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Schematic of network‐based graph embedding neural network framework. (A) Data preparation and integration. Gene interaction networks from multiple sources are merged into a single molecular graph, which is subsequently supplemented with transcriptome (or other omics) data along with information on known cancer driver genes. (B) Graph embedding for training. In this graph, nodes represent genes, edges represent gene interactions, node features correspond to multidimensional gene expression vectors and edge features encode gene interaction data from different sources as n ‐dimensional binary vectors ( n = 3, three sources in this plot). (C) Graph embedding‐based neural network framework for omics data integration. This framework is designed to enhance node embedding extraction within a graph for node classification tasks. The framework processes molecular interaction graphs and is trained on these graphs. The node embeddings from all subgraphs are used to generate features separately that can be coupled with a convolutional neural network or graph attention network model to generate the final gene‐ranked list, representing their likelihood (equivalent to ranking score) of being associated with cancer. CDGs, cancer driver genes.

Journal: Journal of Cellular and Molecular Medicine

Article Title: Enhancing Molecular Network‐Based Cancer Driver Gene Prediction Using Machine Learning Approaches: Current Challenges and Opportunities

doi: 10.1111/jcmm.70351

Figure Lengend Snippet: Schematic of network‐based graph embedding neural network framework. (A) Data preparation and integration. Gene interaction networks from multiple sources are merged into a single molecular graph, which is subsequently supplemented with transcriptome (or other omics) data along with information on known cancer driver genes. (B) Graph embedding for training. In this graph, nodes represent genes, edges represent gene interactions, node features correspond to multidimensional gene expression vectors and edge features encode gene interaction data from different sources as n ‐dimensional binary vectors ( n = 3, three sources in this plot). (C) Graph embedding‐based neural network framework for omics data integration. This framework is designed to enhance node embedding extraction within a graph for node classification tasks. The framework processes molecular interaction graphs and is trained on these graphs. The node embeddings from all subgraphs are used to generate features separately that can be coupled with a convolutional neural network or graph attention network model to generate the final gene‐ranked list, representing their likelihood (equivalent to ranking score) of being associated with cancer. CDGs, cancer driver genes.

Article Snippet: Graph convolutional network , Omics data and gene or protein interaction network , The topology of graphs, including the direct and indirect relationships between nodes (genes), can be learned. , EMOGI [ ], MTGCN [ ], DGMP [ ], MNGCL [ ], NIGCNDriver [ ], CGMega [ ] .

Techniques: Gene Expression, Extraction