Some of the challenges regarding the previous covered topics are
• Validation How do we know the network structure is right?
• How do we know if the network function is right?
• Measuring and modeling protein expression
• Understanding the evolution of regulatory networks
• Mostly it is intractable to compute joint distributions so we focus on marginal distributions.
• Often we have a very large number of regulators or targets making some of the problems require simplifying assumption to be able to make it tractable.