This dissertation is divided into two parts: (i) modeling and the concomitant optimization algorithms for designing Command & Control ( C2) organizations; and (ii) disease diagnosis and discovering organizational networks and their processes from noisy observations (i.e., negative /positive findings, or uncertain message data) using inference techniques from graphical models. In the first part, we seek to design organizational (C2) structures with the ability to conduct dynamic action synchronization, achieve organization agility, and increase speed of command over a robust, decentralized architecture. The key components to design and evaluation of C2 organizational structure are: (i) mathematical modeling of the mission and organization an...