PPT-Exact Computation of Coalescent Likelihood under the Infinite Sites Model

Yufeng Wu University of Connecticut DIMACS Workshop on Algorithmics in Human PopulationGenomics 2009 1 Coalescent Likelihood D a set of binary sequences Coalescent genealogy history with . aka. . deferred execution. aka. call-by-need. What should / does this do? . f n = [ 2*n, g n ] . where. g x = <wildly expensive or . erroneous computation>. ----------------------------------. Lobster Survival by Size in a Tethering Experiment. Source: E.B. Wilkinson, J.H. Grabowski, G.D. Sherwood, P.O. . Yund. (2015). "Influence of Predator Identity on the Strength of Predator Avoidance Response in Lobsters," Journal of Experimental Biology and Ecology, Vol. 465, pp. 107-112.. Februari, 1 2010. Gerrit. Rooks. Sociology of Innovation. Innovation Sciences & Industrial Engineering . Phone: 5509 . email: g.rooks@tue.nl. This. . Lecture. Why. . logistic. . regression. Zhi. -Ming Ma. . ECM2013 . PolyU. . Email: mazm@amt.ac.cn . http://www.amt.ac.cn/member/mazhiming/index.html. A New Method for Coalescent Processes with Recombination . Summary of assumptions so far. We have covered the role of chance (parent choice), demography (population size) and mutation, in shaping genetic diversity. . Neutral Wright-Fisher . models. Parents are always chosen at random. This means no new mutations affect reproductive success of parents, i.e. . Post-mortem. Project presentations in the last 2-3 classes. Start of Statistical Learning. Sanity Test... Max: 52.5 Min: 6 . Avg. : 24.6 . Stdev. : 14.8 . Including those sitting-in: . Avg. CSE280. Vineet Bafna. Expectation, and deviance. Statements such as the ones below can be made only if we have an underlying model that suggests what we should expect. . Recombination rates vary dramatically across the genome. CSE280. Vineet Bafna. Expectation, and deviance. Statements such as the ones below can be made only if we have an underlying model that suggests what we should expect. . Recombination rates vary dramatically across the genome. Genetics (SC1). Simon Myers . . Email: . myers@stats.ox.ac.uk. . Course webpage: . www.stats.ox.ac.uk/~myers/mathgen.html. Class problem sheets . are . posted . online (separate sheets for MSc and Part C). STAT120C. 1. Review of Tests Learned in STAT120C. Which test(s) should be used to answer the following questions?. Is husband’s BMI larger than wife’s?. Is men’s BMI different from women’s?. Do gender and smoking affect human’s weight?. Hypothesis Testing in Binary Choice Models. Hypothesis Tests. Restrictions: Linear or nonlinear functions of the model parameters. Structural ‘change’: Constancy of parameters. Specification Tests: . high-dimensional multiple test. 28 March 2015. London, UK. Youngjo. . Lee. Seoul National University . w. ith Jan F. . Bj. ϕ. rnstad. , . Donghwan. Lee, . Peirong. Xu, Chris Frost,. Gerard . R. Ridgway. 1. Matt Gormley. Lecture . 24. November 21, 2016. School of Computer Science. Readings:. 10-601B Introduction to Machine Learning. Reminders. Final . Exam. in-. class. . Wed. ., . Dec. . 7. 2. Outline. Dr Laura Emery . Laura.Emery@ebi.ac.uk. www.ebi.ac.uk. Objectives. After this . tutorial you . should be able to. …. Discuss . a range of . methods for . phylogenetic . inference, their advantages.