1. Bioinformatics Tea Seminar: Statistical Methods in Bioinformatics Chapter 1Probability Theory (i) : One Random Variable 06/05/2008 Jae Hyun Kim

2. Content • Discrete Random Variable • Discrete Probability Distributions • Probability Generating Functions • Continuous Random Variable • Probability Density Functions • Moment Generating Functions jaekim@ku.edu

3. Discrete Random Variable • Discrete Random Variable • Numerical quantity that, in some experiment(Sample Space) that involves some degree of randomness, takes one value from some discrete set of possible values (EVENT) • Sample Space • Set of all outcomes of an experiment (or observation) • For Example, • Flip a coin { H,T } • Toss a die {1,2,3,4,5,6} • Sum of two dice { 2,3,…,12 } • Event • Any subset of outcome jaekim@ku.edu

4. Discrete Probability Distributions • The probability distribution • Set of values that this random variable can take, together with their associated probabilities • Example, • Y = total number of heads when flip a coin twice • Probability Distribution Function • Cumulative Distribution Function jaekim@ku.edu

5. One Bernoulli Trial • A Bernoulli Trial • Single trial with two possible outcomes • “success” or “failure” • Probability of success = p jaekim@ku.edu

6. The Binomial Distribution • The Binomial Random Variable • The number of success in a fixed number of n independent Bernoulli trials with the same probability of success for each trial • Requirements • Each trial must result in one of two possible outcomes • The various trials must be independent • The probability of success must be the same on all trials • The number n of trials must be fixed in advance jaekim@ku.edu

7. Bernoulli Trail and Binomial Distribution • Comments • Single Bernoulli Trial = special case (n=1) of Binomial Distribution • Probability p is often an unknown parameter • There is no simple formula for the cumulative distribution function for the binomial distribution • There is no unique “binomial distribution,” but rather a family of distributions indexed by n and p jaekim@ku.edu

8. The Hypergeometric Distribution • Hypergeometric Distribution • N objects ( n red, N-n white ) • m objects are taken at random, without replacement • Y = number of red objects taken • Biological example • N lab mice ( n male, N-n female ) • m Mutations • The number Y of mutant males: hypergeometric distribution jaekim@ku.edu

9. The Uniform/Geometric Distribution • The Uniform Distribution • Same values over the range • The Geometric Distribution • Number of Y Bernoulli trials before but not including the first failure • Cumulative distribution function jaekim@ku.edu

10. The Poisson Distribution • The Poisson Distribution • Event occurs randomly in time/space • For example, • The time between phone calls • Approximation of Binomial Distribution • When • n is large • p is small • np is moderate • Binomial (n, p, x ) = Poisson (np, x) ( = np) jaekim@ku.edu

11. Mean • Mean / Expected Value • Expected Value of g(y) • Example • Linearity Property • In general, jaekim@ku.edu

12. Variance • Definition jaekim@ku.edu

13. Summary jaekim@ku.edu

14. General Moments • Moment • r th moment of the probability distribution about zero • Mean : First moment (r = 1) • r th moment about mean • Variance : r = 2 jaekim@ku.edu

15. Probability-Generating Function • PGF • Used to derive moments • Mean • Variance • If two r.v. X and Y have identical probability generating functions, they are identically distributed jaekim@ku.edu

16. Continuous Random Variable • Probability density function f(x) • Probability • Cumulative Distribution Function jaekim@ku.edu

17. Mean and Variance • Mean • Variance • Mean value of the function g(X) jaekim@ku.edu

18. Chebyshev’s Inequality • Chebyshev’s Inequality • Proof jaekim@ku.edu

19. The Uniform Distribution • Pdf • Mean & Variance jaekim@ku.edu

20. The Normal Distribution • Pdf • Mean , Variance 2 jaekim@ku.edu

21. Approximation • Normal Approximation to Binomial • Condition • n is large • Binomial (n,p,x) = Normal (=np, 2=np(1-p), x) • Continuity Correction • Normal Approximation to Poisson • Condition •  is large • Poisson (,x) = Normal(=, 2=, x) jaekim@ku.edu

22. The Exponential Distribution • Pdf • Cdf • Mean 1/, Variance 1/2 jaekim@ku.edu

23. The Gamma Distribution • Pdf • Mean and Variance jaekim@ku.edu

24. The Moment-Generating Function • Definition • Useful to derive • m’(0) = E[X], m’’(0) = E[X2], m(n)(0) = E[Xn] • mgf m(t) = pgf P(et) jaekim@ku.edu

25. Conditional Probability • Conditional Probability • Bayes’ Formula • Independence • Memoryless Property jaekim@ku.edu

26. Entropy • Definition • can be considered as function of PY(y) • a measure of how close to uniform that distribution is, and thus, in a sense, of the unpredictability of any observed value of a random variable having that distribution. • Entropy vs Variance • measure in some sense the uncertainty of the value of a random variable having that distribution • Entropy : Function of pdf • Variance : depends on sample values jaekim@ku.edu