Results indicate that VARION’s GIS-weighted centroid architecture enables individual-patient molecular subtyping that outperforms existing NBS and graph-learning clustering approaches, with high sensitivity for clinically actionable rare subtypes and robust cross- platform generalization.
Accurate survival prediction in cancer remains challenging due to the sparsity of somatic mutation profiles and the failure of existing models to capture higher-order gene-gene dependencies. Network diffusion methods such as Random Walk with Restart (RWR) can propagate mutation signals across protein-protein interactio...
Stuti Kumari, Sakshi Gujral, Abhishek Halder et al.· Journal of Computational Bio...· 0 citations
This chapter provides a comprehensive technical protocol for predicting CDGs using a Graph Convolutional Network (GCN) and guides the reader through hyperparameter optimization, model training, and performance evaluation, while discussing practical considerations related to generalization, computational cost, and inter...
Renan Soares de Andrades, M. Recamonde-Mendoza· Methods in molecular biology· 0 citations
Paired Wilcoxon tests in 39 AURORA-US patients with matched primary and metastatic samples confirm that 4 of the 10 IG-identified TFs are significantly altered during metastatic progression after Bonferroni correction.
C. Fernandez-Lozano, David Ferreiro, Patricia V.-del-Río· bioRxiv· 0 citations
NGM-AML, a modular model predicting ex vivo drug response from BeatAML2 RNA-seq and sensitivity data, achieves mean Pearson and Spearman correlations of 0.324 and 0.326 across drugs, consistent with known AML survival and drug-resistance mechanisms.
Yu-Rung Wu, Yuan Wang, Wen-Jia Zhao et al.· Computational biology and ch...· 0 citations
OncoRAG enables accurate clinical phenotyping from multilingual oncology notes using a locally deployable mid-size model, without model weight fine-tuning or external data sharing.
P. Salome, M. Knoll, David Walz et al.· npj Digital Medicine· 0 citations
An algorithmic Matching Score is described that evaluates cancer drugs’/drug combinations’ ability to address a patients’ entire next-generation sequencing/multi-omic-derived molecular profile and underscores the clinical importance of the precision medicine approach that maximizes matching of multiple molecular altera...
Ally Perlina, Subha Krishnan, K. Bush et al.· npj Genomic Medicine· 0 citations
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