The code of industrial management software typically features few system API calls and a high number of customized variables and structures. This makes the similarity of such codes difficult to compute using text features or traditional neural network methods. In this paper, we propose an FSPS-GNN model, which is based on graph neural networks (GNNs), to address this problem. The model categorizes code features into two types, outer graph and inner graph, and conducts training and prediction with four stages-feature embedding, feature enhancement, feature fusion, and similarity prediction. Moreover, differently structured GNNs were used in the embedding and enhancement stages, respectively, to increase the interaction of code features. Experiments with code from three open-source projects demonstrate that the model achieves an average precision of 87.57% and an 0.5 Score of 89.12%. Compared to existing similarity-computation models based on GNNs, this model exhibits a Mean Squared Error (MSE) that is approximately 0.0041 to 0.0266 lower and an 0.5 Score that is 3.3259% to 6.4392% higher. It broadens the application scope of GNNs and offers additional insights for the study of code-similarity issues.
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http://dx.doi.org/10.3390/e26060505 | DOI Listing |
J Chem Inf Model
January 2025
Department of Computer Science and Technology, Shantou University, Shantou 515063, China.
The human microbiota may influence the effectiveness of drug therapy by activating or inactivating the pharmacological properties of drugs. Computational methods have demonstrated their ability to screen reliable microbe-drug associations and uncover the mechanism by which drugs exert their functions. However, the previous prediction methods failed to completely exploit the neighborhood topologies of the microbe and drug entities and the diverse correlations between the microbe-drug entity pair and the other entities.
View Article and Find Full Text PDFJ Virol
December 2024
1Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA.
Flaviviruses utilize the cellular endoplasmic reticulum (ER) for all aspects of their lifecycle. Genome replication and other viral activities take place in structures called replication organelles (ROs), which are invaginations induced in the ER membrane. Among the required elements for RO formation is the biogenesis of viral nonstructural proteins NS4A and NS4B.
View Article and Find Full Text PDFMicrobiol Spectr
December 2024
Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands.
Metagenomics has revealed the incredible diversity of phages within the human gut. However, very few of these phages have been subjected to in-depth experimental characterization. One promising method of obtaining novel phages for experimental characterization is through induction of the prophages integrated into the genomes of cultured gut bacteria.
View Article and Find Full Text PDFPhytopathology
January 2025
Swedish University of Agricultural Sciences, Plant Protection Biology, Alnarp, Sweden;
Transglutaminases (TGases) are enzymes highly conserved among prokaryotic and eukaryotic organisms, where their role is to catalyze protein cross-linking. One of the putative TGases of has previously been shown to be localized to the cell wall. Based on sequence similarity we were able to identify six more genes annotated as putative TGases and show that these seven genes group together in phylogenetic analysis.
View Article and Find Full Text PDFClin Cancer Res
January 2025
University of Minnesota, Minneapolis, United States.
Purpose: 10-15% of prostate cancers (PCa) harbor recurrent FOXA1 aberrations whereby the alteration type and the effect on the forkhead( FKH) domain impacts protein-function. We developed a FOXA1 classification system to inform clinical management.
Experimental Design: 5,014 PCa were examined using whole exome and transcriptome sequencing from the Caris database.
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