Reading questions
1. Why do we need a probabilistic model for a TF binding site?
2. What is the difference between PSSM and FMM? What are pros and cons of FMM?
3. Describe the proposed computational approach: probabilistic model; training data: observed/ hidden variables; evaluation methods.
4. Is there any room for improvement, either in terms of modeling or learning?
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(optional) 5. Give examples of other problems where replacing a PSSM-type model with FMM-type can improve the performance.