Due date: Oct 24th midnight.
Submission: Please email your critique as a pdf to Prof. Roy (firstname.lastname@example.org) with subject “CS838/BMI826-023: Critique 1”. Please remember to add your name on the Critique.
The goal of this critique assignment is to discuss the papers overlapping the first two topics in class: integrative network inference and modeling dynamics in networks. Please write a critique (1-2 pages) focusing on the ideas and algorithms from the four papers mentioned below.
Reconstructing gene regulatory networks with bayesian networks by combining expression data with multiple sources of prior knowledge
Bayesian Inference of Signaling Network Topology in a Cancer Cell Line
Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks
Reconstructing dynamic regulatory maps
Please keep the following points in mind as you write your critique and address each in a separate section.
1. An overview of the general problem area these methods are addressing.
2. Briefly describe each method
3. How were the methods evaluated?
4. What novel insights were obtained using these methods?
5. What are the strengths and weaknesses of each method?
As an example, you can refer to these example critiques (Example1, Example2) that scored very highly. These critiques were written for a slightly different set of papers, but hopefully you can see these as examples of a good critique.