2024
Vulnerability detection based on transformer and high-quality number embedding.
Concurr. Comput. Pract. Exp., December, 2024
Predicting cell-type specific disease genes of diabetes with the biological network.
Comput. Biol. Medicine, February, 2024
PIORS: Personalized Intelligent Outpatient Reception based on Large Language Model with Multi-Agents Medical Scenario Simulation.
CoRR, 2024
CellAgent: An LLM-driven Multi-Agent Framework for Automated Single-cell Data Analysis.
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CoRR, 2024
Overview of the CAIL 2023 Argument Mining Track.
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CoRR, 2024
Beyond ESM2: Graph-Enhanced Protein Sequence Modeling with Efficient Clustering.
CoRR, 2024
postGWAS: A web server for deciphering the causality post the genome-wide association studies.
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Comput. Biol. Medicine, 2024
Accurately deciphering spatial domains for spatially resolved transcriptomics with stCluster.
Briefings Bioinform., 2024
Identifying brain disease genes via integrating brain imaging and molecular network.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2024
Designing Biological Sequences without Prior Knowledge Using Evolutionary Reinforcement Learning.
Proceedings of the Thirty-Eighth AAAI Conference on Artificial Intelligence, 2024
2023
scMultiGAN: cell-specific imputation for single-cell transcriptomes with multiple deep generative adversarial networks.
Briefings Bioinform., September, 2023
Collaborative deep learning improves disease-related circRNA prediction based on multi-source functional information.
Briefings Bioinform., March, 2023
DFinder: a novel end-to-end graph embedding-based method to identify drug-food interactions.
Bioinform., January, 2023
DxFormer: a decoupled automatic diagnostic system based on decoder-encoder transformer with dense symptom representations.
Bioinform., January, 2023
A benchmark for automatic medical consultation system: frameworks, tasks and datasets.
Bioinform., January, 2023
DISC-MedLLM: Bridging General Large Language Models and Real-World Medical Consultation.
CoRR, 2023
HQProtoPNet: An Evidence-Based Model for Interpretable Image Recognition.
Proceedings of the International Joint Conference on Neural Networks, 2023
2022
Flexibility and rigidity index for chromosome packing, flexibility and dynamics analysis.
Frontiers Comput. Sci., 2022
Hierarchical reinforcement learning for automatic disease diagnosis.
Bioinform., 2022
A review and performance evaluation of clustering frameworks for single-cell Hi-C data.
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Briefings Bioinform., 2022
Correction to: Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation.
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Briefings Bioinform., 2022
Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation.
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Briefings Bioinform., 2022
A network-based method for brain disease gene prediction by integrating brain connectome and molecular network.
Briefings Bioinform., 2022
A Two Stage Adaptation Framework for Frame Detection via Prompt Learning.
Proceedings of the 29th International Conference on Computational Linguistics, 2022
Discovering eQTL Regulatory Patterns Through eQTLMotif.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022
Hypergraph-based Gene Ontology Embedding for Disease Gene Prediction.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022
Deep Representation Debiasing via Mutual Information Minimization and Maximization (Student Abstract).
Proceedings of the Thirty-Sixth AAAI Conference on Artificial Intelligence, 2022
2021
SC2disease: a manually curated database of single-cell transcriptome for human diseases.
Nucleic Acids Res., 2021
ED2: An Environment Dynamics Decomposition Framework for World Model Construction.
CoRR, 2021
A pipeline for RNA-seq based eQTL analysis with automated quality control procedures.
BMC Bioinform., 2021
A novel method for predicting cell abundance based on single-cell RNA-seq data.
BMC Bioinform., 2021
Prediction and collection of protein-metabolite interactions.
Briefings Bioinform., 2021
Identifying drug-target interactions based on graph convolutional network and deep neural network.
Briefings Bioinform., 2021
Integrating multi-network topology for gene function prediction using deep neural networks.
Briefings Bioinform., 2021
An end-to-end heterogeneous graph representation learning-based framework for drug-target interaction prediction.
Briefings Bioinform., 2021
Curriculum Learning for Vision-and-Language Navigation.
Proceedings of the Advances in Neural Information Processing Systems 34: Annual Conference on Neural Information Processing Systems 2021, 2021
Predicting Hepatoma-Related Genes Based on Representation Learning of PPI network and Gene Ontology Annotations.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021
DCAE: Selecting Discriminative Genes on Single-cell RNA-seq Data for Cell-type Quantification.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021
2020
Mining Relationships among Multiple Entities in Biological Networks.
IEEE ACM Trans. Comput. Biol. Bioinform., 2020
A learning-based method for drug-target interaction prediction based on feature representation learning and deep neural network.
BMC Bioinform., 2020
Combining sequence and network information to enhance protein-protein interaction prediction.
BMC Bioinform., 2020
DeepLGP: a novel deep learning method for prioritizing lncRNA target genes.
Bioinform., 2020
Identifying emerging phenomenon in long temporal phenotyping experiments.
Bioinform., 2020
Efficient Deep Reinforcement Learning via Adaptive Policy Transfer.
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Proceedings of the Twenty-Ninth International Joint Conference on Artificial Intelligence, 2020
Automatic Term Name Generation for Gene Ontology: Task and Dataset.
Proceedings of the Findings of the Association for Computational Linguistics: EMNLP 2020, 2020
Efficient Deep Reinforcement Learning through Policy Transfer.
Proceedings of the 19th International Conference on Autonomous Agents and Multiagent Systems, 2020
2019
Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO.
BMC Syst. Biol., 2019
LncDisAP: a computation model for LncRNA-disease association prediction based on multiple biological datasets.
BMC Bioinform., 2019
Prioritizing candidate diseases-related metabolites based on literature and functional similarity.
BMC Bioinform., 2019
Combining gene ontology with deep neural networks to enhance the clustering of single cell RNA-Seq data.
BMC Bioinform., 2019
TS-GOEA: a web tool for tissue-specific gene set enrichment analysis based on gene ontology.
BMC Bioinform., 2019
A learning-based framework for miRNA-disease association identification using neural networks.
Bioinform., 2019
Integrating Multi-Network Topology via Deep Semi-supervised Node Embedding.
Proceedings of the 28th ACM International Conference on Information and Knowledge Management, 2019
A deconvolution method for predicting cell abundance based on single cell RNA-seq data.
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019
Integrating Sequence and Network Information to Enhance Protein-Protein Interaction Prediction Using Graph Convolutional Networks.
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019
Towards Gene Function Prediction via Multi-Networks Representation Learning.
Proceedings of the Thirty-Third AAAI Conference on Artificial Intelligence, 2019
2018
Deep Feature Learning of Multi-Network Topology for Node Classification.
CoRR, 2018
Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach.
BMC Syst. Biol., 2018
Measuring phenotype-phenotype similarity through the interactome.
BMC Bioinform., 2018
Identifying Representative Network Motifs for Inferring Higher-order Structure of Biological Networks.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018
Predicting candidate disease-related lncRNAs based on network random walk.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018
TSGOE: A web tool for tissue-specific gene ontology enrichment.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018
2017
A novel method to measure the semantic similarity of HPO terms.
Int. J. Data Min. Bioinform., 2017
Identifying term relations cross different gene ontology categories.
BMC Bioinform., 2017
Investigations on factors influencing HPO-based semantic similarity calculation.
J. Biomed. Semant., 2017
2016
Extending gene ontology with gene association networks.
Bioinform., 2016
Joint detection of copy number variations in parent-offspring trios.
Bioinform., 2016
Measuring phenotype semantic similarity using Human Phenotype Ontology.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016
Analyzing factors involved in the HPO-based semantic similarity calculation.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016
2015
LncRNA2Target: a database for differentially expressed genes after lncRNA knockdown or overexpression.
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Nucleic Acids Res., 2015
Measuring semantic similarities by combining gene ontology annotations and gene co-function networks.
BMC Bioinform., 2015
A web tool for measuring gene semantic similarities by combining gene ontology and gene co-function networks.
Proceedings of the 6th ACM Conference on Bioinformatics, 2015
2014
An integrative approach for measuring semantic similarities using gene ontology.
BMC Syst. Biol., 2014
Towards integrative gene functional similarity measurement.
BMC Bioinform., 2014
2013
Identifying cross-category relations in gene ontology and constructing genome-specific term association networks.
BMC Bioinform., 2013