Calendar

Event Date Description Course Materials
Pre-course Saturday
October 13
Preparation

Python tutorials
Environment setup

Short Python tutorial
Long Python tutorial
Azure notebooks guide
Anaconda download

Lecture 1 Sunday
October 14
Introduction

Course overview & logistic
Python tutorial

Notebook
Book: Think Python

Lecture 2 Sunday
October 21
Data analysis & visualization 1

NumPy & Matplotlib

NumPy notebook
Matplotlib notebook

Lecture 3 Sunday
October 28
Population Genetics

Discrete-time models for change in allele frequencies
Haldane's model / Wright-Fisher model / Kimura's diffusion equation approximation

Notebook
Book: Otto & Day

A1 Due Sunday
November 04
Assignment #1 due

Discrete time models

A1
Solution

Lecture 4 Sunday
November 04
Data analysis & visualization 2

Pandas dataframes
Seaborn: statistical visualizations

Notebook

Lecture 5 Sunday
November 11
Statistics

Hypothesis testing
Maximum likelihood
Correlation
Fitting distributions

Notebook
Seeing Theory
Book: Think Stats

A2 Due Sunday
November 18
Assignment #2 due

Statistics

A2
Solution

Lecture 6 Sunday
November 18
Generalized Linear models 1

Regression
Maximum likelihood
Gradient descent
Tennis analytics

Notebook

Lecture 7 Sunday
November 25
Generalized Linear models 2

Binomial classification: Logistic model
Titanic survival prediction

Logistic notebook

A3 Due Sunday
December 02
Assignment #3 due

Generalized linear models

A3
Solution

Lecture 8 Sunday
December 02
Population dynamics 1

Deterministic continuous-time models for population growth
Model fitting
Country population size / microbial growth curves

Notebook

Hanuka Sunday
December 09
No class
Lecture 9 Sunday
December 16
Population dynamics 2

Deterministic continuous-time models for species interactions
Equilibria and stability analysis
Numerical integration
SymPy: symbolic mathematics
Lotka-Volterra predator-prey equations

Notebook
Stability analysis

Lecture 10 Sunday
December 23
Population dynamics 3

Stochastic continuous-time models for molecular dynamics
Gillespie algorithm
Numba: JIT for scientific Python
Protein production model

Notebook

Lecture 11 Sunday
December 30
Approximate Bayesian computation

Likelihood-free fitting of complex stochastic models
Markov chain Monte Carlo
Animal social networks

Notebook

A4 Due Sunday
January 06
Assignment #4 due

Continuous time models

A4
Solution

Lecture 12 Sunday
January 06
Feed forward networks

Multinomial classification: Softmax model
Multinomial classification: FFN
Digit image recognition

Softmax notebook
FFN notebook

Lecture 13 Sunday
January 13
Convolutional neural networks

Multinomial classification: CNN
Keras: neural networks library
Digit image recognition

CNN notebook

A5 Due Sunday
January 20
Assignment #5 due

Neural networks

A5
Solution

Project Due Thursday
February 14
Final project due

Project instructions
Final project guidelines