- 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
Special Matrices
Some matrices have interesting properties that allow us either simplify the underlying linear system or to understand more about it.
Square matrices have the same number of columns (usually denoted \(n\)). We refer to an arbitrary square matrix as and \(n\times n\) or we refer to it as a ‘square matrix of dimension \(n\)‘. If an \(n\times n\) matrix \(A\) has full rank (i.e. it has rank \(n\)), then \(A\) is invertible, and its inverse is unique. This is a situation that leads to a unique solution to a linear system.
A diagonal matrix is a matrix with all entries off the diagonal equal to zero. Strictly speaking, such a matrix should be square, but we can also consider rectangular matrices of size \(m\times n\) to be diagonal, if all entries \(a_{ij}\) are zero for \(i\neq j\)
A matrix \(A\) is (skew) symmetric iff \(a_{ij} = (-)a_{ji}\).
Equivalently, \(A\) is (skew) symmetric iff
\[A = (-)A^T\]
A matrix \(A\) is (upper|lower) triangular if \(a_{ij} = 0\) for all \(i (>|<) j\)
These are matrices with lots of zero entries. Banded matrices have non-zero ‘bands’, and this structure can be exploited to simplify computations. Sparse matrices are matrices where there are ‘few’ non-zero entries, but there is no pattern to where non-zero entries are found.
A matrix \(A\) is orthogonal iff
\[A A^T = I\]
In other words, \(A\) is orthogonal iff
\[A^T=A^{-1}\]
Facts:
- The rows and columns of an orthogonal matrix are an orthonormal set of vectors.
- Geometrically speaking, orthogonal transformations preserve lengths and angles between vectors
Positive definite matrices are an important class of matrices with very desirable properties. A square matrix \(A\) is positive definite if
\[\begin{split}u^TA u > 0\end{split}\]
for any non-zero n-dimensional vector \(u\).
A symmetric, positive-definite matrix \(A\) is a positive-definite matrix such that
\[A = A^T\]
IMPORTANT:
- Symmetric, positive-definite matrices have ‘square-roots’ (in a sense)
- Any symmetric, positive-definite matrix is diagonizable!!!
- Co-variance matrices are symmetric and positive-definite
Now that we have the basics down, we can move on to numerical methods for solving systems - aka matrix decompositions.
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