Graph Neural Networks for Cancer Driver Gene Prediction: From Fundamentals to Applications.

Evaluating Graph Neural Network Architectures for Multi-Omics Cancer Subtyping using Methylation and Gene Expression Profiles

A benchmarking study on multiple GNNs on a Protein-Protein Interaction (PPI) network for Kidney Renal Clear Cell Carcinoma and Breast cancer subtype prediction, performing an in-depth investigation of architectures, incorporating skip connections and various data modalities.

Bidirectional network hubs: NT-genes as candidate targets for partial cancer reversal

Background Reversing the tumor phenotype is a long-standing challenge in cancer biology. Although GRNs comprise thousands of genes, normal and tumor tissues occupy distinct, low-dimensional attractors in expression space, raising the possibility that targeting a few key genes could induce widespread transcriptional cha...

A Novel Cancer Driver Genes Identification Method Based on Self-Supervised Dual Masked Graph Autoencoder.

TriOmicNet: A Novel Multi-layer Network Diffusion Approach Integrating Three Types of Scores to Identify Cancer Driver Genes.

Overall, TriOmicNet provides an integrative framework for cancer driver gene prioritization and may support further investigation of cancer biomarkers and therapeutic targets.

Sparse weighted graph convolutional networks for colorectal cancer classification using Hi-C data

Colorectal cancer remains a leading cause of global mortality, driving demand for precise screening methodologies that leverage complex genomic architectures. The functional interplay between spatial chromatin organization and regulatory networks is increasingly recognized as an important component of malignant trans...

Graph neural network-based risk stratification of prostate cancer using gene expression and SHAP interpretability

Accurate risk stratification is essential for guiding treatment decisions and preventing over treatment of prostate cancer, which remains one of the most prevalent cancers among adult men. While the Gleason score, obtained from prostate biopsies, is routinely used to assess tumor aggressiveness, the biopsy procedure ca...