Why do we need a probabilistic model for a TF binding site?
What is the difference between PSSM and FMM? What are pros and cons of FMM?
Describe the proposed computational approach: probabilistic model; training data: observed/ hidden variables; evaluation methods.
Is there any room for improvement, either in terms of modeling or learning?
Give examples of other problems where replacing a PSSM-type model with FMM-type can improve the performance.