In this paper we consider the problem of graph-based transductive classification, and we are particularly interested in the directed graph scenario which is a natural form for many real world applications. Different from existing research efforts that either only deal with undirected graphs or circumvent directionality by means of symmetrization, we propose a novel random walk approach on directed graphs using absorbing Markov chains, which can be regarded as maximizing the accumulated expected number of visits from the unlabeled transient states. Our algorithm is simple, easy to implement, and works with large-scale graphs on binary, multiclass, and multi-label prediction problems. Moreover, it is capable of preserving the graph structure even when the input graph is sparse and changes over time, as well as retaining weak signals presented in the directed edges. We present its intimate connections to a number of existing methods, including graph kernels, graph Laplacian based methods, and spanning forest of graphs. Its computational complexity and the generalization error are also studied. Empirically, our algorithm is evaluated on a wide range of applications, where it has shown to perform competitively comparing to a suite of state-of-the-art methods. In particular, our algorithm is shown to work exceptionally well with large sparse directed graphs with e.g., millions of nodes and tens of millions of edges, where it significantly outperforms other state-of-the-art methods. In the dynamic graph setting involving insertion or deletion of nodes and edge-weight changes over time, it also allows efficient online updates that produce the same results as of the batch update counterparts.
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Int J Mol Sci
January 2025
School of Mathematics and Computer Science, Gannan Normal University, Ganzhou 341000, China.
Due to advances in big data technology, deep learning, and knowledge engineering, biological sequence visualization has been extensively explored. In the post-genome era, biological sequence visualization enables the visual representation of both structured and unstructured biological sequence data. However, a universal visualization method for all types of sequences has not been reported.
View Article and Find Full Text PDFCancers (Basel)
January 2025
Program in Public Health, Stony Brook Medicine, Stony Brook, NY 11794, USA.
Introduction: Colorectal cancer (CRC) is the third most commonly diagnosed cancer in the United States (U.S.).
View Article and Find Full Text PDFBiomedicines
January 2025
CarVasCare Research Group, Facultad de Enfermería de Cuenca, Universidad de Castilla-La Mancha, 16071 Cuenca, Spain.
: Poor metabolic control is associated with increased levels of advanced glycation end products (AGEs), which in turn may lead to increased arterial stiffness. The aim of this study was to estimate the association between glycated haemoglobin A1c (HbA1c) and aortic pulse wave velocity (a-PWV) in healthy subjects and to analyse the mediating effect of AGEs measured by skin autofluorescence (SAF) on this association. : HbA1c, a-PWV and SAF were analysed in 390 healthy Spanish subjects from the EVasCu study (42.
View Article and Find Full Text PDFCommun Biol
January 2025
Applied Mathematics and Computational Biology, IBENS, Ecole Normale Supérieure, PSL University, Paris, France.
Astrocytes form extensive networks with diverse calcium activity, yet the organization and connectivity of these networks across brain regions remain largely unknown. To address this, we developed AstroNet, a data-driven algorithm that uses two-photon calcium imaging to map temporal correlations in astrocyte activation. By organizing individual astrocyte activation events chronologically, our method reconstructs functional networks and extracts local astrocyte correlations.
View Article and Find Full Text PDFNeural Netw
January 2025
Hebei Key Laboratory of Marine Perception Network and Data Processing, Northeastern University (Qinhuangdao), Qinhuangdao 066004, China. Electronic address:
Entity alignment (EA) is a typical strategy for knowledge graph integration, aiming to identify and align different entity pairs representing the same real object from different knowledge graphs. Temporal Knowledge Graph (TKG) extends the static knowledge graph by introducing timestamps. However, since temporal knowledge graphs are constructed based on their own data sources, this usually leads to problems such as missing or redundant entity information in the temporal knowledge graph.
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