Methods and devices for clustering a plurality of sub-networks of a larger interaction network using an enhanced hierarchical clustering algorithm are disclosed. The methods provide expression based sub-network generation using differentially expressed markers. The enhanced hierarchical clustering algorithm clusters the generated sub-networks based on a user defined customizable similarity coefficient. The methods use non-Boolean links to cluster similar sub-networks. This provides consideration of indirect relationships among sub-networks. The customizable similarity coefficient enables the methods to be used for diverse applications such as biomarker detection, patient stratification, personalized therapy, drug efficacy prediction, genetic similarity analysis in genetic diseases. The methods enable patient grouping based on the enhanced hierarchical clustering algorithm.
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