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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