Graph representation learning aims to map nodes or edges within a graph using low-dimensional vectors, while preserving as much topological information as possible. During past decades, numerous algorithms for graph representation learning have emerged. Among them, proximity matrix representation methods have been shown to exhibit excellent performance in experiments and scale to large graphs with millions of nodes. However, with the rapid development of the Internet, information interactions are happening at the scale of billions every moment. Most methods for similarity matrix factorization still focus on static graphs, leading to incomplete similarity descriptions and low embedding quality. To enhance the embedding quality of temporal graph learning, we propose a temporal graph representation learning model based on the matrix factorization of Time-constrained Personalize PageRank (TPPR) matrices. TPPR, an extension of personalized PageRank (PPR) that incorporates temporal information, better captures node similarities in temporal graphs. Based on this, we use Single Value Decomposition or Nonnegative Matrix Factorization to decompose TPPR matrices to obtain embedding vectors for each node. Through experiments on tasks such as link prediction, node classification, and node clustering across multiple temporal graphs, as well as a comparison with various experimental methods, we find that graph representation learning algorithms based on TPPR matrix factorization achieve overall outstanding scores on multiple temporal datasets, highlighting their effectiveness.
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http://dx.doi.org/10.3390/e26070588 | DOI Listing |
J Biomed Inform
January 2025
Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA; Harvard T.H. Chan School of Public Health, Boston, MA, USA. Electronic address:
Motivation: The increasing availability of electronic health record (EHR) systems has created enormous potential for translational research. Recent developments in representation learning techniques have led to effective large-scale representations of EHR concepts along with knowledge graphs that empower downstream EHR studies. However, most existing methods require training with patient-level data, limiting their abilities to expand the training with multi-institutional EHR data.
View Article and Find Full Text PDFSci Rep
January 2025
Department of Electrical and Computer Engineering, Hawassa University, Hawassa 05, Ethiopia.
Understanding human behavior and human action recognition are both essential components of effective surveillance video analysis for the purpose of guaranteeing public safety. However, existing approaches such as three-dimensional convolutional neural networks (3D CNN) and two-stream neural networks (2SNN) have computational hurdles due to the significant parameterization they require. In this paper, we offer HARNet, a specialized lightweight residual 3D CNN that is built on directed acyclic graphs and was created expressly to handle these issues and achieve effective human action detection.
View Article and Find Full Text PDFBrief Bioinform
November 2024
School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072 Shaanxi, China.
The identification of cancer driver genes is crucial for understanding the complex processes involved in cancer development, progression, and therapeutic strategies. Multi-omics data and biological networks provided by numerous databases enable the application of graph deep learning techniques that incorporate network structures into the deep learning framework. However, most existing methods do not account for the heterophily in the biological networks, which hinders the improvement of model performance.
View Article and Find Full Text PDFAlzheimers Dement
December 2024
Cleveland Clinic, Cleveland, OH, USA.
Background: Apolipoprotein E (ApoE) is the primary cholesterol and lipid transporting apolipoprotein in the central nervous system (CNS) and is the greatest genetic risk factor for Alzheimer's Disease (AD). There are three main isoforms differing by single amino acid changes: ε3 is "neutral", ε4 is "risk" (Cys112Arg), and ε2 is "resilience" (Arg158Cys). Rare forms (Christchurch, Jacksonville) have also been proposed as resilience alleles, while an ε4-like allele (with Arg61Thr) is present in non-human primates without AD risk.
View Article and Find Full Text PDFAlzheimers Dement
December 2024
Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany, Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA.
Background: Despite recent breakthroughs, Alzheimer's disease (AD) remains untreatable. In addition, we are still lacking robust biomarkers for early diagnosis and promising novel targets for therapeutic intervention. To enable utilizing the entirety of molecular evidence in the discovery and prioritization of potential novel biomarkers and targets, we have developed the AD Atlas, a network-based multi-omics data integration platform.
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