Likelihood methods in biology - Spring 2019

The course provides an introduction to likelihood-based inference in Biology. We will cover both theoretical and practical aspects of maximum likelihood and Bayesian inference.



Meeting: Monday and Wednesday 10:00-10:50AM in 2025 Haworth


The syllabus is available as a pdf by clicking here .


Instructors (office hours by appointment):

John Kelly jkk@ku.edu 864-3706 5005 Haworth
Mark Holder mtholder@ku.edu 864-5789 6031 Haworth

Grades will be based on class participation and homework assignments. We will have approximately one homework assignment per week.

Slides

Date Topic and Links Assignments
Week 1 Jan 23 Probability, random variables, distributions
Notes on probability by Bálint Tóth
Homework 1: HW1_2019.doc
data: PoissonCounts.xls
Week 2 Jan 28, Jan 29 Random samples, sample distributions, likelihood.
Week 3 Feb 04, Feb 06 Explicitly specifying variability: likelihood examples.
notes on allele freq estimation
Homework 2: HW2_2019.doc (frogs)
Week 4 Feb 11, Feb 13 more Maximum likelihood estimation
notes on population size estimation from sequences
Week 5 Feb 18, Feb 20 Likelihood ratio test statistic and Model Selection
Week 6 Feb 25, Feb 27 Generalized Linear Models (continued)
Week 7 Mar 04, Mar 06 Likelihood ratio test statistic and Model Selection
Week 8 Mar 18, Mar 20 Bayesian methods
Week 9 Mar 25, Mar 27 Parametric bootstrapping
Week 10 Apr 01, Apr 03 Numerical optimization
Week 11 Apr 08, Apr 10 Markov chain Monte Carlo (MCMC)
Week 12 Apr 15, Apr 17 Multiparameter MCMC
Week 13 Apr 22, Apr 24 Hastings ratio and model jumping
Week 14 Apr 29, May 01 TBA
Week 15 May 06, May 08 TBA