The system describes the diagnostic procedures involving the intelligent medical device (iMD) system. After data is collected from a patient by using cellular and molecular samples, the device detects and analyzes pathology. The system uses lab on a chip (LOC) data analysis, including microarrays, to analyze DNA mutations and protein anomalies. The medical pathologies are modeled by the iMD computer system and solutions to multi-objective optimization problems are organized using scenario options. The diagnostic functionality of the iMD system also tracks complex regulatory network pathologies.