This thesis presents a class of graphical models for directly representing the joint cumulative distribution function (CDF) of many random variables, called cumulative distribution networks (CDNs). Unlike graphical models for probability density and mass functions, in a CDN, the marginal...

We investigate the Minimum Evolution Problem (MEP), an NP-hard network design problem arising from computational biology. The MEP consists in finding a weighted unrooted binary tree having n leaves, minimal length, and such that the sum of the edge weights belonging to the unique path between...

Gene Regulatory Networks (GRNs) have become a major focus of interest in recent years. Although much work has been done in elucidating the transcriptional regulatory network, the underlying mechanisms that have possibly influenced the evolution of these GRNs are still debatable. We have...