- Introduction to Python
- Getting started with Python and the IPython notebook
- Functions are first class objects
- Data science is OSEMN
- Working with text
- Preprocessing text data
- Working with structured data
- Using SQLite3
- Using HDF5
- Using numpy
- Using Pandas
- Computational problems in statistics
- Computer numbers and mathematics
- Algorithmic complexity
- Linear Algebra and Linear Systems
- Linear Algebra and Matrix Decompositions
- Change of Basis
- Optimization and Non-linear Methods
- Practical Optimizatio Routines
- Finding roots
- Optimization Primer
- Using scipy.optimize
- Gradient deescent
- Newton’s method and variants
- Constrained optimization
- Curve fitting
- Finding paraemeters for ODE models
- Optimization of graph node placement
- Optimization of standard statistical models
- Fitting ODEs with the Levenberg–Marquardt algorithm
- 1D example
- 2D example
- Algorithms for Optimization and Root Finding for Multivariate Problems
- Expectation Maximizatio (EM) Algorithm
- Monte Carlo Methods
- Resampling methods
- Resampling
- Simulations
- Setting the random seed
- Sampling with and without replacement
- Calculation of Cook’s distance
- Permutation resampling
- Design of simulation experiments
- Example: Simulations to estimate power
- Check with R
- Estimating the CDF
- Estimating the PDF
- Kernel density estimation
- Multivariate kerndel density estimation
- Markov Chain Monte Carlo (MCMC)
- Using PyMC2
- Using PyMC3
- Using PyStan
- C Crash Course
- Code Optimization
- Using C code in Python
- Using functions from various compiled languages in Python
- Julia and Python
- Converting Python Code to C for speed
- Optimization bake-off
- Writing Parallel Code
- Massively parallel programming with GPUs
- Writing CUDA in C
- Distributed computing for Big Data
- Hadoop MapReduce on AWS EMR with mrjob
- Spark on a local mahcine using 4 nodes
- Modules and Packaging
- Tour of the Jupyter (IPython3) notebook
- Polyglot programming
- What you should know and learn more about
- Wrapping R libraries with Rpy
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Some examples of numbers behaving badly
Normalizing weights
Given a set of weights, we want to nromalize them so that the sum = 1.
def normalize(ws): """Returns normalized set of weights that sum to 1.""" s = sum(ws) return [w/s for w in ws]
ws = [1,2,3,4,5] normalize(ws)
[0, 0, 0, 0, 0]
Comparing likleihoods
Assuming indepdnece, the likelihood of observing some data points given a distributional model for each data point is the product of the likelihood for each data point.
from scipy.stats import norm rv1 = norm(0, 1) rv2 = norm(0, 3) xs = np.random.normal(0, 3, 1000) likelihood1 = np.prod(rv1.pdf(xs)) likelihood2 = np.prod(rv2.pdf(xs)) likelihood2 > likelihood1
False
Equality comparisons
We use an equality condition to exit some loop.
s = 0.0 for i in range(1000): s += 1.0/10.0 if s == 1.0: break print i
999
Calculating variance
\[s^2 = \frac{\sum_{i=1}^{n} x_i^2 - (\sum_{i=1}^n x_i)^2/n}{n-1}\]
def var(xs): """Returns variance of sample data.""" n = 0 s = 0 ss = 0 for x in xs: n +=1 s += x ss += x*x v = (ss - (s*s)/n)/(n-1) return v
# What is the sample variance for numbers from a normal distribution with variance 1? np.random.seed(4) xs = np.random.normal(1e9, 1, 1000) var(xs)
-262.4064
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