# Date Topics Slides Matlab Homework 1 Jan 16 Class logistics Two reasons we need probability and statistics in BIOE Lecture 1 2 Jan 18 Random experiments. Sample space. Events Venn diagrams Definitions of probability: statistical Lecture 2 coin_toss_template.m coin_toss.m 3 Jan 23 Definitions of probability: inductive or logical Combinatorics Birthday problem Lecture 3 Video recording 4 Jan 25 Combinatorics: Polya Urn problem Axioms of probability Conditional probability Event independence Lecture 4 5 Jan 30 Circuit problems Bayes theorem.  Example of cancer tests Lecture 5 6 Feb 1 Simpson's paradox Monty Hall problem Lecture 6 7 Feb 6 Random variables: discrete vs continuous PMF, CDF, CCDF, mean, variance, standard deviation, skewness, geometric mean Uniformly distributed random variables Lecture 7 hw1.pdf 8 Feb 8 Bernoulli trial Binomial distribution Matlab exercises Lecture 8 uniform_discrete_template.m uniform_discrete.m   binomial_template.m binomial.m 9 Feb 13 Poisson Distribution Genome Assembly. Applications of the Poisson distribution Lecture 9 hw1 solutions 10 Feb 15 Geometric Distribution. Mitochondrial Eve and Y-chromosome Adam Lecture 10 11 Feb 20 MRCA in nuclear part of the genome Negative binomial distribution. Driver and passesnger mutations in cancer Lecture 11 12 Feb 22 Continuous random variables: PDF Continuous uniform distribution Lecture 12 hw2.pdf 13 Feb 27 Gaussian or Normal Distribution. Standardizing random variables. Lecture 13 exponential_gamma_template.m 14 Feb 29 Erlang distribution Lecture 14 15 Mar 5 Protein Protein Interations (PPIs) Lognormal Distribution Two random variables Joint Distributions Marginal, conditional probabilities Lecture 15 PINT_binding_energy.mat 16 Mar 7 Continuous Joint Distributions Covariance and Correlation Lecture 16 correlation_template.m hw2_solutions 17 Mar 19 Descriptive statistics Samples of i.i.d. random variables Median, quartiles, percentiles Lecture 17 cancer_wdbc.mat cancer_wdbc_cc_analysis_template.m quartiles_template.m 18 Mar 21 Misterm review Lecture 18 Mar 26 MIDTERM during regular lecture hours 19 Mar 28 Boxplot, vase and violin diagrams Probability plots: light- and heavy-tailed distributions Sample statistic:Sample mean, its average value and standard deviation. Sampling distribution of the sample mean: Central Limit Theorem. Lecture 19 boxplot_template.m central_limit_theorem_template.m 20 Apr 2 Parameter point estimation Sample variance Method of Moments Lecture 20 moment_estimators_template.m 21 Apr 4 Method of Maximum Likelihood Estimation Confidence intervals. T-statistic and Student's T-distribution Lecture 21 confidence_intervals_template.m Student t-distribution hw3.pdf 22 Apr 9 Chi-squared distribution Hypothesis testing : one- and two-sided. Type I and Type-II errors Lecture 22 Chi-squared distribution 23 Apr 11 Hypothesis testing with two samples Bonferroni correction for multiple hypotheses Chi-squared goodness of fit test with k classes. Test of statistical independence. Lecture 23 m_and_m_analysis_template.m 24 Apr 16 Two variable linear regression Lecture 24 25 Apr 18 How to avoid overfitting the data.  Training and testing datasets Double descent Multiple linear regression Adjusted R-squared Lecture 25 expression_table.mat regression_template.m regression_multiple_template.m hw4.pdf 26 Apr 23 Clustering data Lecture 26 clustering_template.m 27 Apr 25 gephi_network_analysis_exercise.pdf coexpression_network_random start.gephi disease_disease_random_start.gephi 28 Apr 30 FINAL EXAM