AI

EpiGePT: a pretrained transformer-basedlanguage model for context-specific humanepigenomics
Zijing Gao*, Qiao Liu*,†, Wanwen Zeng, Rui Jiang†, Wing Hung Wong†. Genome Biology, 2024.
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EpiGePT: a pretrained transformer-basedlanguage model for context-specific humanepigenomics
DeepDrug: A general graph-based deep learning framework for drug-drug interactions and drug-target interactions prediction
Qijin Yin, Rui Fan, Xusheng Cao Qiao Liu#, Rui Jiang# and Wanwen Zeng#. Quantitative Biology, 2023.
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DeepDrug: A general graph-based deep learning framework for drug-drug interactions and drug-target interactions prediction
Applications of transformer-based language models in bioinformatics: a survey
Shuang Zhang, Yuti Liu, Shuang Chen, Qiao Liu, Wanwen Zeng. Bioinformatics Advances, 2023.
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Deep generative modeling and clustering of single cell Hi-C data
Qiao Liu, Wanwen Zeng, Wei Zhang, Sicheng Wang, Hongyang Chen, Rui Jiang, Mu Zhou, Shaoting Zhang. Brief. Bioinform, 2022.
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Deep generative modeling and clustering of single cell Hi-C data
AggEnhance: Aggregation Enhancement by Class Interior Points in Federated Learning with Non-IID Data
Jinxiang Ou, Yunheng Shen, Feng Wang, Qiao Liu, Xuegong Zhang, Hairong Lv. ACM Transactions on Intelligent Systems and Technology, 2022.
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DualGCN: a dual graph convolutional network model to predict cancer drug response
Tianxing Ma, Qiao Liu, Haochen Li, Mu Zhou, Rui Jiang & Xuegong Zhang. BMC Bioinformatics, 2022.
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scGraph: a graph neural network-based approach to automatically identify cell types
Qijin Yin, Qiao Liu, Zhuoran Fu, Rui Jiang. Bioinformatics, 2022.
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DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility
Qiao Liu, Kui Hua, Xuegong Zhang, Wing Hung Wong, Rui Jiang. Genomics, Proteomics & Bioinformatics, 2022.
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DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility
Multimodal single cell data integration challenge: Results and lessons learned
Christopher Lance, Malte D Luecken, Daniel B Burkhardt,…,Qiao Liu,…,Fabian J Theis. Proceedings of Machine Learning Research(PMLR), 2022.
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Simultaneous deep generative modelling and clustering of single-cell genomic data
Qiao Liu, Shengquan Chen, Rui Jiang, Wing Hung Wong. Nature Machine Intelligence, 2021.
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Simultaneous deep generative modelling and clustering of single-cell genomic data