Early warning and diagnosis of liver cancer based on dynamic network biomarker and deep learning

• Published in: Computational and structural biotechnology journal Vol. 21; pp. 3478 - 3489
• Main Authors: Han, Yukun, Akhtar, Javed, Liu, Guozhen, Li, Chenzhong, Wang, Guanyu
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.01.2023; Research Network of Computational and Structural Biotechnology; Elsevier
• Subjects: Dynamic network biomarkers; Early warning of diseases; Graph convolutional neural networks; Hepatocellular carcinoma; Latency detection; Hepatocellular carcinoma; Graph convolutional neural networks; Dynamic network biomarkers; Latency detection; Early warning of diseases
• ISSN: 2001-0370; 2001-0370
• DOI: 10.1016/j.csbj.2023.07.002

Early detection of complex diseases like hepatocellular carcinoma remains challenging due to their network-driven pathology. Dynamic network biomarkers (DNB) based on monitoring changes in molecular correlations may enable earlier predictions. However, DNB analysis often overlooks disease heterogeneity. We integrated DNB analysis with graph convolutional neural networks (GCN) to identify critical transitions during hepatocellular carcinoma development in a mouse model. A DNB-GCN model was constructed using transcriptomic data and gene expression levels as node features. DNB analysis identified a critical transition point at 7 weeks of age despite histological examinations being unable to detect cancerous changes at that time point. The DNB-GCN model achieved 100% accuracy in classifying healthy and cancerous mice, and was able to accurately predict the health status of newly introduced mice. The integration of DNB analysis and GCN demonstrates potential for the early detection of complex diseases by capturing network structures and molecular features that conventional biomarker discovery methods overlook. The approach warrants further development and validation. [Display omitted]