware Scheduling on Heterogeneous Computing Systems.
Proceedings of the Bio-Inspired Computing - Theories and Applications, 2015

2014
On Some Classes of Sequential Spiking Neural P Systems.
Neural Comput., 2014

Spiking Neural P Systems with Thresholds.
Neural Comput., 2014

Decision Tree Classification Model for Popularity Forecast of Chinese Colleges.
J. Appl. Math., 2014

Solving Multidimensional 0-1 Knapsack Problem with Time-Free Tissue P Systems.
J. Appl. Math., 2014

On languages generated by spiking neural P systems with weights.
Inf. Sci., 2014

Weighted Spiking Neural P Systems with Rules on Synapses.
Fundam. Informaticae, 2014

A hybrid heuristic algorithm for the 2D variable-sized bin packing problem.
Eur. J. Oper. Res., 2014

Small universal simple spiking neural P systems with weights.
Sci. China Inf. Sci., 2014

nDNA-prot: identification of DNA-binding proteins based on unbalanced classification.
BMC Bioinform., 2014

A New Graphical Representation of Protein Sequences Based on Dual-Vector Model.
Proceedings of the Bio-Inspired Computing - Theories and Applications, 2014

Time-Free Tissue P Systems for Solving the Hamilton Path Problem.
Proceedings of the Bio-Inspired Computing - Theories and Applications, 2014

2013
A Polynomial-Time Solution to Constraint Satisfaction Problems by Neural-like P Systems.
Int. J. Unconv. Comput., 2013

Spiking neural P systems with anti-spikes and without annihilating priority working in a 'flip-flop' way.
Int. J. Comput. Sci. Math., 2013

A Bayesian Investment Model for Online P2P Lending.
Proceedings of the Frontiers in Internet Technologies, 2013

Stock Price Forecast Using Tree Augmented Naïve (TAN) Bayes.
Proceedings of The Eighth International Conference on Bio-Inspired Computing: Theories and Applications, 2013

2012
Spiking Neural P Systems with Weighted Synapses.
Neural Process. Lett., 2012

A uniform solution to the independent set problem through tissue P systems with cell separation.
Frontiers Comput. Sci., 2012

2011
Time-Free Spiking Neural P Systems.
Neural Comput., 2011

A Novel Membrane Algorithm Based on Differential Evolution for Numerical Optimization.
Int. J. Unconv. Comput., 2011

Spiking Neural P Systems for Arithmetic Operations.
Proceedings of the Sixth International Conference on Bio-Inspired Computing: Theories and Applications, 2011

P Systems with 2D Picture Grammars.
Proceedings of the Sixth International Conference on Bio-Inspired Computing: Theories and Applications, 2011

A Modified Estimation of Distribution Algorithm for Numeric Optimization.
Proceedings of the Sixth International Conference on Bio-Inspired Computing: Theories and Applications, 2011

2010
Deterministic solutions to QSAT and Q3SAT by spiking neural P systems with pre-computed resources.
Theor. Comput. Sci., 2010

A weakly universal spiking neural P system.
Math. Comput. Model., 2010

Matrix Representation of Spiking Neural P Systems.
Proceedings of the Membrane Computing, 2010

Small universal asynchronous spiking neural P systems.
Proceedings of the Fifth International Conference on Bio-Inspired Computing: Theories and Applications, 2010

2009
On languages generated by asynchronous spiking neural P systems.
Theor. Comput. Sci., 2009

Homogeneous Spiking Neural P Systems.
Fundam. Informaticae, 2009

A Note on Small Universal Spiking Neural P Systems.
Proceedings of the Membrane Computing, 10th International Workshop, 2009

2008
On string languages generated by spiking neural P systems with exhaustive use of rules.
Nat. Comput., 2008

Smaller Universal Spiking Neural P Systems.
Fundam. Informaticae, 2008


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