#

Date

Topics

Slides

Matlab

Homework
(not graded)

Exams
1

Aug 27

 Why probability and statistics in comutational bioengineering? Lecture 1      
2

Aug 29

Random experiments. Sample space, Events, Venn diagramms. 

Definitions of probability:
Statistical (part 1)

 Lecture 2

coin_toss_template.m

coin_toss.m

    
3

Sep 3

Definitions of probability:
Statistical (continued)

Definitions of probability:
Inductive. 

Paradoxes of inductive definition of probability

Combinatorics

 Lecture 3      
4

Sep 5

Combinatorics (continued)

Probability axioms

Conditional probability

Independence of events

Circuit diagrams

 Lecture 4      
5

Sep 10

Circuit diagrams (continued)

Bayes' theorem

Specificity/Sensitivity of tests

 Lecture 5

circuit_template.m

circuit.m

    
6

Sep 12

Secretary problem

Simpson's paradox

Monty Hall problem

 Lecture 6

monty_hall_template.m

monty_hall.m

  


 
7 Sep 17

 

Discrete random varibales,

PMF. CDF, CCDF, 
Mean, Variance, Skewness

Uniform distribution

The distribution of the
Ct value in COVID-19
PCR tests

 Lecture 7

 

 HW 1  
8 Sep 19

Uniform Distribution (Matlab exercise)

Bernoulli trials

Binomial Distribution

 Lecture 8

uniform_discrete_template.m

uniform_discrete.m

    
9

Sep 24

 Poisson Distribution

Genome Assembly		 Lecture 9

poisson_template.m

poisson.m

 HW_1_with_solutions  
10

Sep 26

 Genome Assembly (cont)
 

Geometric distribution.

Phylogenetic trees and time to the most recent common ancestor. 

Mitochondrial Eve

 Lecture 10

 

    
11

Oct 1

Mitochondrial Eveen (continued)

Negative Binomial Distribution

Cancer: Driver and Passenger genes

 Lecture 11

negative_binomial_template.m

negative_binomial.m

    
12

Oct 3

Continuous random variables.

Probability Density Function, CDF, CCDF, Mean, Variance, Std

Uniform continuous distribution. 

 Lecture 12

 

    
13 Oct 8

 

Constant rate (Poisson) process.

Exponential distribution.

Erlang and Gamma distributions

 Lecture 13

exponential_template.m

exponential.m

 hw2_part1.pdf  
14

Oct 10

Gaussian distribution

Standardizing and working with the CDF table

 Lecture 14

exponential_gamma.m

gaussian_template.m

gaussian.m

    
 

Oct 15

NO LECTURE


Study homework

    

hw2_part2.pdf

  
15

Oct 17

Fitting Gaussian distribution to the data for binding energies of protein-protein interactions 

Multiple random variables. Joint, Marginal, and Conditional PMFs

Statistical independence of random variables

 Lecture 15

PINT_binding_energy.mat

PINT_binding_energy.m

    
16

Oct 22

Covariance

Correlation coefficients:
Pearson, Spearman

 Lecture 16

correlation_template.m

cancer_wdbc_cc_analysis_template.m

cancer_wdbc.mat

hw2_part1_solutions.pdf

hw2_part2_solutions.pdf

  
17

Oct 24

 Misterm review Lecture 17       
18

Oct 29

 MIDTERM EXAM 
in class regular time		        
19

Oct 31

 Samples, histograms, 
median, quartiles, percentiles
Box-and-whisker plots		 Lecture 18 boxplot_template.m    
20 Nov 5

 

 Sample mean. Its mean and variance (standard error). Central limit theorem Lecture 19

https://onlinestatbook.com/stat_sim/sampling_dist/

central_limit_theorem_template.m

    
21

Nov 7

 Parameter point estimation. Method of moments and Maximum Likelihood Estimator Lecture 20 moment_estimators_template.m    
22

Nov 12

Confidence intervals of population mean and variance

Student-t and chi-squared distributions

Confidence interval of population proportion

 Lecture 21 confidence_intervals_template.m    
23

Nov 14

Confidence intervals (continued).

Hypothesis testing

 Lecture 22 dark_vs_milk_chocolate_analysis_template.m    
24

Nov 19

 Pearson's chi-square Goodness of Fit (GOF) test Lecture 23

m_and_m_analysis_template.m

    
25

Nov 21

Linear regression: two variables.

Multiple linear regression (part one).

Nonlinear regression.

Training and testing/validation sets.

Overfitting.

Double descent.

 Lecture 24

expression_table.mat

regression_template.m

    
26 Dec 3

 

Multiple Linear Regression.

Principle Component Analysis 
(PCA) 

 Lecture 25

regression_multiple_template.m

    
27 Dec 5

 

 Clustering and Network Analysis Lecture 26

coexpression_network_random start.gephi

disease_disease_random_start.gephi

gephi_network_analysis_exercise.pdf

    
28

Dec 10

 Final exam review Lecture 27  

hw3
hw4

hw3_with_solutions
hw4_with_solutions

 

  

FINAL EXAM

Dec 17

7pm-9pm

 0018 Campus Instructional Facility