mtholder.github.io/home/

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

3

Date	Topic and Links	Assignments
Week 1 Jan 23	Probability, random variables, distributions
Week 2 Jan 28, Jan 30	Random samples, sample distributions, likelihood	HW1_2013.doc
Week 3 Feb 04, Feb 06	Explicitly specifying variability: likelihood examples and Bayes' rule. Notes on probability by Bálint Tóth	HW2_Likelihood_2013.pdf
Week 4 Feb 11, Feb 13	Likelihood examples and maximum likelihood estimation
Week 5 Feb 18, Feb 20	Review / Likelihood ratio test statistic	HW3_2013.doc (due Wed., Feb. 27)
Week 6 Feb 25, Feb 27	Generalized Linear Models	Mark's notes on the lecture about testing with nuisance parameters
Week 7 Mar 04, Mar 06	Generalized Linear Models (continued)	HW4_2013.doc (due March 13)
Week 8 Mar 11, Mar 13	Numerical Optimization/Parametric bootstrapping	numerical_opt.pdf notes num_opt_summary_example_code_intro.pdf generalMismatchedFights.py.txt Save this as generalMismatchedFights.py and run using: python generalMismatchedFights.py 0.5 1000 You'll need Python and you'll need to install SciPy Of you can check out the R version generalMismatchedFights.R.txt which requires the data in a separate file: simpleData.txt
Mar 18 - Mar 22	SPRING BREAK
Week 9 Mar 25, Mar 27	Programming Intro, MCMC	Homework5-2013.pdf (due Wed, April 3rd) "https://phylo.bio.ku.edu/slides/templateParametricBoot.py.txt Notes: BayesianMCMC-2013.pdf
Week 10 Apr 01, Apr 03	MCMC continued	coin_contamination.py
Week 11 Apr 08, Apr 10	Multiparameter MCMC	latent_variable_MCMC.pdf (notes) Homework6-2013.pdf See coin_contamination.py for a Python template. An R template is at coin_contamination.R it will write files called MCMC-output.txt and MCMC-samples.txt to its working directory. Code snippet for running Gelman-Rubin diagnostic on tabular MCMC output. Convergence Diagnostics Notes by Patrick K. Lam .
Week 12 Apr 15, Apr 17	Hastings ratio and model jumping	hastingsRatio.pdf
Week 13 Apr 22, Apr 24		MTH's notes on JKK's lecture: source code and pdf The homework from 2011 that we discussed in class is here and this is a link to the GLM ML code that I discussed in class.
Week 14 Apr 29, May 01	Special topics: based on student suggestions	Lewis et al paper with reversible jump move. Updated multi_parameter_mcmc.pdf notes. First part of the last homework: Homework7-2013-preview.pdf Homework7-2013.pdf (with corrections May 17th) See https://gist.github.com/mtholder/5587724 (python) or https://gist.github.com/mtholder/5587706 (R) as your language preference dictates.
Week 15 May 06, May 08	Special topics: based on student suggestions