- 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
Spark
Spark provides a much richer set of programming constructs and libraries that greatly simplify concurrent programming. In addition, because Spark data can be persistent over a session (unliike MapReduce which reads/writes data at each step in the job chain), it can be much faster for iteratvie programs and also enables interactive concurrent programming. See official documenttion for details, including setting up on Amazon . This article on how to set up Spark on EMR may also be helpful.
Very conceniently for learning, Spark provides an REPL shell where you can interactively type and run Spark programs. For example, this will open a Spark shell as an IPython Notebook (if spark is installed and pyspark is on your path):
IPYTHON_OPTS="notebook" pyspark
To whet your appetite, here is the stadnalone Spark version for the word count program.
%%file spark_count.py from pyspark import SparkConf, SparkContext conf = SparkConf().setMaster("local").setAppName("Word Count") sc = SparkContext(conf = conf) rdd = sc.textFile("<path_to_books>") words = rdd.flatMap(lambda x: x.split()) result = words.countByValue()
Writing spark_count.py
And this is run by typing on the command line
bin/spark-submit spark_count.py
Of course, spark-submit
has many options that can be provided to configure the job.
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