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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     midterm_with_solutions.pdf
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

 hw3_solutions
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

Topics in network analysis:
Degree (in- and out-degree)
PageRank
Betweenness-centrality
Clustering coefficient​

Co-expression networks

Visualization of large networks using Gephi

 Lecture 27

gephi_network_analysis_exercise.pdf

coexpression_network_random start.gephi

disease_disease_random_start.gephi

  
28 Apr 30 Final exam reviw

Lecture 28

Zoom recording

   hw4_solutions

FINAL EXAM