Deep graph clustering, which aims to reveal the underlying graph structure and divide the nodes into different clusters without human annotations, is a fundamental yet challenging task. However, we observe that the existing methods suffer from the representation collapse problem and tend to encode samples with different classes into the same latent embedding. Consequently, the discriminative capability of nodes is limited, resulting in suboptimal clustering performance. To address this problem, we propose a novel deep graph clustering algorithm termed improved dual correlation reduction network (IDCRN) through improving the discriminative capability of samples. Specifically, by approximating the cross-view feature correlation matrix to an identity matrix, we reduce the redundancy between different dimensions of features, thus improving the discriminative capability of the latent space explicitly. Meanwhile, the cross-view sample correlation matrix is forced to approximate the designed clustering-refined adjacency matrix to guide the learned latent representation to recover the affinity matrix even across views, thus enhancing the discriminative capability of features implicitly. Moreover, we avoid the collapsed representation caused by the oversmoothing issue in graph convolutional networks (GCNs) through an introduced propagation regularization term, enabling IDCRN to capture the long-range information with the shallow network structure. Extensive experimental results on six benchmarks have demonstrated the effectiveness and efficiency of IDCRN compared with the existing state-of-the-art deep graph clustering algorithms. The code of IDCRN is released at https://github.com/yueliu1999/IDCRN. Besides, we share a collection of deep graph clustering, including papers, codes, and datasets at https://github.com/yueliu1999/Awesome-Deep-Graph-Clustering.
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http://dx.doi.org/10.1109/TNNLS.2024.3406538 | DOI Listing |
J Chem Inf Model
January 2025
Key Laboratory for Bio-Electromagnetic Environment and Advanced Medical Theranostics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Longmian Avenue No. 101, Jiangsu 211166, China.
Predicting drug-target binding affinity (DTA) is a crucial task in drug discovery research. Recent studies have demonstrated that pocket features and interactions between targets and drugs significantly improve the understanding of DTA. However, challenges remain, particularly in the detailed consideration of both global and local information and the further modeling of pocket features.
View Article and Find Full Text PDFBrief Bioinform
November 2024
College of Communication Engineering, Jilin University, No. 2699 Qianjin Street, Chaoyang District, Changchun 130012, China.
Antibiotic resistance poses a significant threat to global health, making the development of alternative strategies to combat bacterial pathogens increasingly urgent. One such promising approach is the strategic use of bacteriophages (or phages) to specifically target and eradicate antibiotic-resistant bacteria. Phages, being among the most prevalent life forms on Earth, play a critical role in maintaining ecological balance by regulating bacterial communities and driving genetic diversity.
View Article and Find Full Text PDFJ Biomed Inform
January 2025
School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058 China; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA. Electronic address:
Objective: Current studies leveraging social media data for disease monitoring face challenges like noisy colloquial language and insufficient tracking of user disease progression in longitudinal data settings. This study aims to develop a pipeline for collecting, cleaning, and analyzing large-scale longitudinal social media data for disease monitoring, with a focus on COVID-19 pandemic.
Materials And Methods: This pipeline initiates by screening COVID-19 cases from tweets spanning February 1, 2020, to April 30, 2022.
Research (Wash D C)
January 2025
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Spatially resolved transcriptomics enable comprehensive measurement of gene expression at subcellular resolution while preserving the spatial context of the tissue microenvironment. While deep learning has shown promise in analyzing SCST datasets, most efforts have focused on sequence data and spatial localization, with limited emphasis on leveraging rich histopathological insights from staining images. We introduce GIST, a deep learning-enabled gene expression and histology integration for spatial cellular profiling.
View Article and Find Full Text PDFFront Pharmacol
January 2025
Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA, United States.
Introduction: Recent advances in 3D structure-based deep learning approaches demonstrate improved accuracy in predicting protein-ligand binding affinity in drug discovery. These methods complement physics-based computational modeling such as molecular docking for virtual high-throughput screening. Despite recent advances and improved predictive performance, most methods in this category primarily rely on utilizing co-crystal complex structures and experimentally measured binding affinities as both input and output data for model training.
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