<!-- dom:TITLE: Week 35: From Ordinary Linear Regression to Ridge and Lasso Regression -->
# Week 35: From Ordinary Linear Regression to Ridge and Lasso Regression
<!-- dom:AUTHOR: Morten Hjorth-Jensen at Department of Physics, University of Oslo & Department of Physics and Astronomy and National Superconducting Cyclotron Laboratory, Michigan State University -->
<!-- Author: -->
**Morten Hjorth-Jensen**, Department of Physics, University of Oslo and Department of Physics and Astronomy and National Superconducting Cyclotron Laboratory, Michigan State University

Date: **Sep 6, 2021**

Copyright 1999-2021, Morten Hjorth-Jensen. Released under CC Attribution-NonCommercial 4.0 license

## Plans for week 35, August 30 -September 3

* Thursday: Review of  ordinary Least Squares with applications and discussion of Ridge Regression and Singular Value Decomposition

* [Video of lecture Thursday](https://www.uio.no/studier/emner/matnat/fys/FYS-STK3155/h21/forelesningsvideoer/LectureSeptember2.mp4?vrtx=view-as-webpage).

* Friday: Analysis of Ridge and Lasso Regression and links with Singular Value Decomposition

* [Video of lecture Friday](https://www.uio.no/studier/emner/matnat/fys/FYS-STK3155/h21/forelesningsvideoer/LectureSeptember3.mp4?vrtx=view-as-webpage)

## Thursday September 2

The main topics on Thursday are:
1. Repetition from last week on linear regression

2. Discussion of how to prepare data and examples of applications of linear regression

3. Mathematical interpretations of Linear Regression

4. Start discussing Ridge and Lasso regression and Singular Value Decomposition

## Why Linear Regression (aka Ordinary Least Squares and family), repeat from last week

We need first a reminder from last week about linear regression.

Fitting a continuous function with linear parameterization in terms of the parameters  $\boldsymbol{\beta}$.
* Method of choice for fitting a continuous function!

* Gives an excellent introduction to central Machine Learning features with **understandable pedagogical** links to other methods like **Neural Networks**, **Support Vector Machines** etc

* Analytical expression for the fitting parameters $\boldsymbol{\beta}$

* Analytical expressions for statistical propertiers like mean values, variances, confidence intervals and more

* Analytical relation with probabilistic interpretations

* Easy to introduce basic concepts like bias-variance tradeoff, cross-validation, resampling and regularization techniques and many other ML topics

* Easy to code! And links well with classification problems and logistic regression and neural networks

* Allows for **easy** hands-on understanding of gradient descent methods

* and many more features

For more discussions of Ridge and Lasso regression, [Wessel van Wieringen's](https://arxiv.org/abs/1509.09169) article is highly recommended.
Similarly, [Mehta et al's article](https://arxiv.org/abs/1803.08823) is also recommended.

## Regression analysis, overarching aims

Regression modeling deals with the description of  the sampling distribution of a given random variable $y$ and how it varies as function of another variable or a set of such variables $\boldsymbol{x} =[x_0, x_1,\dots, x_{n-1}]^T$.
The first variable is called the **dependent**, the **outcome** or the **response** variable while the set of variables $\boldsymbol{x}$ is called the independent variable, or the predictor variable or the explanatory variable.

A regression model aims at finding a likelihood function $p(\boldsymbol{y}\vert \boldsymbol{x})$, that is the conditional distribution for $\boldsymbol{y}$ with a given $\boldsymbol{x}$. The estimation of  $p(\boldsymbol{y}\vert \boldsymbol{x})$ is made using a data set with
* $n$ cases $i = 0, 1, 2, \dots, n-1$

* Response (target, dependent or outcome) variable $y_i$ with $i = 0, 1, 2, \dots, n-1$

* $p$ so-called explanatory (independent or predictor) variables $\boldsymbol{x}_i=[x_{i0}, x_{i1}, \dots, x_{ip-1}]$ with $i = 0, 1, 2, \dots, n-1$ and explanatory variables running from $0$ to $p-1$. See below for more explicit examples.

 The goal of the regression analysis is to extract/exploit relationship between $\boldsymbol{y}$ and $\boldsymbol{x}$ in or to infer causal dependencies, approximations to the likelihood functions, functional relationships and to make predictions, making fits and many other things.

## Regression analysis, overarching aims II

Consider an experiment in which $p$ characteristics of $n$ samples are
measured. The data from this experiment, for various explanatory variables $p$ are normally represented by a matrix
$\mathbf{X}$.

The matrix $\mathbf{X}$ is called the *design
matrix*. Additional information of the samples is available in the
form of $\boldsymbol{y}$ (also as above). The variable $\boldsymbol{y}$ is
generally referred to as the *response variable*. The aim of
regression analysis is to explain $\boldsymbol{y}$ in terms of
$\boldsymbol{X}$ through a functional relationship like $y_i =
f(\mathbf{X}_{i,\ast})$. When no prior knowledge on the form of
$f(\cdot)$ is available, it is common to assume a linear relationship
between $\boldsymbol{X}$ and $\boldsymbol{y}$. This assumption gives rise to
the *linear regression model* where $\boldsymbol{\beta} = [\beta_0, \ldots,
\beta_{p-1}]^{T}$ are the *regression parameters*.

Linear regression gives us a set of analytical equations for the parameters $\beta_j$.

## Examples
In order to understand the relation among the predictors $p$, the set of data $n$ and the target (outcome, output etc) $\boldsymbol{y}$,
consider the model we discussed for describing nuclear binding energies.

There we assumed that we could parametrize the data using a polynomial approximation based on the liquid drop model.
Assuming

```python

```

$$
BE(A) = a_0+a_1A+a_2A^{2/3}+a_3A^{-1/3}+a_4A^{-1},
$$

we have five predictors, that is the intercept, the $A$ dependent term, the $A^{2/3}$ term and the $A^{-1/3}$ and $A^{-1}$ terms.
This gives $p=0,1,2,3,4$. Furthermore we have $n$ entries for each predictor. It means that our design matrix is a
$p\times n$ matrix $\boldsymbol{X}$.

Here the predictors are based on a model we have made. A popular data set which is widely encountered in ML applications is the
so-called [credit card default data from Taiwan](https://www.sciencedirect.com/science/article/pii/S0957417407006719?via%3Dihub). The data set contains data on $n=30000$ credit card holders with predictors like gender, marital status, age, profession, education, etc. In total there are $24$ such predictors or attributes leading to a design matrix of dimensionality $24 \times 30000$. This is however a classification problem and we will come back to it when we discuss Logistic Regression.

## General linear models
Before we proceed let us study a case from linear algebra where we aim at fitting a set of data $\boldsymbol{y}=[y_0,y_1,\dots,y_{n-1}]$. We could think of these data as a result of an experiment or a complicated numerical experiment. These data are functions of a series of variables $\boldsymbol{x}=[x_0,x_1,\dots,x_{n-1}]$, that is $y_i = y(x_i)$ with $i=0,1,2,\dots,n-1$. The variables $x_i$ could represent physical quantities like time, temperature, position etc. We assume that $y(x)$ is a smooth function.

Since obtaining these data points may not be trivial, we want to use these data to fit a function which can allow us to make predictions for values of $y$ which are not in the present set. The perhaps simplest approach is to assume we can parametrize our function in terms of a polynomial of degree $n-1$ with $n$ points, that is

$$
y=y(x) \rightarrow y(x_i)=\tilde{y}_i+\epsilon_i=\sum_{j=0}^{n-1} \beta_j x_i^j+\epsilon_i,
$$

where $\epsilon_i$ is the error in our approximation.

## Rewriting the fitting procedure as a linear algebra problem
For every set of values $y_i,x_i$ we have thus the corresponding set of equations

$$
\begin{align*}
y_0&=\beta_0+\beta_1x_0^1+\beta_2x_0^2+\dots+\beta_{n-1}x_0^{n-1}+\epsilon_0\\
y_1&=\beta_0+\beta_1x_1^1+\beta_2x_1^2+\dots+\beta_{n-1}x_1^{n-1}+\epsilon_1\\
y_2&=\beta_0+\beta_1x_2^1+\beta_2x_2^2+\dots+\beta_{n-1}x_2^{n-1}+\epsilon_2\\
\dots & \dots \\
y_{n-1}&=\beta_0+\beta_1x_{n-1}^1+\beta_2x_{n-1}^2+\dots+\beta_{n-1}x_{n-1}^{n-1}+\epsilon_{n-1}.\\
\end{align*}
$$

## Rewriting the fitting procedure as a linear algebra problem, more details
Defining the vectors

$$
\boldsymbol{y} = [y_0,y_1, y_2,\dots, y_{n-1}]^T,
$$

and

$$
\boldsymbol{\beta} = [\beta_0,\beta_1, \beta_2,\dots, \beta_{n-1}]^T,
$$

and

$$
\boldsymbol{\epsilon} = [\epsilon_0,\epsilon_1, \epsilon_2,\dots, \epsilon_{n-1}]^T,
$$

and the design matrix

$$
\boldsymbol{X}=
\begin{bmatrix}
1& x_{0}^1 &x_{0}^2& \dots & \dots &x_{0}^{n-1}\\
1& x_{1}^1 &x_{1}^2& \dots & \dots &x_{1}^{n-1}\\
1& x_{2}^1 &x_{2}^2& \dots & \dots &x_{2}^{n-1}\\
\dots& \dots &\dots& \dots & \dots &\dots\\
1& x_{n-1}^1 &x_{n-1}^2& \dots & \dots &x_{n-1}^{n-1}\\
\end{bmatrix}
$$

we can rewrite our equations as

$$
\boldsymbol{y} = \boldsymbol{X}\boldsymbol{\beta}+\boldsymbol{\epsilon}.
$$

The above design matrix is called a [Vandermonde matrix](https://en.wikipedia.org/wiki/Vandermonde_matrix).

## Generalizing the fitting procedure as a linear algebra problem

We are obviously not limited to the above polynomial expansions.  We
could replace the various powers of $x$ with elements of Fourier
series or instead of $x_i^j$ we could have $\cos{(j x_i)}$ or $\sin{(j
x_i)}$, or time series or other orthogonal functions.  For every set
of values $y_i,x_i$ we can then generalize the equations to

$$
\begin{align*}
y_0&=\beta_0x_{00}+\beta_1x_{01}+\beta_2x_{02}+\dots+\beta_{n-1}x_{0n-1}+\epsilon_0\\
y_1&=\beta_0x_{10}+\beta_1x_{11}+\beta_2x_{12}+\dots+\beta_{n-1}x_{1n-1}+\epsilon_1\\
y_2&=\beta_0x_{20}+\beta_1x_{21}+\beta_2x_{22}+\dots+\beta_{n-1}x_{2n-1}+\epsilon_2\\
\dots & \dots \\
y_{i}&=\beta_0x_{i0}+\beta_1x_{i1}+\beta_2x_{i2}+\dots+\beta_{n-1}x_{in-1}+\epsilon_i\\
\dots & \dots \\
y_{n-1}&=\beta_0x_{n-1,0}+\beta_1x_{n-1,2}+\beta_2x_{n-1,2}+\dots+\beta_{n-1}x_{n-1,n-1}+\epsilon_{n-1}.\\
\end{align*}
$$

**Note that we have $p=n$ here. The matrix is symmetric. This is generally not the case!**

## Generalizing the fitting procedure as a linear algebra problem
We redefine in turn the matrix $\boldsymbol{X}$ as

$$
\boldsymbol{X}=
\begin{bmatrix}
x_{00}& x_{01} &x_{02}& \dots & \dots &x_{0,n-1}\\
x_{10}& x_{11} &x_{12}& \dots & \dots &x_{1,n-1}\\
x_{20}& x_{21} &x_{22}& \dots & \dots &x_{2,n-1}\\
\dots& \dots &\dots& \dots & \dots &\dots\\
x_{n-1,0}& x_{n-1,1} &x_{n-1,2}& \dots & \dots &x_{n-1,n-1}\\
\end{bmatrix}
$$

and without loss of generality we rewrite again  our equations as

$$
\boldsymbol{y} = \boldsymbol{X}\boldsymbol{\beta}+\boldsymbol{\epsilon}.
$$

The left-hand side of this equation is kwown. Our error vector $\boldsymbol{\epsilon}$ and the parameter vector $\boldsymbol{\beta}$ are our unknow quantities. How can we obtain the optimal set of $\beta_i$ values?

## Optimizing our parameters
We have defined the matrix $\boldsymbol{X}$ via the equations

$$
\begin{align*}
y_0&=\beta_0x_{00}+\beta_1x_{01}+\beta_2x_{02}+\dots+\beta_{n-1}x_{0n-1}+\epsilon_0\\
y_1&=\beta_0x_{10}+\beta_1x_{11}+\beta_2x_{12}+\dots+\beta_{n-1}x_{1n-1}+\epsilon_1\\
y_2&=\beta_0x_{20}+\beta_1x_{21}+\beta_2x_{22}+\dots+\beta_{n-1}x_{2n-1}+\epsilon_1\\
\dots & \dots \\
y_{i}&=\beta_0x_{i0}+\beta_1x_{i1}+\beta_2x_{i2}+\dots+\beta_{n-1}x_{in-1}+\epsilon_1\\
\dots & \dots \\
y_{n-1}&=\beta_0x_{n-1,0}+\beta_1x_{n-1,2}+\beta_2x_{n-1,2}+\dots+\beta_{n-1}x_{n-1,n-1}+\epsilon_{n-1}.\\
\end{align*}
$$

As we noted above, we stayed with a system with the design matrix
 $\boldsymbol{X}\in {\mathbb{R}}^{n\times n}$, that is we have $p=n$. For reasons to come later (algorithmic arguments) we will hereafter define
our matrix as $\boldsymbol{X}\in {\mathbb{R}}^{n\times p}$, with the predictors refering to the column numbers and the entries $n$ being the row elements.

## Our model for the nuclear binding energies

In our [introductory notes](https://compphysics.github.io/MachineLearning/doc/pub/How2ReadData/html/How2ReadData.html) we looked at the so-called [liquid drop model](https://en.wikipedia.org/wiki/Semi-empirical_mass_formula). Let us remind ourselves about what we did by looking at the code.

We restate the parts of the code we are most interested in.

```python
%matplotlib inline

# Common imports
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from IPython.display import display
import os

# Where to save the figures and data files
PROJECT_ROOT_DIR = "Results"
FIGURE_ID = "Results/FigureFiles"
DATA_ID = "DataFiles/"

if not os.path.exists(PROJECT_ROOT_DIR):
    os.mkdir(PROJECT_ROOT_DIR)

if not os.path.exists(FIGURE_ID):
    os.makedirs(FIGURE_ID)

if not os.path.exists(DATA_ID):
    os.makedirs(DATA_ID)

def image_path(fig_id):
    return os.path.join(FIGURE_ID, fig_id)

def data_path(dat_id):
    return os.path.join(DATA_ID, dat_id)

def save_fig(fig_id):
    plt.savefig(image_path(fig_id) + ".png", format='png')

infile = open(data_path("MassEval2016.dat"),'r')

# Read the experimental data with Pandas
Masses = pd.read_fwf(infile, usecols=(2,3,4,6,11),
              names=('N', 'Z', 'A', 'Element', 'Ebinding'),
              widths=(1,3,5,5,5,1,3,4,1,13,11,11,9,1,2,11,9,1,3,1,12,11,1),
              header=39,
              index_col=False)

# Extrapolated values are indicated by '#' in place of the decimal place, so
# the Ebinding column won't be numeric. Coerce to float and drop these entries.
Masses['Ebinding'] = pd.to_numeric(Masses['Ebinding'], errors='coerce')
Masses = Masses.dropna()
# Convert from keV to MeV.
Masses['Ebinding'] /= 1000

# Group the DataFrame by nucleon number, A.
Masses = Masses.groupby('A')
# Find the rows of the grouped DataFrame with the maximum binding energy.
Masses = Masses.apply(lambda t: t[t.Ebinding==t.Ebinding.max()])
A = Masses['A']
Z = Masses['Z']
N = Masses['N']
Element = Masses['Element']
Energies = Masses['Ebinding']

# Now we set up the design matrix X
X = np.zeros((len(A),5))
X[:,0] = 1
X[:,1] = A
X[:,2] = A**(2.0/3.0)
X[:,3] = A**(-1.0/3.0)
X[:,4] = A**(-1.0)
# Then nice printout using pandas
DesignMatrix = pd.DataFrame(X)
DesignMatrix.index = A
DesignMatrix.columns = ['1', 'A', 'A^(2/3)', 'A^(-1/3)', '1/A']
display(DesignMatrix)
```

With $\boldsymbol{\beta}\in {\mathbb{R}}^{p\times 1}$, it means that we will hereafter write our equations for the approximation as

$$
\boldsymbol{\tilde{y}}= \boldsymbol{X}\boldsymbol{\beta},
$$

throughout these lectures.

## Optimizing our parameters, more details
With the above we use the design matrix to define the approximation $\boldsymbol{\tilde{y}}$ via the unknown quantity $\boldsymbol{\beta}$ as

$$
\boldsymbol{\tilde{y}}= \boldsymbol{X}\boldsymbol{\beta},
$$

and in order to find the optimal parameters $\beta_i$ instead of solving the above linear algebra problem, we define a function which gives a measure of the spread between the values $y_i$ (which represent hopefully the exact values) and the parameterized values $\tilde{y}_i$, namely

$$
C(\boldsymbol{\beta})=\frac{1}{n}\sum_{i=0}^{n-1}\left(y_i-\tilde{y}_i\right)^2=\frac{1}{n}\left\{\left(\boldsymbol{y}-\boldsymbol{\tilde{y}}\right)^T\left(\boldsymbol{y}-\boldsymbol{\tilde{y}}\right)\right\},
$$

or using the matrix $\boldsymbol{X}$ and in a more compact matrix-vector notation as

$$
C(\boldsymbol{\beta})=\frac{1}{n}\left\{\left(\boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta}\right)^T\left(\boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta}\right)\right\}.
$$

This function is one possible way to define the so-called cost function.

It is also common to define
the function $C$ as

$$
C(\boldsymbol{\beta})=\frac{1}{2n}\sum_{i=0}^{n-1}\left(y_i-\tilde{y}_i\right)^2,
$$

since when taking the first derivative with respect to the unknown parameters $\beta$, the factor of $2$ cancels out.

## Interpretations and optimizing our parameters

The function

$$
C(\boldsymbol{\beta})=\frac{1}{n}\left\{\left(\boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta}\right)^T\left(\boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta}\right)\right\},
$$

can be linked to the variance of the quantity $y_i$ if we interpret the latter as the mean value.
When linking (see the discussion below) with the maximum likelihood approach below, we will indeed interpret $y_i$ as a mean value

$$
y_{i}=\langle y_i \rangle = \beta_0x_{i,0}+\beta_1x_{i,1}+\beta_2x_{i,2}+\dots+\beta_{n-1}x_{i,n-1}+\epsilon_i,
$$

where $\langle y_i \rangle$ is the mean value. Keep in mind also that
till now we have treated $y_i$ as the exact value. Normally, the
response (dependent or outcome) variable $y_i$ the outcome of a
numerical experiment or another type of experiment and is thus only an
approximation to the true value. It is then always accompanied by an
error estimate, often limited to a statistical error estimate given by
the standard deviation discussed earlier. In the discussion here we
will treat $y_i$ as our exact value for the response variable.

In order to find the parameters $\beta_i$ we will then minimize the spread of $C(\boldsymbol{\beta})$, that is we are going to solve the problem

$$
{\displaystyle \min_{\boldsymbol{\beta}\in
{\mathbb{R}}^{p}}}\frac{1}{n}\left\{\left(\boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta}\right)^T\left(\boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta}\right)\right\}.
$$

In practical terms it means we will require

$$
\frac{\partial C(\boldsymbol{\beta})}{\partial \beta_j} = \frac{\partial }{\partial \beta_j}\left[ \frac{1}{n}\sum_{i=0}^{n-1}\left(y_i-\beta_0x_{i,0}-\beta_1x_{i,1}-\beta_2x_{i,2}-\dots-\beta_{n-1}x_{i,n-1}\right)^2\right]=0,
$$

which results in

$$
\frac{\partial C(\boldsymbol{\beta})}{\partial \beta_j} = -\frac{2}{n}\left[ \sum_{i=0}^{n-1}x_{ij}\left(y_i-\beta_0x_{i,0}-\beta_1x_{i,1}-\beta_2x_{i,2}-\dots-\beta_{n-1}x_{i,n-1}\right)\right]=0,
$$

or in a matrix-vector form as

$$
\frac{\partial C(\boldsymbol{\beta})}{\partial \boldsymbol{\beta}} = 0 = \boldsymbol{X}^T\left( \boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta}\right).
$$

## Interpretations and optimizing our parameters
We can rewrite

$$
\frac{\partial C(\boldsymbol{\beta})}{\partial \boldsymbol{\beta}} = 0 = \boldsymbol{X}^T\left( \boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta}\right),
$$

as

$$
\boldsymbol{X}^T\boldsymbol{y} = \boldsymbol{X}^T\boldsymbol{X}\boldsymbol{\beta},
$$

and if the matrix $\boldsymbol{X}^T\boldsymbol{X}$ is invertible we have the solution

$$
\boldsymbol{\beta} =\left(\boldsymbol{X}^T\boldsymbol{X}\right)^{-1}\boldsymbol{X}^T\boldsymbol{y}.
$$

We note also that since our design matrix is defined as $\boldsymbol{X}\in
{\mathbb{R}}^{n\times p}$, the product $\boldsymbol{X}^T\boldsymbol{X} \in
{\mathbb{R}}^{p\times p}$.  In the above case we have that $p \ll n$,
in our case $p=5$ meaning that we end up with inverting a small
$5\times 5$ matrix. This is a rather common situation, in many cases we end up with low-dimensional
matrices to invert. The methods discussed here and for many other
supervised learning algorithms like classification with logistic
regression or support vector machines, exhibit dimensionalities which
allow for the usage of direct linear algebra methods such as **LU** decomposition or **Singular Value Decomposition** (SVD) for finding the inverse of the matrix
$\boldsymbol{X}^T\boldsymbol{X}$.

**Small question**: Do you think the example we have at hand here (the nuclear binding energies) can lead to problems in inverting the matrix  $\boldsymbol{X}^T\boldsymbol{X}$? What kind of problems can we expect?

## Some useful matrix and vector expressions

The following matrix and vector relation will be useful here and for the rest of the course. Vectors are always written as boldfaced lower case letters and
matrices as upper case boldfaced letters.

(vedi slides: ripasso lin alg)

2
7

<
<
<
!
!
M
A
T
H
_
B
L
O
C
K

2
8

<
<
<
!
!
M
A
T
H
_
B
L
O
C
K

$$
\frac{\partial \log{\vert\boldsymbol{A}\vert}}{\partial \boldsymbol{A}} = (\boldsymbol{A}^{-1})^T.
$$

## Meet the Hessian Matrix

A very important matrix we will meet again and again in Machine
Learning is the Hessian.  It is given by the second derivative of the
cost function with respect to the parameter $\beta$. Using the above
expression for derivatives of vectors and matrices, we find that the
second derivative of the cost function is,

$$
\frac{\partial}{\partial \boldsymbol{\beta}^T}\frac{\partial C(\boldsymbol{\beta})}{\partial \boldsymbol{\beta}} =\frac{\partial}{\partial \boldsymbol{\beta}}\left[-\frac{2}{n}\boldsymbol{X}^T\left( \boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta}\right)\right]=\frac{2}{n}\boldsymbol{X}^T\boldsymbol{X}.
$$

The Hessian matrix plays an important role and is defined here as

$$
\boldsymbol{H}=\boldsymbol{X}^T\boldsymbol{X}.
$$

For ordinary least squares, it is inversely proportional (derivation
next week) with the variance of the optimal parameters
$\hat{\boldsymbol{\beta}}$. Furthermore, we will see later this week that is
(beside $1/n$) equal to the covariance matrix. It plays also a very
important role in optmization algorithms and Principal Component
Analysis as a way to reduce the dimensionality of a machine learning
problem.

**Linear algebra question:**  Can we use the Hessian matrix to say something about properties of the cost function (our optmization  problem)? (hint: think about convex or concave problems and how to relate these to a matrix!).

## Interpretations and optimizing our parameters
The residuals $\boldsymbol{\epsilon}$ are in turn given by

$$
\boldsymbol{\epsilon} = \boldsymbol{y}-\boldsymbol{\tilde{y}} = \boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta},
$$

and with

$$
\boldsymbol{X}^T\left( \boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta}\right)= 0,
$$

we have

$$
\boldsymbol{X}^T\boldsymbol{\epsilon}=\boldsymbol{X}^T\left( \boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta}\right)= 0,
$$

meaning that the solution for $\boldsymbol{\beta}$ is the one which minimizes the residuals.  Later we will link this with the maximum likelihood approach.

## Own code for Ordinary Least Squares

It is rather straightforward to implement the matrix inversion and obtain the parameters $\boldsymbol{\beta}$. After having defined the matrix $\boldsymbol{X}$ we simply need to
write

```python
# matrix inversion to find beta
beta = np.linalg.inv(X.T.dot(X)).dot(X.T).dot(Energies)
# and then make the prediction
ytilde = X @ beta
```

Alternatively, you can use the least squares functionality in **Numpy** as

```python
fit = np.linalg.lstsq(X, Energies, rcond =None)[0]
ytildenp = np.dot(fit,X.T)
```

And finally we plot our fit with and compare with data

```python
Masses['Eapprox']  = ytilde
# Generate a plot comparing the experimental with the fitted values values.
fig, ax = plt.subplots()
ax.set_xlabel(r'$A = N + Z$')
ax.set_ylabel(r'$E_\mathrm{bind}\,/\mathrm{MeV}$')
ax.plot(Masses['A'], Masses['Ebinding'], alpha=0.7, lw=2,
            label='Ame2016')
ax.plot(Masses['A'], Masses['Eapprox'], alpha=0.7, lw=2, c='m',
            label='Fit')
ax.legend()
save_fig("Masses2016OLS")
plt.show()
```

## Adding error analysis and training set up

We can easily test our fit by computing the $R2$ score that we discussed in connection with the functionality of **Scikit-Learn** in the introductory slides.
Since we are not using **Scikit-Learn** here we can define our own $R2$ function as

```python
def R2(y_data, y_model):
    return 1 - np.sum((y_data - y_model) ** 2) / np.sum((y_data - np.mean(y_data)) ** 2)
```

and we would be using it as

```python
print(R2(Energies,ytilde))
```

We can easily add our **MSE** score as

```python
def MSE(y_data,y_model):
    n = np.size(y_model)
    return np.sum((y_data-y_model)**2)/n

print(MSE(Energies,ytilde))
```

and finally the relative error as

```python
def RelativeError(y_data,y_model):
    return abs((y_data-y_model)/y_data)
print(RelativeError(Energies, ytilde))
```

## Splitting our Data in Training and Test data

It is normal in essentially all Machine Learning studies to split the
data in a training set and a test set (sometimes also an additional
validation set).  **Scikit-Learn** has an own function for this. There
is no explicit recipe for how much data should be included as training
data and say test data.  An accepted rule of thumb is to use
approximately $2/3$ to $4/5$ of the data as training data. We will
postpone a discussion of this splitting to the end of these notes and
our discussion of the so-called **bias-variance** tradeoff. Here we
limit ourselves to repeat the above equation of state fitting example
but now splitting the data into a training set and a test set.

## Examples

```python
import os
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn.model_selection import train_test_split

def R2(y_data, y_model):
    return 1 - np.sum((y_data - y_model) ** 2) / np.sum((y_data - np.mean(y_data)) ** 2)
def MSE(y_data,y_model):
    n = np.size(y_model)
    return np.sum((y_data-y_model)**2)/n

x = np.random.rand(100)
y = 2.0+5*x*x+0.1*np.random.randn(100)

#  The design matrix now as function of a given polynomial
X = np.zeros((len(x),3))
X[:,0] = 1.0
X[:,1] = x
X[:,2] = x**2
# We split the data in test and training data
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2)
# matrix inversion to find beta
beta = np.linalg.inv(X_train.T @ X_train) @ X_train.T @ y_train
print(beta)
# and then make the prediction
ytilde = X_train @ beta
print("Training R2")
print(R2(y_train,ytilde))
print("Training MSE")
print(MSE(y_train,ytilde))
ypredict = X_test @ beta
print("Test R2")
print(R2(y_test,ypredict))
print("Test MSE")
print(MSE(y_test,ypredict))
```

    [1.99003335 0.15101684 4.82667929]
    Training R2
    0.9932513421630478
    Training MSE
    0.010531495229523572
    Test R2
    0.9913891012083176
    Test MSE
    0.018528772890231096

## Making your own test-train splitting

```python
# equivalently in numpy
def train_test_split_numpy(inputs, labels, train_size, test_size):
    n_inputs = len(inputs)
    inputs_shuffled = inputs.copy()
    labels_shuffled = labels.copy()

    np.random.shuffle(inputs_shuffled)
    np.random.shuffle(labels_shuffled)

    train_end = int(n_inputs*train_size)
    X_train, X_test = inputs_shuffled[:train_end], inputs_shuffled[train_end:]
    Y_train, Y_test = labels_shuffled[:train_end], labels_shuffled[train_end:]

    return X_train, X_test, Y_train, Y_test
```

But since **scikit-learn** has its own function for doing this and since
it interfaces easily with **tensorflow** and other libraries, we
normally recommend using the latter functionality.

<!-- !split  -->
## The Boston housing data example

The Boston housing
data set was originally a part of UCI Machine Learning Repository
and has been removed now. The data set is now included in **Scikit-Learn**'s
library.  There are 506 samples and 13 feature (predictor) variables
in this data set. The objective is to predict the value of prices of
the house using the features (predictors) listed here.

The features/predictors are
1. CRIM: Per capita crime rate by town

2. ZN: Proportion of residential land zoned for lots over 25000 square feet

3. INDUS: Proportion of non-retail business acres per town

4. CHAS: Charles River dummy variable (= 1 if tract bounds river; 0 otherwise)

5. NOX: Nitric oxide concentration (parts per 10 million)

6. RM: Average number of rooms per dwelling

7. AGE: Proportion of owner-occupied units built prior to 1940

8. DIS: Weighted distances to five Boston employment centers

9. RAD: Index of accessibility to radial highways

10. TAX: Full-value property tax rate per USD10000

11. B: $1000(Bk - 0.63)^2$, where $Bk$ is the proportion of [people of African American descent] by town

12. LSTAT: Percentage of lower status of the population

13. MEDV: Median value of owner-occupied homes in USD 1000s

## Housing data, the code
We start by importing the libraries

```python
import numpy as np
import matplotlib.pyplot as plt

import pandas as pd
import seaborn as sns
```

and load the Boston Housing DataSet from **Scikit-Learn**

```python
from sklearn.datasets import load_boston

boston_dataset = load_boston()

# boston_dataset is a dictionary
# let's check what it contains
boston_dataset.keys()
```

    dict_keys(['data', 'target', 'feature_names', 'DESCR', 'filename'])

Then we invoke Pandas

```python
boston = pd.DataFrame(boston_dataset.data, columns=boston_dataset.feature_names)
boston.head()
boston['MEDV'] = boston_dataset.target
```

and preprocess the data

```python
# check for missing values in all the columns
boston.isnull().sum()
```

    CRIM       0
    ZN         0
    INDUS      0
    CHAS       0
    NOX        0
    RM         0
    AGE        0
    DIS        0
    RAD        0
    TAX        0
    PTRATIO    0
    B          0
    LSTAT      0
    MEDV       0
    dtype: int64

We can then visualize the data

```python
# set the size of the figure
sns.set(rc={'figure.figsize':(11.7,8.27)})

# plot a histogram showing the distribution of the target values
sns.distplot(boston['MEDV'], bins=30)
plt.show()
```

It is now useful to look at the correlation matrix

```python
# compute the pair wise correlation for all columns
correlation_matrix = boston.corr().round(2)
# use the heatmap function from seaborn to plot the correlation matrix
# annot = True to print the values inside the square
sns.heatmap(data=correlation_matrix, annot=True)
```

From the above coorelation plot we can see that **MEDV** is strongly correlated to **LSTAT** and  **RM**. We see also that **RAD** and **TAX** are stronly correlated, but we don't include this in our features together to avoid multi-colinearity

```python
plt.figure(figsize=(20, 5))

features = ['LSTAT', 'RM']
target = boston['MEDV']

for i, col in enumerate(features):
    plt.subplot(1, len(features) , i+1)
    x = boston[col]
    y = target
    plt.scatter(x, y, marker='o')
    plt.title(col)
    plt.xlabel(col)
    plt.ylabel('MEDV')
```

**Now we start training our model**

```python
X = pd.DataFrame(np.c_[boston['LSTAT'], boston['RM']], columns = ['LSTAT','RM'])
Y = boston['MEDV']
```

We split the data into training and test sets

```python
from sklearn.model_selection import train_test_split

# splits the training and test data set in 80% : 20%
# assign random_state to any value.This ensures consistency.
X_train, X_test, Y_train, Y_test = train_test_split(X, Y, test_size = 0.2, random_state=5)
print(X_train.shape)
print(X_test.shape)
print(Y_train.shape)
print(Y_test.shape)
```

    (404, 2)
    (102, 2)
    (404,)
    (102,)

Then we use the linear regression functionality from **Scikit-Learn**

```python
from sklearn.linear_model import LinearRegression
from sklearn.metrics import mean_squared_error, r2_score

lin_model = LinearRegression()
lin_model.fit(X_train, Y_train)

# model evaluation for training set

y_train_predict = lin_model.predict(X_train)
rmse = (np.sqrt(mean_squared_error(Y_train, y_train_predict)))
r2 = r2_score(Y_train, y_train_predict)

print("The model performance for training set")
print("--------------------------------------")
print('RMSE is {}'.format(rmse))
print('R2 score is {}'.format(r2))
print("\n")

# model evaluation for testing set

y_test_predict = lin_model.predict(X_test)
# root mean square error of the model
rmse = (np.sqrt(mean_squared_error(Y_test, y_test_predict)))

# r-squared score of the model
r2 = r2_score(Y_test, y_test_predict)

print("The model performance for testing set")
print("--------------------------------------")
print('RMSE is {}'.format(rmse))
print('R2 score is {}'.format(r2))
```

    The model performance for training set
    --------------------------------------
    RMSE is 5.6371293350711955
    R2 score is 0.6300745149331701

    The model performance for testing set
    --------------------------------------
    RMSE is 5.137400784702911
    R2 score is 0.6628996975186953

*"Not really a good result. You wouldn't present to a party."*

```python
# plotting the y_test vs y_pred
# ideally should have been a straight line
plt.scatter(Y_test, y_test_predict)
plt.show()
```

## Reducing the number of degrees of freedom, overarching view

Many Machine Learning problems involve thousands or even millions of
features for each training instance. <font color='red'>Not only does this make training
extremely slow, it can also make it much harder to find a good
solution, </font> as we will see. This problem is often referred to as the
curse of dimensionality.  Fortunately, in real-world problems, it is
often possible to reduce the number of features considerably, turning
an intractable problem into a tractable one.

Later  we will discuss some of the most popular dimensionality reduction
techniques: the <font color='blue'>principal component analysis (PCA), Kernel PCA, and
Locally Linear Embedding (LLE)</font>.

<font color='red'>**$\rightarrow$**</font>Principal component analysis and its various variants deal with the
problem of fitting a low-dimensional [affine
subspace](https://en.wikipedia.org/wiki/Affine_space) to a set of of
data points in a high-dimensional space. With its family of methods it
is one of the most used tools in data modeling, compression and
visualization.

## Preprocessing our data

Before we proceed however, we will discuss how to preprocess our
data. Till now and in connection with our previous examples we have
not met so many cases where we are too sensitive to the scaling of our
data. Normally the data may need a rescaling and/or may be <font color='green'>sensitive
to extreme values. **Scaling the data renders our inputs much more
suitable for the algorithms** we want to employ</font>.

<font color='grey'>For data sets gathered for real world applications, it is rather normal that
different features have very different units and
numerical scales. For example, a data set detailing health habits may include
features such as **age** in the range $0-80$, and **caloric intake** of order $2000$.
Many machine learning methods sensitive to the scales of the features and may perform poorly if they
are very different scales. Therefore, it is typical to scale
the features in a way to avoid such outlier values.</font>

## Functionality in Scikit-Learn

**Scikit-Learn** has several functions which allow us to rescale the
data, normally resulting in much better results in terms of various
accuracy scores.  The<font color='purple'> **StandardScaler**</font> function in **Scikit-Learn**
ensures that for each feature/predictor we study the <font color='purple'>mean value is
zero and the variance is one</font> (every column in the design/feature
matrix).  This scaling has the drawback that it does <font color='purple'>not ensure that
we have a particular maximum or minimum in our data set</font>. Another
function included in **Scikit-Learn** is the <font color='purple'>**MinMaxScaler** </font> which
ensures that all features are exactly <font color='purple'>between $0$ and $1$ </font>. The

## More preprocessing

The <font color='purple'>**Normalizer** </font>scales each data
point such that the <font color='purple'>feature vector has a euclidean length of one</font>. In other words, it
projects a data point on the circle (or sphere in the case of higher dimensions) with a
radius of 1. This means every data point is scaled by a different number (by the
inverse of it’s length).
This normalization is often <font color='purple'>used when only the direction (or angle) of the data matters,
not the length of the feature vector</font>.

The <font color='purple'>**RobustScaler** </font> works similarly to the StandardScaler in that it
ensures statistical properties for each feature that guarantee that
they are on the same scale. However, the RobustScaler <font color='purple'>uses the median
and quartiles, instead of mean and variance</font>. This makes the
RobustScaler <font color='purple'>ignore data points that are very different from the rest
(like measurement errors)</font>. These odd data points are also called
<font color='purple'>outliers</font>, and might often lead to trouble for other scaling
techniques.

## Frequently used scaling functions

### 1) StandardScaler

Many features are often scaled using standardization to improve performance. In **Scikit-Learn** this is given by the **StandardScaler** function as discussed above. It is easy however to write your own.
Mathematically, this involves subtracting the mean and divide by the standard deviation over the data set, for each feature:

$$
x_j^{(i)} \rightarrow \frac{x_j^{(i)} - \overline{x}_j}{\sigma(x_j)},
$$

where $\overline{x}_j$ and $\sigma(x_j)$ are the mean and standard deviation, respectively,  of the feature $x_j$.
This ensures that each feature has zero mean and unit standard deviation.  For data sets where  we do not have the standard deviation or don't wish to calculate it,  it is then common to simply set it to one.

## Example of own Standard scaling

Let us consider the following vanilla example where we use both
**Scikit-Learn** and write our own function as well.  We produce a
simple test design matrix with random numbers. Each column could then
represent a specific feature whose mean value is subracted.

```python
import sklearn.linear_model as skl
from sklearn.metrics import mean_squared_error
from sklearn.model_selection import  train_test_split
from sklearn.preprocessing import MinMaxScaler, StandardScaler, Normalizer
import numpy as np
import pandas as pd
from IPython.display import display
np.random.seed(100)
# setting up a 10 x 5 matrix
rows = 10
cols = 5
X = np.random.randn(rows,cols)
XPandas = pd.DataFrame(X)
display(XPandas)
print(XPandas.mean())
print(XPandas.std())
XPandas = (XPandas -XPandas.mean())
display(XPandas)
#  This option does not include the standard deviation
scaler = StandardScaler(with_std=False)
scaler.fit(X)
Xscaled = scaler.transform(X)
display(XPandas-Xscaled)
```

<div>
<style scoped>
    .dataframe tbody tr th:only-of-type {
        vertical-align: middle;
    }

    .dataframe tbody tr th {
        vertical-align: top;
    }

    .dataframe thead th {
        text-align: right;
    }
</style>
<table border="1" class="dataframe">
  <thead>
    <tr style="text-align: right;">
      <th></th>
      <th>0</th>
      <th>1</th>
      <th>2</th>
      <th>3</th>
      <th>4</th>
    </tr>
  </thead>
  <tbody>
    <tr>
      <th>0</th>
      <td>-1.749765</td>
      <td>0.342680</td>
      <td>1.153036</td>
      <td>-0.252436</td>
      <td>0.981321</td>
    </tr>
    <tr>
      <th>1</th>
      <td>0.514219</td>
      <td>0.221180</td>
      <td>-1.070043</td>
      <td>-0.189496</td>
      <td>0.255001</td>
    </tr>
    <tr>
      <th>2</th>
      <td>-0.458027</td>
      <td>0.435163</td>
      <td>-0.583595</td>
      <td>0.816847</td>
      <td>0.672721</td>
    </tr>
    <tr>
      <th>3</th>
      <td>-0.104411</td>
      <td>-0.531280</td>
      <td>1.029733</td>
      <td>-0.438136</td>
      <td>-1.118318</td>
    </tr>
    <tr>
      <th>4</th>
      <td>1.618982</td>
      <td>1.541605</td>
      <td>-0.251879</td>
      <td>-0.842436</td>
      <td>0.184519</td>
    </tr>
    <tr>
      <th>5</th>
      <td>0.937082</td>
      <td>0.731000</td>
      <td>1.361556</td>
      <td>-0.326238</td>
      <td>0.055676</td>
    </tr>
    <tr>
      <th>6</th>
      <td>0.222400</td>
      <td>-1.443217</td>
      <td>-0.756352</td>
      <td>0.816454</td>
      <td>0.750445</td>
    </tr>
    <tr>
      <th>7</th>
      <td>-0.455947</td>
      <td>1.189622</td>
      <td>-1.690617</td>
      <td>-1.356399</td>
      <td>-1.232435</td>
    </tr>
    <tr>
      <th>8</th>
      <td>-0.544439</td>
      <td>-0.668172</td>
      <td>0.007315</td>
      <td>-0.612939</td>
      <td>1.299748</td>
    </tr>
    <tr>
      <th>9</th>
      <td>-1.733096</td>
      <td>-0.983310</td>
      <td>0.357508</td>
      <td>-1.613579</td>
      <td>1.470714</td>
    </tr>
  </tbody>
</table>
</div>

    0   -0.175300
    1    0.083527
    2   -0.044334
    3   -0.399836
    4    0.331939
    dtype: float64
    0    1.069584
    1    0.965548
    2    1.018232
    3    0.793167
    4    0.918992
    dtype: float64

<div>
<style scoped>
    .dataframe tbody tr th:only-of-type {
        vertical-align: middle;
    }

    .dataframe tbody tr th {
        vertical-align: top;
    }

    .dataframe thead th {
        text-align: right;
    }
</style>
<table border="1" class="dataframe">
  <thead>
    <tr style="text-align: right;">
      <th></th>
      <th>0</th>
      <th>1</th>
      <th>2</th>
      <th>3</th>
      <th>4</th>
    </tr>
  </thead>
  <tbody>
    <tr>
      <th>0</th>
      <td>-1.574465</td>
      <td>0.259153</td>
      <td>1.197370</td>
      <td>0.147400</td>
      <td>0.649382</td>
    </tr>
    <tr>
      <th>1</th>
      <td>0.689519</td>
      <td>0.137652</td>
      <td>-1.025709</td>
      <td>0.210340</td>
      <td>-0.076938</td>
    </tr>
    <tr>
      <th>2</th>
      <td>-0.282727</td>
      <td>0.351636</td>
      <td>-0.539261</td>
      <td>1.216683</td>
      <td>0.340782</td>
    </tr>
    <tr>
      <th>3</th>
      <td>0.070889</td>
      <td>-0.614808</td>
      <td>1.074067</td>
      <td>-0.038300</td>
      <td>-1.450257</td>
    </tr>
    <tr>
      <th>4</th>
      <td>1.794282</td>
      <td>1.458078</td>
      <td>-0.207545</td>
      <td>-0.442600</td>
      <td>-0.147420</td>
    </tr>
    <tr>
      <th>5</th>
      <td>1.112383</td>
      <td>0.647473</td>
      <td>1.405890</td>
      <td>0.073598</td>
      <td>-0.276263</td>
    </tr>
    <tr>
      <th>6</th>
      <td>0.397700</td>
      <td>-1.526744</td>
      <td>-0.712018</td>
      <td>1.216290</td>
      <td>0.418506</td>
    </tr>
    <tr>
      <th>7</th>
      <td>-0.280647</td>
      <td>1.106095</td>
      <td>-1.646283</td>
      <td>-0.956563</td>
      <td>-1.564374</td>
    </tr>
    <tr>
      <th>8</th>
      <td>-0.369139</td>
      <td>-0.751699</td>
      <td>0.051649</td>
      <td>-0.213103</td>
      <td>0.967809</td>
    </tr>
    <tr>
      <th>9</th>
      <td>-1.557795</td>
      <td>-1.066837</td>
      <td>0.401842</td>
      <td>-1.213743</td>
      <td>1.138775</td>
    </tr>
  </tbody>
</table>
</div>

<div>
<style scoped>
    .dataframe tbody tr th:only-of-type {
        vertical-align: middle;
    }

    .dataframe tbody tr th {
        vertical-align: top;
    }

    .dataframe thead th {
        text-align: right;
    }
</style>
<table border="1" class="dataframe">
  <thead>
    <tr style="text-align: right;">
      <th></th>
      <th>0</th>
      <th>1</th>
      <th>2</th>
      <th>3</th>
      <th>4</th>
    </tr>
  </thead>
  <tbody>
    <tr>
      <th>0</th>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
    </tr>
    <tr>
      <th>1</th>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
    </tr>
    <tr>
      <th>2</th>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
    </tr>
    <tr>
      <th>3</th>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
    </tr>
    <tr>
      <th>4</th>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
    </tr>
    <tr>
      <th>5</th>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
    </tr>
    <tr>
      <th>6</th>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
    </tr>
    <tr>
      <th>7</th>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
    </tr>
    <tr>
      <th>8</th>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
    </tr>
    <tr>
      <th>9</th>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
      <td>0.0</td>
    </tr>
  </tbody>
</table>
</div>

Small exercise: perform the standard scaling by including the standard deviation and compare with what Scikit-Learn gives.

### 2) Min-Max Scaling

Another commonly used scaling method is min-max scaling. This is very
useful for when we want the features to lie in a certain interval. To
scale the feature $x_j$ to the interval $[a, b]$, we can apply the
transformation

$$
x_j^{(i)} \rightarrow (b-a)\frac{x_j^{(i)} - \min(x_j)}{\max(x_j) - \min(x_j)} - a
$$

where $\min(x_j)$ and $\max(x_j)$ return the minimum and maximum value of $x_j$ over the data set, respectively.

## Testing the Means Squared Error as function of Complexity
One of
the aims is to reproduce Figure 2.11 of [Hastie et al](https://github.com/CompPhysics/MLErasmus/blob/master/doc/Textbooks/elementsstat.pdf).
We will also use Ridge and Lasso regression.

Our data is defined by $x\in [-3,3]$ with a total of for example $100$ data points.

```python
np.random.seed()
n = 100
maxdegree = 14
# Make data set.
x = np.linspace(-3, 3, n).reshape(-1, 1)
y = np.exp(-x**2) + 1.5 * np.exp(-(x-2)**2)+ np.random.normal(0, 0.1, x.shape)
```

where $y$ is the function we want to fit with a given polynomial.

Write a first code which sets up a design matrix $X$ defined by a fifth-order polynomial.  Scale your data and split it in training and test data.

```python
import matplotlib.pyplot as plt
import numpy as np
from sklearn.linear_model import LinearRegression, Ridge, Lasso
from sklearn.preprocessing import PolynomialFeatures
from sklearn.model_selection import train_test_split
from sklearn.pipeline import make_pipeline

np.random.seed(2018)
n = 50
maxdegree = 5
# Make data set.
x = np.linspace(-3, 3, n).reshape(-1, 1)
y = np.exp(-x**2) + 1.5 * np.exp(-(x-2)**2)+ np.random.normal(0, 0.1, x.shape)
TestError = np.zeros(maxdegree)
TrainError = np.zeros(maxdegree)
polydegree = np.zeros(maxdegree)
x_train, x_test, y_train, y_test = train_test_split(x, y, test_size=0.2)
scaler = StandardScaler()
scaler.fit(x_train)
x_train_scaled = scaler.transform(x_train)
x_test_scaled = scaler.transform(x_test)

for degree in range(maxdegree):
    model = make_pipeline(PolynomialFeatures(degree=degree), LinearRegression(fit_intercept=False))
    clf = model.fit(x_train_scaled,y_train)
    y_fit = clf.predict(x_train_scaled)
    y_pred = clf.predict(x_test_scaled)
    polydegree[degree] = degree
    TestError[degree] = np.mean( np.mean((y_test - y_pred)**2) )
    TrainError[degree] = np.mean( np.mean((y_train - y_fit)**2) )

plt.plot(polydegree, TestError, label='Test Error')
plt.plot(polydegree, TrainError, label='Train Error')
plt.legend()
plt.show()
```

## More preprocessing examples, Franke function and regression

```python
# Common imports
import os
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import sklearn.linear_model as skl
from sklearn.metrics import mean_squared_error
from sklearn.model_selection import  train_test_split
from sklearn.preprocessing import MinMaxScaler, StandardScaler, Normalizer

# Where to save the figures and data files
PROJECT_ROOT_DIR = "Results"
FIGURE_ID = "Results/FigureFiles"
DATA_ID = "DataFiles/"

if not os.path.exists(PROJECT_ROOT_DIR):
    os.mkdir(PROJECT_ROOT_DIR)

if not os.path.exists(FIGURE_ID):
    os.makedirs(FIGURE_ID)

if not os.path.exists(DATA_ID):
    os.makedirs(DATA_ID)

def image_path(fig_id):
    return os.path.join(FIGURE_ID, fig_id)

def data_path(dat_id):
    return os.path.join(DATA_ID, dat_id)

def save_fig(fig_id):
    plt.savefig(image_path(fig_id) + ".png", format='png')

def FrankeFunction(x,y):
	term1 = 0.75*np.exp(-(0.25*(9*x-2)**2) - 0.25*((9*y-2)**2))
	term2 = 0.75*np.exp(-((9*x+1)**2)/49.0 - 0.1*(9*y+1))
	term3 = 0.5*np.exp(-(9*x-7)**2/4.0 - 0.25*((9*y-3)**2))
	term4 = -0.2*np.exp(-(9*x-4)**2 - (9*y-7)**2)
	return term1 + term2 + term3 + term4

def create_X(x, y, n ):
	if len(x.shape) > 1:
		x = np.ravel(x)
		y = np.ravel(y)

	N = len(x)
	l = int((n+1)*(n+2)/2)		# Number of elements in beta
	X = np.ones((N,l))

	for i in range(1,n+1):
		q = int((i)*(i+1)/2)
		for k in range(i+1):
			X[:,q+k] = (x**(i-k))*(y**k)

	return X

# Making meshgrid of datapoints and compute Franke's function
n = 5
N = 1000
x = np.sort(np.random.uniform(0, 1, N))
y = np.sort(np.random.uniform(0, 1, N))
z = FrankeFunction(x, y)
X = create_X(x, y, n=n)
# split in training and test data
X_train, X_test, y_train, y_test = train_test_split(X,z,test_size=0.2)

clf = skl.LinearRegression().fit(X_train, y_train)

# The mean squared error and R2 score
print("MSE before scaling: {:.2f}".format(mean_squared_error(clf.predict(X_test), y_test)))
print("R2 score before scaling {:.2f}".format(clf.score(X_test,y_test)))

scaler = StandardScaler()
scaler.fit(X_train)
X_train_scaled = scaler.transform(X_train)
X_test_scaled = scaler.transform(X_test)

print("Feature min values before scaling:\n {}".format(X_train.min(axis=0)))
print("Feature max values before scaling:\n {}".format(X_train.max(axis=0)))

print("Feature min values after scaling:\n {}".format(X_train_scaled.min(axis=0)))
print("Feature max values after scaling:\n {}".format(X_train_scaled.max(axis=0)))

clf = skl.LinearRegression().fit(X_train_scaled, y_train)

print("MSE after  scaling: {:.2f}".format(mean_squared_error(clf.predict(X_test_scaled), y_test)))
print("R2 score for  scaled data: {:.2f}".format(clf.score(X_test_scaled,y_test)))
```

    MSE before scaling: 0.00
    R2 score before scaling 1.00
    Feature min values before scaling:
     [1.00000000e+00 6.97906022e-03 2.43639284e-03 4.87072815e-05
     1.70037324e-05 5.93601008e-06 3.39931051e-07 1.18670072e-07
     4.14277718e-08 1.44624525e-08 2.37239927e-09 8.28205578e-10
     2.89126914e-10 1.00934327e-10 3.52362157e-11 1.65571174e-11
     5.78009660e-12 2.01783414e-12 7.04426744e-13 2.45915671e-13
     8.58492636e-14]
    Feature max values before scaling:
     [1.         0.99970894 0.99978365 0.99941797 0.99949266 0.99956735
     0.99912709 0.99920175 0.99927642 0.9993511  0.99883628 0.99891093
     0.99898558 0.99906023 0.99913489 0.99854557 0.99862019 0.99869482
     0.99876945 0.99884409 0.99891873]
    Feature min values after scaling:
     [ 0.         -1.71761101 -1.75770568 -1.12330033 -1.12591227 -1.12871842
     -0.88613493 -0.884669   -0.88323026 -0.88182591 -0.75269037 -0.75050135
     -0.74829661 -0.74607851 -0.74384949 -0.6652177  -0.66294408 -0.66064822
     -0.65833132 -0.65599456 -0.6536392 ]
    Feature max values after scaling:
     [0.         1.71737253 1.75576555 2.20916295 2.23971032 2.26995402
     2.60543038 2.63162342 2.65743689 2.68286725 2.94273542 2.96631321
     2.98947894 3.01222822 3.034557   3.24159785 3.26297455 3.28391978
     3.30442964 3.32450054 3.34412923]
    MSE after  scaling: 0.00
    R2 score for  scaled data: 1.00

## Mathematical Interpretation of Ordinary Least Squares (no)

What is presented here is a mathematical analysis of various regression algorithms (ordinary least  squares, Ridge and Lasso Regression). The analysis is based on an important algorithm in linear algebra, the so-called Singular Value Decomposition (SVD).

We have shown that in ordinary least squares the optimal parameters $\beta$ are given by

$$
\hat{\boldsymbol{\beta}} = \left(\boldsymbol{X}^T\boldsymbol{X}\right)^{-1}\boldsymbol{X}^T\boldsymbol{y}.
$$

The **hat** over $\boldsymbol{\beta}$ means we have the optimal parameters after minimization of the cost function.

This means that our best model is defined as

$$
\tilde{\boldsymbol{y}}=\boldsymbol{X}\hat{\boldsymbol{\beta}} = \boldsymbol{X}\left(\boldsymbol{X}^T\boldsymbol{X}\right)^{-1}\boldsymbol{X}^T\boldsymbol{y}.
$$

We now define a matrix

$$
\boldsymbol{A}=\boldsymbol{X}\left(\boldsymbol{X}^T\boldsymbol{X}\right)^{-1}\boldsymbol{X}^T.
$$

We can rewrite

$$
\tilde{\boldsymbol{y}}=\boldsymbol{X}\hat{\boldsymbol{\beta}} = \boldsymbol{A}\boldsymbol{y}.
$$

The matrix $\boldsymbol{A}$ has the important property that $\boldsymbol{A}^2=\boldsymbol{A}$. This is the definition of a projection matrix.
We can then interpret our optimal model $\tilde{\boldsymbol{y}}$ as being represented  by an orthogonal  projection of $\boldsymbol{y}$ onto a space defined by the column vectors of $\boldsymbol{X}$.  In our case here the matrix $\boldsymbol{A}$ is a square matrix. If it is a general rectangular matrix we have an oblique projection matrix.

## Residual Error

We have defined the residual error as

$$
\boldsymbol{\epsilon}=\boldsymbol{y}-\tilde{\boldsymbol{y}}=\left[\boldsymbol{I}-\boldsymbol{X}\left(\boldsymbol{X}^T\boldsymbol{X}\right)^{-1}\boldsymbol{X}^T\right]\boldsymbol{y}.
$$

The residual errors are then the projections of $\boldsymbol{y}$ onto the orthogonal component of the space defined by the column vectors of $\boldsymbol{X}$.

## Simple case

If the matrix $\boldsymbol{X}$ is an orthogonal (or unitary in case of complex values) matrix, we have

$$
\boldsymbol{X}^T\boldsymbol{X}=\boldsymbol{X}\boldsymbol{X}^T = \boldsymbol{I}.
$$

In this case the matrix $\boldsymbol{A}$ becomes

$$
\boldsymbol{A}=\boldsymbol{X}\left(\boldsymbol{X}^T\boldsymbol{X}\right)^{-1}\boldsymbol{X}^T)=\boldsymbol{I},
$$

and we have the obvious case

$$
\boldsymbol{\epsilon}=\boldsymbol{y}-\tilde{\boldsymbol{y}}=0.
$$

This serves also as a useful test of our codes.

## The singular value decomposition

The examples we have looked at so far are cases where we normally can
invert the matrix $\boldsymbol{X}^T\boldsymbol{X}$. Using a polynomial expansion where we fit of various functions leads to
row vectors of the design matrix which are essentially orthogonal due
to the polynomial character of our model. Obtaining the inverse of the
design matrix is then often done via a so-called LU, QR or Cholesky
decomposition.

As we will also see in the first project,
this may
however not the be case in general and a standard matrix inversion
algorithm based on say LU, QR or Cholesky decomposition may lead to singularities. We will see examples of this below.

There is however a way to circumvent this problem and also
gain some insights about the ordinary least squares approach, and
later shrinkage methods like Ridge and Lasso regressions.

This is given by the **Singular Value Decomposition** (SVD) algorithm,
perhaps the most powerful linear algebra algorithm.  The SVD provides
a numerically stable matrix decomposition that is used in a large
swath oc applications and the decomposition is always stable
numerically.

In machine learning it plays a central role in dealing with for
example design matrices that may be near singular or singular.
Furthermore, as we will see here, the singular values can be related
to the covariance matrix (and thereby the correlation matrix) and in
turn the variance of a given quantity. It plays also an important role
in the principal component analysis where high-dimensional data can be
reduced to the statistically relevant features.

## $\rightarrow$ Linear Regression Problems

One of the typical problems we encounter with linear regression, in particular
when the matrix $\boldsymbol{X}$ (our so-called design matrix) is high-dimensional,
are problems with near singular or singular matrices. The column vectors of $\boldsymbol{X}$
may be linearly dependent, normally referred to as super-collinearity.
This means that the matrix may be rank deficient and it is basically impossible to
to model the data using linear regression. As an example, consider the matrix

$$
\begin{align*}
\mathbf{X} & =  \left[
\begin{array}{rrr}
1 & -1 & 2
\\
1 & 0 & 1
\\
1 & 2  & -1
\\
1 & 1  & 0
\end{array} \right]
\end{align*}
$$

The columns of $\boldsymbol{X}$ are linearly dependent. We see this easily since the
the first column is the row-wise sum of the other two columns. The rank (more correct,
the column rank) of a matrix is the dimension of the space spanned by the
column vectors. Hence, the rank of $\mathbf{X}$ is equal to the number
of linearly independent columns. In this particular case the matrix has rank 2.

Super-collinearity of an $(n \times p)$-dimensional design matrix $\mathbf{X}$ implies
that the inverse of the matrix $\boldsymbol{X}^T\boldsymbol{X}$ (the matrix we need to invert to solve the linear regression equations) is non-invertible. If we have a square matrix that does not have an inverse, we say this matrix singular. The example here demonstrates this

$$
\begin{align*}
\boldsymbol{X} & =  \left[
\begin{array}{rr}
1 & -1
\\
1 & -1
\end{array} \right].
\end{align*}
$$

We see easily that  $\mbox{det}(\boldsymbol{X}) = x_{11} x_{22} - x_{12} x_{21} = 1 \times (-1) - 1 \times (-1) = 0$. Hence, $\mathbf{X}$ is singular and its inverse is undefined.
This is equivalent to saying that the matrix $\boldsymbol{X}$ has at least an eigenvalue which is zero.

## 1) Fixing the singularity: add a non-zero scalar $\lambda$ in the diagonal

If our design matrix $\boldsymbol{X}$ which enters the linear regression problem

<!-- Equation labels as ordinary links -->
<div id="_auto1"></div>

$$
\begin{equation}
\boldsymbol{\beta}  =  (\boldsymbol{X}^{T} \boldsymbol{X})^{-1} \boldsymbol{X}^{T} \boldsymbol{y},
\label{_auto1} \tag{1}
\end{equation}
$$

has linearly dependent column vectors, we will not be able to compute the inverse
of $\boldsymbol{X}^T\boldsymbol{X}$ and we cannot find the parameters (estimators) $\beta_i$.
The estimators are only well-defined if $(\boldsymbol{X}^{T}\boldsymbol{X})^{-1}$ exits.
This is more likely to happen when the matrix $\boldsymbol{X}$ is high-dimensional. In this case it is likely to encounter a situation where
the regression parameters $\beta_i$ cannot be estimated.

A cheap  *ad hoc* approach is  simply to add a small diagonal component to the matrix to invert, that is we change

$$
\boldsymbol{X}^{T} \boldsymbol{X} \rightarrow \boldsymbol{X}^{T} \boldsymbol{X}+\lambda \boldsymbol{I},
$$

where $\boldsymbol{I}$ is the identity matrix.  When we discuss **Ridge** regression this is actually what we end up evaluating. The parameter $\lambda$ is called a hyperparameter. More about this later.

## 2) Basic math of the SVD (!!!)

From standard linear algebra we know that a square matrix $\boldsymbol{X}$ can be diagonalized if and only it is
a so-called [normal matrix](https://en.wikipedia.org/wiki/Normal_matrix), that is if $\boldsymbol{X}\in {\mathbb{R}}^{n\times n}$
we have $\boldsymbol{X}\boldsymbol{X}^T=\boldsymbol{X}^T\boldsymbol{X}$ or if $\boldsymbol{X}\in {\mathbb{C}}^{n\times n}$ we have $\boldsymbol{X}\boldsymbol{X}^{\dagger}=\boldsymbol{X}^{\dagger}\boldsymbol{X}$.
The matrix has then a set of eigenpairs

$$
(\lambda_1,\boldsymbol{u}_1),\dots, (\lambda_n,\boldsymbol{u}_n),
$$

and the eigenvalues are given by the diagonal matrix

$$
\boldsymbol{\Sigma}=\mathrm{Diag}(\lambda_1, \dots,\lambda_n).
$$

The matrix $\boldsymbol{X}$ can be written in terms of an orthogonal/unitary transformation $\boldsymbol{U}$

$$
\boldsymbol{X} = \boldsymbol{U}\boldsymbol{\Sigma}\boldsymbol{V}^T,
$$

with $\boldsymbol{U}\boldsymbol{U}^T=\boldsymbol{I}$ or $\boldsymbol{U}\boldsymbol{U}^{\dagger}=\boldsymbol{I}$.

Not all square matrices are diagonalizable. A matrix like the one discussed above

$$
\boldsymbol{X} = \begin{bmatrix}
1&  -1 \\
1& -1\\
\end{bmatrix}
$$

is not diagonalizable, it is a so-called [defective matrix](https://en.wikipedia.org/wiki/Defective_matrix). It is easy to see that the condition
$\boldsymbol{X}\boldsymbol{X}^T=\boldsymbol{X}^T\boldsymbol{X}$ is not fulfilled.

## The SVD, a Fantastic Algorithm

However, and this is the strength of the SVD algorithm, any general
matrix $\boldsymbol{X}$ can be decomposed in terms of a diagonal matrix and
two orthogonal/unitary matrices.  The [Singular Value Decompostion
(SVD) theorem](https://en.wikipedia.org/wiki/Singular_value_decomposition)
states that a general $m\times n$ matrix $\boldsymbol{X}$ can be written in
terms of a diagonal matrix $\boldsymbol{\Sigma}$ of dimensionality $m\times n$
and two orthognal matrices $\boldsymbol{U}$ and $\boldsymbol{V}$, where the first has
dimensionality $m \times m$ and the last dimensionality $n\times n$.
We have then

$$
\boldsymbol{X} = \boldsymbol{U}\boldsymbol{\Sigma}\boldsymbol{V}^T
$$

As an example, the above defective matrix can be decomposed as

$$
\boldsymbol{X} = \frac{1}{\sqrt{2}}\begin{bmatrix}  1&  1 \\ 1& -1\\ \end{bmatrix} \begin{bmatrix}  2&  0 \\ 0& 0\\ \end{bmatrix}    \frac{1}{\sqrt{2}}\begin{bmatrix}  1&  -1 \\ 1& 1\\ \end{bmatrix}=\boldsymbol{U}\boldsymbol{\Sigma}\boldsymbol{V}^T,
$$

with eigenvalues $\sigma_1=2$ and $\sigma_2=0$.
The SVD exits always!

The SVD
decomposition (singular values) gives eigenvalues
$\sigma_i\geq\sigma_{i+1}$ for all $i$ and for dimensions larger than $i=p$, the
eigenvalues (singular values) are zero.

In the general case, where our design matrix $\boldsymbol{X}$ has dimension
$n\times p$, the matrix is thus decomposed into an $n\times n$
orthogonal matrix $\boldsymbol{U}$, a $p\times p$ orthogonal matrix $\boldsymbol{V}$
and a diagonal matrix $\boldsymbol{\Sigma}$ with $r=\mathrm{min}(n,p)$
singular values $\sigma_i\geq 0$ on the main diagonal and zeros filling
the rest of the matrix.  There are at most $p$ singular values
assuming that $n > p$. In our regression examples for the nuclear
masses and the equation of state this is indeed the case, while for
the Ising model we have $p > n$. These are often cases that lead to
near singular or singular matrices.

The columns of $\boldsymbol{U}$ are called the left singular vectors while the columns of $\boldsymbol{V}$ are the right singular vectors.

## Economy-size SVD

If we assume that $n > p$, then our matrix $\boldsymbol{U}$ has dimension $n
\times n$. The last $n-p$ columns of $\boldsymbol{U}$ become however
irrelevant in our calculations since they are multiplied with the
zeros in $\boldsymbol{\Sigma}$.

The economy-size decomposition removes extra rows or columns of zeros
from the diagonal matrix of singular values, $\boldsymbol{\Sigma}$, along with the columns
in either $\boldsymbol{U}$ or $\boldsymbol{V}$ that multiply those zeros in the expression.
Removing these zeros and columns can improve execution time
and reduce storage requirements without compromising the accuracy of
the decomposition.

If $n > p$, we keep only the first $p$ columns of $\boldsymbol{U}$ and $\boldsymbol{\Sigma}$ has dimension $p\times p$.
If $p > n$, then only the first $n$ columns of $\boldsymbol{V}$ are computed and $\boldsymbol{\Sigma}$ has dimension $n\times n$.
The $n=p$ case is obvious, we retain the full SVD.
In general the economy-size SVD leads to less FLOPS and still conserving the desired accuracy.

## Codes for the SVD

```python
import numpy as np
# SVD inversion
def SVD(A):
    ''' Takes as input a numpy matrix A and returns inv(A) based on singular value decomposition (SVD).
    SVD is numerically more stable than the inversion algorithms provided by
    numpy and scipy.linalg at the cost of being slower.
    '''
    U, S, VT = np.linalg.svd(A,full_matrices=True)
    print('test U')
    print( (np.transpose(U) @ U - U @np.transpose(U)))
    print('test VT')
    print( (np.transpose(VT) @ VT - VT @np.transpose(VT)))
    print(U)
    print(S)
    print(VT)

    D = np.zeros((len(U),len(VT)))
    for i in range(0,len(VT)):
        D[i,i]=S[i]
    return U @ D @ VT

X = np.array([ [1.0,-1.0], [1.0,-1.0]])
#X = np.array([[1, 2], [3, 4], [5, 6]])

print(X)
C = SVD(X)
# Print the difference between the original matrix and the SVD one
print(C-X)
```

    [[ 1. -1.]
     [ 1. -1.]]
    test U
    [[0. 0.]
     [0. 0.]]
    test VT
    [[0. 0.]
     [0. 0.]]
    [[-0.70710678 -0.70710678]
     [-0.70710678  0.70710678]]
    [2.00000000e+00 3.35470445e-17]
    [[-0.70710678  0.70710678]
     [ 0.70710678  0.70710678]]
    [[-3.33066907e-16  4.44089210e-16]
     [ 0.00000000e+00  2.22044605e-16]]

The matrix $\boldsymbol{X}$ has columns that are linearly dependent. The first
column is the row-wise sum of the other two columns. The rank of a
matrix (the column rank) is the dimension of space spanned by the
column vectors. The rank of the matrix is the number of linearly
independent columns, in this case just $2$. We see this from the
singular values when running the above code. Running the standard
inversion algorithm for matrix inversion with $\boldsymbol{X}^T\boldsymbol{X}$ results
in the program terminating due to a singular matrix.

## Note about SVD Calculations

The $U$, $S$, and $V$ matrices returned from the **svd()** function
cannot be multiplied directly.

As you can see from the code, the $S$ vector must be converted into a
diagonal matrix. This may cause a problem as the size of the matrices
do not fit the rules of matrix multiplication, where the number of
columns in a matrix must match the number of rows in the subsequent
matrix.

If you wish to include the zero singular values, you will need to
resize the matrices and set up a diagonal matrix as done in the above
example

## Friday September 3

[Video of Lecture from 2020](https://www.uio.no/studier/emner/matnat/fys/FYS-STK4155/h20/forelesningsvideoer/LectureSeptember11.mp4?vrtx=view-as-webpage) and [handwritten notes](https://github.com/CompPhysics/MachineLearning/blob/master/doc/HandWrittenNotes/NotesSeptember11.pdf)

More material will be added here, see handwritten notes also.   Note that this material will be cleaned up after the lecture of Friday September 3.   See the handwritten notes from Friday's lecture at <https://github.com/CompPhysics/MachineLearning/tree/master/doc/HandWrittenNotes/2021>.

## Mathematics of the SVD and implications

Let us take a closer look at the mathematics of the SVD and the various implications for machine learning studies.

Our starting point is our design matrix $\boldsymbol{X}$ of dimension $n\times p$

$$
\boldsymbol{X}=\begin{bmatrix}
x_{0,0} & x_{0,1} & x_{0,2}& \dots & \dots x_{0,p-1}\\
x_{1,0} & x_{1,1} & x_{1,2}& \dots & \dots x_{1,p-1}\\
x_{2,0} & x_{2,1} & x_{2,2}& \dots & \dots x_{2,p-1}\\
\dots & \dots & \dots & \dots \dots & \dots \\
x_{n-2,0} & x_{n-2,1} & x_{n-2,2}& \dots & \dots x_{n-2,p-1}\\
x_{n-1,0} & x_{n-1,1} & x_{n-1,2}& \dots & \dots x_{n-1,p-1}\\
\end{bmatrix}.
$$

We can SVD decompose our matrix as

$$
\boldsymbol{X}=\boldsymbol{U}\boldsymbol{\Sigma}\boldsymbol{V}^T,
$$

where $\boldsymbol{U}$ is an orthogonal matrix of dimension $n\times n$, meaning that $\boldsymbol{U}\boldsymbol{U}^T=\boldsymbol{U}^T\boldsymbol{U}=\boldsymbol{I}_n$. Here $\boldsymbol{I}_n$ is the unit matrix of dimension $n \times n$.

Similarly, $\boldsymbol{V}$ is an orthogonal matrix of dimension $p\times p$, meaning that $\boldsymbol{V}\boldsymbol{V}^T=\boldsymbol{V}^T\boldsymbol{V}=\boldsymbol{I}_p$. Here $\boldsymbol{I}_n$ is the unit matrix of dimension $p \times p$.

Finally $\boldsymbol{\Sigma}$ contains the singular values $\sigma_i$. This matrix has dimension $n\times p$ and the singular values $\sigma_i$ are all positive. The non-zero values are ordered in descending order, that is

$$
\sigma_0 > \sigma_1 > \sigma_2 > \dots > \sigma_{p-1} > 0.
$$

All values beyond $p-1$ are all zero.

## Example Matrix

As an example, consider the following $3\times 2$ example for the matrix $\boldsymbol{\Sigma}$

$$
\boldsymbol{\Sigma}=
\begin{bmatrix}
2& 0 \\
0 & 1 \\
0 & 0 \\
\end{bmatrix}
$$

The singular values are $\sigma_0=2$ and $\sigma_1=1$. It is common to rewrite the matrix $\boldsymbol{\Sigma}$ as

$$
\boldsymbol{\Sigma}=
\begin{bmatrix}
\boldsymbol{\tilde{\Sigma}}\\
\boldsymbol{0}\\
\end{bmatrix},
$$

where

$$
\boldsymbol{\tilde{\Sigma}}=
\begin{bmatrix}
2& 0 \\
0 & 1 \\
\end{bmatrix},
$$

contains only the singular values.   Note also (and we will use this below) that

$$
\boldsymbol{\Sigma}^T\boldsymbol{\Sigma}=
\begin{bmatrix}
4& 0 \\
0 & 1 \\
\end{bmatrix},
$$

which is a $2\times 2 $ matrix while

$$
\boldsymbol{\Sigma}\boldsymbol{\Sigma}^T=
\begin{bmatrix}
4& 0 & 0\\
0 & 1 & 0\\
0 & 0 & 0\\
\end{bmatrix},
$$

is a $3\times 3 $ matrix. The last row and column of this last matrix
contain only zeros. This will have important consequences for our SVD
decomposition of the design matrix.

## Setting up the Matrix to be inverted

The matrix that may cause problems for us is $\boldsymbol{X}^T\boldsymbol{X}$. Using the SVD we can rewrite this matrix as

$$
\boldsymbol{X}^T\boldsymbol{X}=\boldsymbol{V}\boldsymbol{\Sigma}^T\boldsymbol{U}^T\boldsymbol{U}\boldsymbol{\Sigma}\boldsymbol{V}^T,
$$

and using the orthogonality of the matrix $\boldsymbol{U}$ we have

$$
\boldsymbol{X}^T\boldsymbol{X}=\boldsymbol{V}\boldsymbol{\Sigma}^T\boldsymbol{\Sigma}\boldsymbol{V}^T.
$$

We define $\boldsymbol{\Sigma}^T\boldsymbol{\Sigma}=\tilde{\boldsymbol{\Sigma}}^2$ which is  a diagonal matrix containing only the singular values squared. It has dimensionality $p \times p$.

This means, using the orthogonality of $\boldsymbol{V}$,  that we get

$$
\boldsymbol{X}^T\boldsymbol{X}=\tilde{\boldsymbol{\Sigma}}^2.
$$

We can now insert the result for the matrix $\boldsymbol{X}^T\boldsymbol{X}$ into our equation for ordinary least squares where

$$
\tilde{y}_{\mathrm{OLS}}=\boldsymbol{X}\left(\boldsymbol{X}^T\boldsymbol{X}\right)^{-1}\boldsymbol{X}^T\boldsymbol{y},
$$

and using our SVD decomposition of $\boldsymbol{X}$ we have

$$
\tilde{y}_{\mathrm{OLS}}=\boldsymbol{U}\boldsymbol{\Sigma}\boldsymbol{V}^T\tilde{\boldsymbol{\Sigma}}^{-2}\boldsymbol{V}\boldsymbol{\Sigma}^T\boldsymbol{U}^T\boldsymbol{y},
$$

which gives us, using the orthogonality of the matrices $\boldsymbol{U}$ and $\boldsymbol{V}$,

$$
\tilde{y}_{\mathrm{OLS}}=\boldsymbol{U}\boldsymbol{U}^T\boldsymbol{y}=\sum_{i=0}^{p-1}\boldsymbol{u}_i\boldsymbol{u}^T_j\boldsymbol{y},
$$

Note here that when we perform the  multiplication of the various matrices, the orthogonal vectors of the matrix $\boldsymbol{U}$

$$
\boldsymbol{U}=[\boldsymbol{u}_0,\boldsymbol{u}_1,\dots,\boldsymbol{u}_{n-1}],
$$

that belong to $i>p-1$, result in only  zeros when we perform the multiplications. This means that the sum above has non-zero elements only up to $i=p-1$. This corresponds also to the number of singular values (these are all non-zero).

<font color=purple> It means that the **ordinary least square model**(with the optimal parameters) $\boldsymbol{\tilde{y}}$, corresponds to an **orthogonal transformation** of the **output (or target) vector** $\boldsymbol{y}$ by the **(orthogonal) vectors of the matrix** $\boldsymbol{U}$. </font>

## Further properties (important for our analyses later)

Let us study again $\boldsymbol{X}^T\boldsymbol{X}$ in terms of our SVD,

$$
\boldsymbol{X}^T\boldsymbol{X}=\boldsymbol{V}\boldsymbol{\Sigma}^T\boldsymbol{U}^T\boldsymbol{U}\boldsymbol{\Sigma}\boldsymbol{V}^T=\boldsymbol{V}\boldsymbol{\Sigma}^T\boldsymbol{\Sigma}\boldsymbol{V}^T.
$$

If we now multiply from the right with $\boldsymbol{V}$ (using the orthogonality of $\boldsymbol{V}$) we get

$$
\left(\boldsymbol{X}^T\boldsymbol{X}\right)\boldsymbol{V}=\boldsymbol{V}\boldsymbol{\Sigma}^T\boldsymbol{\Sigma}.
$$

This means the vectors $\boldsymbol{v}_i$ of the orthogonal matrix $\boldsymbol{V}$ are the eigenvectors of the matrix $\boldsymbol{X}^T\boldsymbol{X}$
with eigenvalues given by the singular values squared, that is

$$
\left(\boldsymbol{X}^T\boldsymbol{X}\right)\boldsymbol{v}_i=\boldsymbol{v}_i\sigma_i^2.
$$

Similarly, if we use the SVD decomposition for the matrix $\boldsymbol{X}\boldsymbol{X}^T$, we have

$$
\boldsymbol{X}\boldsymbol{X}^T=\boldsymbol{U}\boldsymbol{\Sigma}\boldsymbol{V}^T\boldsymbol{V}\boldsymbol{\Sigma}^T\boldsymbol{U}^T=\boldsymbol{U}\boldsymbol{\Sigma}\boldsymbol{\Sigma}^T\boldsymbol{U}^T.
$$

If we now multiply from the right with $\boldsymbol{U}$ (using the orthogonality of $\boldsymbol{U}$) we get

$$
\left(\boldsymbol{X}\boldsymbol{X}^T\right)\boldsymbol{U}=\boldsymbol{U}\boldsymbol{\Sigma}\boldsymbol{\Sigma}^T.
$$

This means the vectors $\boldsymbol{u}_i$ of the orthogonal matrix $\boldsymbol{U}$ are the eigenvectors of the matrix $\boldsymbol{X}\boldsymbol{X}^T$
with eigenvalues given by the singular values squared, that is

$$
\left(\boldsymbol{X}\boldsymbol{X}^T\right)\boldsymbol{u}_i=\boldsymbol{u}_i\sigma_i^2.
$$

**Important note**: we have defined our design matrix $\boldsymbol{X}$ to be an
$n\times p$ matrix. In most supervised learning cases we have that $n
\ge p$, and quite often we have <font color=blue>$n >> p$</font>. For linear algebra based methods like ordinary least squares or Ridge regression, this leads to a matrix <font color=blue> $\boldsymbol{X}^T\boldsymbol{X}$ which is small and thereby easier to handle from a computational point of view </font>(in terms of number of floating point operations).

In our lectures, the number of columns will
always refer to the number of features in our data set, while the
number of rows represents the number of data inputs. Note that in
other texts you may find the opposite notation. This has consequences
for the definition of for example the covariance matrix and its relation to the SVD.

## Meet the Covariance Matrix

Before we move on to a discussion of Ridge and Lasso regression, we want to show an important example of the above.

We have already noted that the matrix $\boldsymbol{X}^T\boldsymbol{X}$ in ordinary
least squares is proportional to the second derivative of the cost
function, that is we have

$$
\frac{\partial^2 C(\boldsymbol{\beta})}{\partial \boldsymbol{\beta}^T\partial \boldsymbol{\beta}} =\frac{2}{n}\boldsymbol{X}^T\boldsymbol{X}.
$$

This quantity defines was what is called the Hessian matrix (the second derivative of a function we want to optimize).

The Hessian matrix plays an important role and is defined in this course as

$$
\boldsymbol{H}=\boldsymbol{X}^T\boldsymbol{X}.
$$

The Hessian matrix for ordinary least squares is also proportional to
the covariance matrix. This means also that we can use the SVD to find
the eigenvalues of the covariance matrix and the Hessian matrix in
terms of the singular values.   Let us develop these arguments, as they will play an important role in our machine learning studies.

## Introducing the Covariance and Correlation functions

Before we discuss the link between for example Ridge regression and the singular value decomposition, we need to remind ourselves about
the definition of the covariance and the correlation function. These are quantities that play a central role in machine learning methods.

Suppose we have defined two vectors
$\hat{x}$ and $\hat{y}$ with $n$ elements each. The covariance matrix $\boldsymbol{C}$ is defined as

$$
\boldsymbol{C}[\boldsymbol{x},\boldsymbol{y}] = \begin{bmatrix} \mathrm{cov}[\boldsymbol{x},\boldsymbol{x}] & \mathrm{cov}[\boldsymbol{x},\boldsymbol{y}] \\
                              \mathrm{cov}[\boldsymbol{y},\boldsymbol{x}] & \mathrm{cov}[\boldsymbol{y},\boldsymbol{y}] \\
             \end{bmatrix},
$$

where for example

$$
\mathrm{cov}[\boldsymbol{x},\boldsymbol{y}] =\frac{1}{n} \sum_{i=0}^{n-1}(x_i- \overline{x})(y_i- \overline{y}).
$$

With this definition and recalling that the variance is defined as

$$
\mathrm{var}[\boldsymbol{x}]=\frac{1}{n} \sum_{i=0}^{n-1}(x_i- \overline{x})^2,
$$

we can rewrite the covariance matrix as

$$
\boldsymbol{C}[\boldsymbol{x},\boldsymbol{y}] = \begin{bmatrix} \mathrm{var}[\boldsymbol{x}] & \mathrm{cov}[\boldsymbol{x},\boldsymbol{y}] \\
                              \mathrm{cov}[\boldsymbol{x},\boldsymbol{y}] & \mathrm{var}[\boldsymbol{y}] \\
             \end{bmatrix}.
$$

**Note:** we have used $1/n$ in the above definitions of the *sample* variance and covariance. We assume then that we can calculate the exact mean value.
What you will find in essentially all statistics texts are equations
with a factor $1/(n-1)$. This is called [Bessel's correction](https://mathworld.wolfram.com/BesselsCorrection.html). This
method corrects the bias in the estimation of the population variance
and covariance. It also partially corrects the bias in the estimation
of the population standard deviation. If you use a library like
**Scikit-Learn** or **nunmpy's** function calculate the covariance, this
quantity will be computed with a factor $1/(n-1)$.

## Covariance and Correlation Matrix

The covariance takes values between zero and infinity and may thus
lead to problems with loss of numerical precision for particularly
large values. It is common to scale the covariance matrix by
introducing instead the correlation matrix defined via the so-called
correlation function

$$
\mathrm{corr}[\boldsymbol{x},\boldsymbol{y}]=\frac{\mathrm{cov}[\boldsymbol{x},\boldsymbol{y}]}{\sqrt{\mathrm{var}[\boldsymbol{x}] \mathrm{var}[\boldsymbol{y}]}}.
$$

The correlation function is then given by values $\mathrm{corr}[\boldsymbol{x},\boldsymbol{y}]
\in [-1,1]$. This avoids eventual problems with too large values. We
can then define the correlation matrix for the two vectors $\boldsymbol{x}$
and $\boldsymbol{y}$ as

$$
\boldsymbol{K}[\boldsymbol{x},\boldsymbol{y}] = \begin{bmatrix} 1 & \mathrm{corr}[\boldsymbol{x},\boldsymbol{y}] \\
                              \mathrm{corr}[\boldsymbol{y},\boldsymbol{x}] & 1 \\
             \end{bmatrix},
$$

In the above example this is the function we constructed using **pandas**.

## Correlation Function and Design/Feature Matrix

In our derivation of the various regression algorithms like **Ordinary Least Squares** or **Ridge regression**
we defined the design/feature matrix $\boldsymbol{X}$ as

$$
\boldsymbol{X}=\begin{bmatrix}
x_{0,0} & x_{0,1} & x_{0,2}& \dots & \dots x_{0,p-1}\\
x_{1,0} & x_{1,1} & x_{1,2}& \dots & \dots x_{1,p-1}\\
x_{2,0} & x_{2,1} & x_{2,2}& \dots & \dots x_{2,p-1}\\
\dots & \dots & \dots & \dots \dots & \dots \\
x_{n-2,0} & x_{n-2,1} & x_{n-2,2}& \dots & \dots x_{n-2,p-1}\\
x_{n-1,0} & x_{n-1,1} & x_{n-1,2}& \dots & \dots x_{n-1,p-1}\\
\end{bmatrix},
$$

with $\boldsymbol{X}\in {\mathbb{R}}^{n\times p}$, with the predictors/features $p$  refering to the column numbers and the
entries $n$ being the row elements.
We can rewrite the design/feature matrix in terms of its column vectors as

$$
\boldsymbol{X}=\begin{bmatrix} \boldsymbol{x}_0 & \boldsymbol{x}_1 & \boldsymbol{x}_2 & \dots & \dots & \boldsymbol{x}_{p-1}\end{bmatrix},
$$

with a given vector

$$
\boldsymbol{x}_i^T = \begin{bmatrix}x_{0,i} & x_{1,i} & x_{2,i}& \dots & \dots x_{n-1,i}\end{bmatrix}.
$$

With these definitions, we can now rewrite our $2\times 2$
correlation/covariance matrix in terms of a moe general design/feature
matrix $\boldsymbol{X}\in {\mathbb{R}}^{n\times p}$. This leads to a $p\times p$
covariance matrix for the vectors $\boldsymbol{x}_i$ with $i=0,1,\dots,p-1$

$$
\boldsymbol{C}[\boldsymbol{x}] = \begin{bmatrix}
\mathrm{var}[\boldsymbol{x}_0] & \mathrm{cov}[\boldsymbol{x}_0,\boldsymbol{x}_1]  & \mathrm{cov}[\boldsymbol{x}_0,\boldsymbol{x}_2] & \dots & \dots & \mathrm{cov}[\boldsymbol{x}_0,\boldsymbol{x}_{p-1}]\\
\mathrm{cov}[\boldsymbol{x}_1,\boldsymbol{x}_0] & \mathrm{var}[\boldsymbol{x}_1]  & \mathrm{cov}[\boldsymbol{x}_1,\boldsymbol{x}_2] & \dots & \dots & \mathrm{cov}[\boldsymbol{x}_1,\boldsymbol{x}_{p-1}]\\
\mathrm{cov}[\boldsymbol{x}_2,\boldsymbol{x}_0]   & \mathrm{cov}[\boldsymbol{x}_2,\boldsymbol{x}_1] & \mathrm{var}[\boldsymbol{x}_2] & \dots & \dots & \mathrm{cov}[\boldsymbol{x}_2,\boldsymbol{x}_{p-1}]\\
\dots & \dots & \dots & \dots & \dots & \dots \\
\dots & \dots & \dots & \dots & \dots & \dots \\
\mathrm{cov}[\boldsymbol{x}_{p-1},\boldsymbol{x}_0]   & \mathrm{cov}[\boldsymbol{x}_{p-1},\boldsymbol{x}_1] & \mathrm{cov}[\boldsymbol{x}_{p-1},\boldsymbol{x}_{2}]  & \dots & \dots  & \mathrm{var}[\boldsymbol{x}_{p-1}]\\
\end{bmatrix},
$$

and the correlation matrix

$$
\boldsymbol{K}[\boldsymbol{x}] = \begin{bmatrix}
1 & \mathrm{corr}[\boldsymbol{x}_0,\boldsymbol{x}_1]  & \mathrm{corr}[\boldsymbol{x}_0,\boldsymbol{x}_2] & \dots & \dots & \mathrm{corr}[\boldsymbol{x}_0,\boldsymbol{x}_{p-1}]\\
\mathrm{corr}[\boldsymbol{x}_1,\boldsymbol{x}_0] & 1  & \mathrm{corr}[\boldsymbol{x}_1,\boldsymbol{x}_2] & \dots & \dots & \mathrm{corr}[\boldsymbol{x}_1,\boldsymbol{x}_{p-1}]\\
\mathrm{corr}[\boldsymbol{x}_2,\boldsymbol{x}_0]   & \mathrm{corr}[\boldsymbol{x}_2,\boldsymbol{x}_1] & 1 & \dots & \dots & \mathrm{corr}[\boldsymbol{x}_2,\boldsymbol{x}_{p-1}]\\
\dots & \dots & \dots & \dots & \dots & \dots \\
\dots & \dots & \dots & \dots & \dots & \dots \\
\mathrm{corr}[\boldsymbol{x}_{p-1},\boldsymbol{x}_0]   & \mathrm{corr}[\boldsymbol{x}_{p-1},\boldsymbol{x}_1] & \mathrm{corr}[\boldsymbol{x}_{p-1},\boldsymbol{x}_{2}]  & \dots & \dots  & 1\\
\end{bmatrix},
$$

## Covariance Matrix Examples

The Numpy function **np.cov** calculates the covariance elements using
the factor $1/(n-1)$ instead of $1/n$ since it assumes we do not have
the exact mean values.  The following simple function uses the
**np.vstack** function which takes each vector of dimension $1\times n$
and produces a $2\times n$ matrix $\boldsymbol{W}$

Note that this assumes you have the features as the rows, and the inputs as columns, that is

$$
\boldsymbol{W} = \begin{bmatrix} x_0 & x_1 & x_2 & \dots & x_{n-2} & x_{n-1} \\
                     y_0 & y_1 & y_2 & \dots & y_{n-2} & y_{n-1} \\
             \end{bmatrix},
$$

which in turn is converted into into the $2\times 2$ covariance matrix
$\boldsymbol{C}$ via the Numpy function **np.cov()**. We note that we can also calculate
the mean value of each set of samples $\boldsymbol{x}$ etc using the Numpy
function **np.mean(x)**. We can also extract the eigenvalues of the
covariance matrix through the **np.linalg.eig()** function.

```python
# Importing various packages
import numpy as np
n = 100
x = np.random.normal(size=n)
print(np.mean(x))
y = 4+3*x+np.random.normal(size=n)
print(np.mean(y))
W = np.vstack((x, y))
C = np.cov(W)
print(C)
```

    0.037174616325398424
    4.038906048738624
    [[ 1.1362171   3.60990608]
     [ 3.60990608 12.36658807]]

## Correlation Matrix

The previous example can be converted into the correlation matrix by
simply scaling the matrix elements with the variances.  We should also
subtract the mean values for each column. This leads to the following
code which sets up the correlations matrix for the previous example in
a more brute force way. Here we scale the mean values for each column of the design matrix, calculate the relevant mean values and variances and then finally set up the $2\times 2$ correlation matrix (since we have only two vectors).

```python
import numpy as np
n = 100
# define two vectors
x = np.random.random(size=n)
y = 4+3*x+np.random.normal(size=n)
#scaling the x and y vectors
x = x - np.mean(x)
y = y - np.mean(y)
variance_x = np.sum(x@x)/n
variance_y = np.sum(y@y)/n
print(variance_x)
print(variance_y)
cov_xy = np.sum(x@y)/n
cov_xx = np.sum(x@x)/n
cov_yy = np.sum(y@y)/n
C = np.zeros((2,2))
C[0,0]= cov_xx/variance_x
C[1,1]= cov_yy/variance_y
C[0,1]= cov_xy/np.sqrt(variance_y*variance_x)
C[1,0]= C[0,1]
print(C)
```

    0.07927324359762601
    1.5533957209864064
    [[1.         0.69178491]
     [0.69178491 1.        ]]

We see that the matrix elements along the diagonal are one as they
should be and that the matrix is symmetric. Furthermore, diagonalizing
this matrix we easily see that it is a positive definite matrix.

The above procedure with **numpy** can be made more compact if we use **pandas**.

## Correlation Matrix with Pandas

We whow here how we can set up the correlation matrix using **pandas**, as done in this simple code

```python
import numpy as np
import pandas as pd
n = 10
x = np.random.normal(size=n)
x = x - np.mean(x)
y = 4+3*x+np.random.normal(size=n)
y = y - np.mean(y)
# Note that we transpose the matrix in order to stay with our ordering n x p
X = (np.vstack((x, y))).T
print(X)
Xpd = pd.DataFrame(X)
print(Xpd)
correlation_matrix = Xpd.corr()
print(correlation_matrix)
```

    [[-0.40353261 -0.34219479]
     [ 0.27456763 -0.39740405]
     [ 0.31066489  1.7217131 ]
     [-1.03536949 -3.69986916]
     [-1.56583936 -4.46342118]
     [ 1.75459736  6.5538312 ]
     [-0.49550208 -2.34795091]
     [-0.52420593 -0.7992669 ]
     [ 1.00509918  3.12332646]
     [ 0.67952042  0.65123623]]
              0         1
    0 -0.403533 -0.342195
    1  0.274568 -0.397404
    2  0.310665  1.721713
    3 -1.035369 -3.699869
    4 -1.565839 -4.463421
    5  1.754597  6.553831
    6 -0.495502 -2.347951
    7 -0.524206 -0.799267
    8  1.005099  3.123326
    9  0.679520  0.651236
              0         1
    0  1.000000  0.957273
    1  0.957273  1.000000

We expand this model to the Franke function discussed above.

## $\rightarrow$ Correlation Matrix with Pandas and the Franke function

```python
# Common imports
import numpy as np
import pandas as pd

def FrankeFunction(x,y):
	term1 = 0.75*np.exp(-(0.25*(9*x-2)**2) - 0.25*((9*y-2)**2))
	term2 = 0.75*np.exp(-((9*x+1)**2)/49.0 - 0.1*(9*y+1))
	term3 = 0.5*np.exp(-(9*x-7)**2/4.0 - 0.25*((9*y-3)**2))
	term4 = -0.2*np.exp(-(9*x-4)**2 - (9*y-7)**2)
	return term1 + term2 + term3 + term4

def create_X(x, y, n ):
	if len(x.shape) > 1:
		x = np.ravel(x)
		y = np.ravel(y)

	N = len(x)
	l = int((n+1)*(n+2)/2)		# Number of elements in beta
	X = np.ones((N,l))

	for i in range(1,n+1):
		q = int((i)*(i+1)/2)
		for k in range(i+1):
			X[:,q+k] = (x**(i-k))*(y**k)

	return X

# Making meshgrid of datapoints and compute Franke's function
n = 4
N = 100
x = np.sort(np.random.uniform(0, 1, N))
y = np.sort(np.random.uniform(0, 1, N))
z = FrankeFunction(x, y)
X = create_X(x, y, n=n)

Xpd = pd.DataFrame(X)
# subtract the mean values and set up the covariance matrix
Xpd = Xpd - Xpd.mean()
covariance_matrix = Xpd.cov()
print(covariance_matrix)
```

         0         1         2         3         4         5         6         7   \
    0   0.0  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000
    1   0.0  0.090181  0.070482  0.091723  0.074512  0.060864  0.084671  0.069625
    2   0.0  0.070482  0.056898  0.071391  0.059326  0.049634  0.066302  0.055635
    3   0.0  0.091723  0.071391  0.099932  0.081405  0.066702  0.095940  0.079300
    4   0.0  0.074512  0.059326  0.081405  0.067421  0.056211  0.078671  0.065998
    5   0.0  0.060864  0.049634  0.066702  0.056211  0.047705  0.064924  0.055309
    6   0.0  0.084671  0.066302  0.095940  0.078671  0.064924  0.094424  0.078581
    7   0.0  0.069625  0.055635  0.079300  0.065998  0.055309  0.078581  0.066268
    8   0.0  0.057671  0.047046  0.066039  0.055798  0.047481  0.065900  0.056320
    9   0.0  0.048125  0.040094  0.055414  0.047541  0.041071  0.055694  0.048236
    10  0.0  0.077111  0.061024  0.089602  0.074084  0.061671  0.089728  0.075232
    11  0.0  0.063892  0.051546  0.074693  0.062632  0.052893  0.075303  0.063929
    12  0.0  0.053350  0.043884  0.062755  0.053369  0.045712  0.063697  0.054751
    13  0.0  0.044898  0.037656  0.053143  0.045834  0.039803  0.054306  0.047253
    14  0.0  0.038087  0.032564  0.045362  0.039669  0.034911  0.046663  0.041092

              8         9         10        11        12        13        14
    0   0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000
    1   0.057671  0.048125  0.077111  0.063892  0.053350  0.044898  0.038087
    2   0.047046  0.040094  0.061024  0.051546  0.043884  0.037656  0.032564
    3   0.066039  0.055414  0.089602  0.074693  0.062755  0.053143  0.045362
    4   0.055798  0.047541  0.074084  0.062632  0.053369  0.045834  0.039669
    5   0.047481  0.041071  0.061671  0.052893  0.045712  0.039803  0.034911
    6   0.065900  0.055694  0.089728  0.075303  0.063697  0.054306  0.046663
    7   0.056320  0.048236  0.075232  0.063929  0.054751  0.047253  0.041092
    8   0.048501  0.042081  0.063569  0.054694  0.047414  0.041406  0.036419
    9   0.042081  0.036969  0.054131  0.047150  0.041359  0.036529  0.032476
    10  0.063569  0.054131  0.086370  0.072987  0.062163  0.053357  0.046149
    11  0.054694  0.047150  0.072987  0.062402  0.053762  0.046667  0.040805
    12  0.047414  0.041359  0.062163  0.053762  0.046837  0.041095  0.036306
    13  0.041406  0.036529  0.053357  0.046667  0.041095  0.036428  0.032496
    14  0.036419  0.032476  0.046149  0.040805  0.036306  0.032496  0.029253

We note here that the covariance is zero for the first rows and
columns since all matrix elements in the design matrix were set to one
(we are fitting the function in terms of a polynomial of degree $n$).

This means that the variance for these elements will be zero and will
cause problems when we set up the correlation matrix.  We can simply
drop these elements and construct a correlation
matrix without these elements.

## Rewriting the Covariance and/or Correlation Matrix

We can rewrite the covariance matrix in a more compact form in terms of the design/feature matrix $\boldsymbol{X}$ as

$$
\boldsymbol{C}[\boldsymbol{x}] = \frac{1}{n}\boldsymbol{X}^T\boldsymbol{X}= \mathbb{E}[\boldsymbol{X}^T\boldsymbol{X}].
$$

To see this let us simply look at a design matrix $\boldsymbol{X}\in {\mathbb{R}}^{2\times 2}$

$$
\boldsymbol{X}=\begin{bmatrix}
x_{00} & x_{01}\\
x_{10} & x_{11}\\
\end{bmatrix}=\begin{bmatrix}
\boldsymbol{x}_{0} & \boldsymbol{x}_{1}\\
\end{bmatrix}.
$$

If we then compute the expectation value (note the $1/n$ factor instead of $1/(n-1)$)

$$
\mathbb{E}[\boldsymbol{X}^T\boldsymbol{X}] = \frac{1}{n}\boldsymbol{X}^T\boldsymbol{X}=\frac{1}{n}\begin{bmatrix}
x_{00}^2+x_{10}^2 & x_{00}x_{01}+x_{10}x_{11}\\
x_{01}x_{00}+x_{11}x_{10} & x_{01}^2+x_{11}^2\\
\end{bmatrix},
$$

which is just

$$
\boldsymbol{C}[\boldsymbol{x}_0,\boldsymbol{x}_1] = \boldsymbol{C}[\boldsymbol{x}]=\begin{bmatrix} \mathrm{var}[\boldsymbol{x}_0] & \mathrm{cov}[\boldsymbol{x}_0,\boldsymbol{x}_1] \\
                              \mathrm{cov}[\boldsymbol{x}_1,\boldsymbol{x}_0] & \mathrm{var}[\boldsymbol{x}_1] \\
             \end{bmatrix},
$$

where we wrote $$\boldsymbol{C}[\boldsymbol{x}_0,\boldsymbol{x}_1] = \boldsymbol{C}[\boldsymbol{x}]$$ to indicate that this is the covariance of the vectors $\boldsymbol{x}$ of the design/feature matrix $\boldsymbol{X}$.

It is easy to generalize this to a matrix $\boldsymbol{X}\in {\mathbb{R}}^{n\times p}$.

## Linking with the SVD

We saw earlier that

$$
\boldsymbol{X}^T\boldsymbol{X}=\boldsymbol{V}\boldsymbol{\Sigma}^T\boldsymbol{U}^T\boldsymbol{U}\boldsymbol{\Sigma}\boldsymbol{V}^T=\boldsymbol{V}\boldsymbol{\Sigma}^T\boldsymbol{\Sigma}\boldsymbol{V}^T.
$$

Since the matrices here have dimension $p\times p$, with $p$ corresponding to the singular values, we defined earlier the matrix

$$
\boldsymbol{\Sigma}^T\boldsymbol{\Sigma} = \begin{bmatrix} \tilde{\boldsymbol{\Sigma}} & \boldsymbol{0}\\ \end{bmatrix}\begin{bmatrix} \tilde{\boldsymbol{\Sigma}} \\ \boldsymbol{0}\\ \end{bmatrix},
$$

where the tilde-matrix $\tilde{\boldsymbol{\Sigma}}$ is a matrix of dimension $p\times p$ containing only the singular values $\sigma_i$, that is

$$
\tilde{\boldsymbol{\Sigma}}=\begin{bmatrix} \sigma_0 & 0 & 0 & \dots & 0 & 0 \\
                                    0 & \sigma_1 & 0 & \dots & 0 & 0 \\
				    0 & 0 & \sigma_2 & \dots & 0 & 0 \\
				    0 & 0 & 0 & \dots & \sigma_{p-2} & 0 \\
				    0 & 0 & 0 & \dots & 0 & \sigma_{p-1} \\
\end{bmatrix},
$$

meaning we can write

$$
\boldsymbol{X}^T\boldsymbol{X}=\boldsymbol{V}\tilde{\boldsymbol{\Sigma}}^2\boldsymbol{V}^T.
$$

Multiplying from the right with $\boldsymbol{V}$ (using the orthogonality of $\boldsymbol{V}$) we get

$$
\left(\boldsymbol{X}^T\boldsymbol{X}\right)\boldsymbol{V}=\boldsymbol{V}\tilde{\boldsymbol{\Sigma}}^2.
$$

## What does it mean?

This means the vectors $\boldsymbol{v}_i$ of the orthogonal matrix $\boldsymbol{V}$
are the eigenvectors of the matrix $\boldsymbol{X}^T\boldsymbol{X}$ with eigenvalues
given by the singular values squared, that is

$$
\left(\boldsymbol{X}^T\boldsymbol{X}\right)\boldsymbol{v}_i=\boldsymbol{v}_i\sigma_i^2.
$$

In other words, each non-zero singular value of $\boldsymbol{X}$ is a positive
square root of an eigenvalue of $\boldsymbol{X}^T\boldsymbol{X}$.  It means also that
the columns of $\boldsymbol{V}$ are the eigenvectors of
$\boldsymbol{X}^T\boldsymbol{X}$. Since we have ordered the singular values of
$\boldsymbol{X}$ in a descending order, it means that the column vectors
$\boldsymbol{v}_i$ are hierarchically ordered by how much correlation they
encode from the columns of $\boldsymbol{X}$.

Note that these are also the eigenvectors and eigenvalues of the
Hessian matrix.

If we now recall the definition of the covariance matrix (not using
Bessel's correction) we have

$$
\boldsymbol{C}[\boldsymbol{X}]=\frac{1}{n}\boldsymbol{X}^T\boldsymbol{X},
$$

meaning that every squared non-singular value of $\boldsymbol{X}$ divided by $n$ (
the number of samples) are the eigenvalues of the covariance
matrix. Every singular value of $\boldsymbol{X}$ is thus a positive square
root of an eigenvalue of $\boldsymbol{X}^T\boldsymbol{X}$. If the matrix $\boldsymbol{X}$ is
self-adjoint, the singular values of $\boldsymbol{X}$ are equal to the
absolute value of the eigenvalues of $\boldsymbol{X}$.

## And finally  $\boldsymbol{X}\boldsymbol{X}^T$

For $\boldsymbol{X}\boldsymbol{X}^T$ we found

$$
\boldsymbol{X}\boldsymbol{X}^T=\boldsymbol{U}\boldsymbol{\Sigma}\boldsymbol{V}^T\boldsymbol{V}\boldsymbol{\Sigma}^T\boldsymbol{U}^T=\boldsymbol{U}\boldsymbol{\Sigma}^T\boldsymbol{\Sigma}\boldsymbol{U}^T.
$$

Since the matrices here have dimension $n\times n$, we have

$$
\boldsymbol{\Sigma}\boldsymbol{\Sigma}^T = \begin{bmatrix} \tilde{\boldsymbol{\Sigma}} \\ \boldsymbol{0}\\ \end{bmatrix}\begin{bmatrix} \tilde{\boldsymbol{\Sigma}}  \boldsymbol{0}\\ \end{bmatrix}=\begin{bmatrix} \tilde{\boldsymbol{\Sigma}} & \boldsymbol{0} \\ \boldsymbol{0} & \boldsymbol{0}\\ \end{bmatrix},
$$

leading to

$$
\boldsymbol{X}\boldsymbol{X}^T=\boldsymbol{U}\begin{bmatrix} \tilde{\boldsymbol{\Sigma}} & \boldsymbol{0} \\ \boldsymbol{0} & \boldsymbol{0}\\ \end{bmatrix}\boldsymbol{U}^T.
$$

Multiplying with $\boldsymbol{U}$ from the right gives us the eigenvalue problem

$$
(\boldsymbol{X}\boldsymbol{X}^T)\boldsymbol{U}=\boldsymbol{U}\begin{bmatrix} \tilde{\boldsymbol{\Sigma}} & \boldsymbol{0} \\ \boldsymbol{0} & \boldsymbol{0}\\ \end{bmatrix}.
$$

It means that the eigenvalues of $\boldsymbol{X}\boldsymbol{X}^T$ are again given by
the non-zero singular values plus now a series of zeros.  The column
vectors of $\boldsymbol{U}$ are the eigenvectors of $\boldsymbol{X}\boldsymbol{X}^T$ and
measure how much correlations are contained in the rows of $\boldsymbol{X}$.

Since we will mainly be interested in the correlations among the features
of our data (the columns of $\boldsymbol{X}$, the quantity of interest for us are the non-zero singular
values and the column vectors of $\boldsymbol{V}$.

## Ridge and LASSO Regression

Let us remind ourselves about the expression for the standard Mean Squared Error (MSE) which we used to define our cost function and the equations for the ordinary least squares (OLS) method, that is
our optimization problem is

$$
{\displaystyle \min_{\boldsymbol{\beta}\in {\mathbb{R}}^{p}}}\frac{1}{n}\left\{\left(\boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta}\right)^T\left(\boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta}\right)\right\}.
$$

or we can state it as

$$
{\displaystyle \min_{\boldsymbol{\beta}\in
{\mathbb{R}}^{p}}}\frac{1}{n}\sum_{i=0}^{n-1}\left(y_i-\tilde{y}_i\right)^2=\frac{1}{n}\vert\vert \boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta}\vert\vert_2^2,
$$

where we have used the definition of  a norm-2 vector, that is

$$
\vert\vert \boldsymbol{x}\vert\vert_2 = \sqrt{\sum_i x_i^2}.
$$

By minimizing the above equation with respect to the parameters
$\boldsymbol{\beta}$ we could then obtain an analytical expression for the
parameters $\boldsymbol{\beta}$.  We can add a regularization parameter $\lambda$ by
defining a new cost function to be optimized, that is

$$
{\displaystyle \min_{\boldsymbol{\beta}\in
{\mathbb{R}}^{p}}}\frac{1}{n}\vert\vert \boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta}\vert\vert_2^2+\lambda\vert\vert \boldsymbol{\beta}\vert\vert_2^2
$$

which leads to the Ridge regression minimization problem where we
require that $\vert\vert \boldsymbol{\beta}\vert\vert_2^2\le t$, where $t$ is
a finite number larger than zero. By defining

$$
C(\boldsymbol{X},\boldsymbol{\beta})=\frac{1}{n}\vert\vert \boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta}\vert\vert_2^2+\lambda\vert\vert \boldsymbol{\beta}\vert\vert_1,
$$

we have a new optimization equation

$$
{\displaystyle \min_{\boldsymbol{\beta}\in
{\mathbb{R}}^{p}}}\frac{1}{n}\vert\vert \boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta}\vert\vert_2^2+\lambda\vert\vert \boldsymbol{\beta}\vert\vert_1
$$

which leads to Lasso regression. Lasso stands for least absolute shrinkage and selection operator.

Here we have defined the norm-1 as

$$
\vert\vert \boldsymbol{x}\vert\vert_1 = \sum_i \vert x_i\vert.
$$

## Deriving the  Ridge Regression Equations

Using the matrix-vector expression for Ridge regression and dropping the parameter $1/n$ in front of the standard means squared error equation, we have

$$
C(\boldsymbol{X},\boldsymbol{\beta})=\left\{(\boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta})^T(\boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta})\right\}+\lambda\boldsymbol{\beta}^T\boldsymbol{\beta},
$$

and
taking the derivatives with respect to $\boldsymbol{\beta}$ we obtain then
a slightly modified matrix inversion problem which for finite values
of $\lambda$ does not suffer from singularity problems. We obtain
the optimal parameters

$$
\hat{\boldsymbol{\beta}}_{\mathrm{Ridge}} = \left(\boldsymbol{X}^T\boldsymbol{X}+\lambda\boldsymbol{I}\right)^{-1}\boldsymbol{X}^T\boldsymbol{y},
$$

with $\boldsymbol{I}$ being a $p\times p$ identity matrix with the constraint that

$$
\sum_{i=0}^{p-1} \beta_i^2 \leq t,
$$

with $t$ a finite positive number.

When we compare this with the ordinary least squares result we have

$$
\hat{\boldsymbol{\beta}}_{\mathrm{OLS}} = \left(\boldsymbol{X}^T\boldsymbol{X}\right)^{-1}\boldsymbol{X}^T\boldsymbol{y},
$$

which can lead to singular matrices. However, with the SVD, we can always compute the inverse of the matrix $\boldsymbol{X}^T\boldsymbol{X}$.

We see that Ridge regression is nothing but the standard OLS with a
modified diagonal term added to $\boldsymbol{X}^T\boldsymbol{X}$. The consequences, in
particular for our discussion of the bias-variance tradeoff are rather
interesting. We will see that for specific values of $\lambda$, we may
even reduce the variance of the optimal parameters $\boldsymbol{\beta}$. These topics and other related ones, will be discussed after the more linear algebra oriented analysis here.

Using our insights about the SVD of the design matrix $\boldsymbol{X}$
We have already analyzed the OLS solutions in terms of the eigenvectors (the columns) of the right singular value matrix $\boldsymbol{U}$ as

$$
\tilde{\boldsymbol{y}}_{\mathrm{OLS}}=\boldsymbol{X}\boldsymbol{\beta}  =\boldsymbol{U}\boldsymbol{U}^T\boldsymbol{y}.
$$

For Ridge regression this becomes

$$
\tilde{\boldsymbol{y}}_{\mathrm{Ridge}}=\boldsymbol{X}\boldsymbol{\beta}_{\mathrm{Ridge}} = \boldsymbol{U\Sigma V^T}\left(\boldsymbol{V}\boldsymbol{\Sigma}^2\boldsymbol{V}^T+\lambda\boldsymbol{I} \right)^{-1}(\boldsymbol{U\Sigma V^T})^T\boldsymbol{y}=\sum_{j=0}^{p-1}\boldsymbol{u}_j\boldsymbol{u}_j^T\frac{\sigma_j^2}{\sigma_j^2+\lambda}\boldsymbol{y},
$$

with the vectors $\boldsymbol{u}_j$ being the columns of $\boldsymbol{U}$ from the SVD of the matrix $\boldsymbol{X}$.

## Interpreting the Ridge results

Since $\lambda \geq 0$, it means that compared to OLS, we have

$$
\frac{\sigma_j^2}{\sigma_j^2+\lambda} \leq 1.
$$

Ridge regression finds the coordinates of $\boldsymbol{y}$ with respect to the
orthonormal basis $\boldsymbol{U}$, it then shrinks the coordinates by
$\frac{\sigma_j^2}{\sigma_j^2+\lambda}$. Recall that the SVD has
eigenvalues ordered in a descending way, that is $\sigma_i \geq
\sigma_{i+1}$.

For small eigenvalues $\sigma_i$ it means that their contributions become less important, a fact which can be used to reduce the number of degrees of freedom. More about this when we have covered the material on a statistical interpretation of various linear regression methods.

## More interpretations

For the sake of simplicity, let us assume that the design matrix is orthonormal, that is

$$
\boldsymbol{X}^T\boldsymbol{X}=(\boldsymbol{X}^T\boldsymbol{X})^{-1} =\boldsymbol{I}.
$$

In this case the standard OLS results in

$$
\boldsymbol{\beta}^{\mathrm{OLS}} = \boldsymbol{X}^T\boldsymbol{y}=\sum_{i=0}^{p-1}\boldsymbol{u}_j\boldsymbol{u}_j^T\boldsymbol{y},
$$

and

$$
\boldsymbol{\beta}^{\mathrm{Ridge}} = \left(\boldsymbol{I}+\lambda\boldsymbol{I}\right)^{-1}\boldsymbol{X}^T\boldsymbol{y}=\left(1+\lambda\right)^{-1}\boldsymbol{\beta}^{\mathrm{OLS}},
$$

that is the Ridge estimator scales the OLS estimator by the inverse of a factor $1+\lambda$, and
the Ridge estimator converges to zero when the hyperparameter goes to
infinity.

We will come back to more interpreations after we have gone through some of the statistical analysis part.

For more discussions of Ridge and Lasso regression, [Wessel van Wieringen's](https://arxiv.org/abs/1509.09169) article is highly recommended.
Similarly, [Mehta et al's article](https://arxiv.org/abs/1803.08823) is also recommended.

## Deriving the  Lasso Regression Equations

Using the matrix-vector expression for Lasso regression and dropping the parameter $1/n$ in front of the standard means squared error equation, we have the following **cost** function

$$
C(\boldsymbol{X},\boldsymbol{\beta})=\left\{(\boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta})^T(\boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta})\right\}+\lambda\vert\vert\boldsymbol{\beta}\vert\vert_1,
$$

Taking the derivative with respect to $\boldsymbol{\beta}$ and recalling that the derivative of the absolute value is (we drop the boldfaced vector symbol for simplicty)

$$
\frac{d \vert \beta\vert}{d \boldsymbol{\beta}}=\mathrm{sgn}(\boldsymbol{\beta})=\left\{\begin{array}{cc} 1 & \beta > 0 \\ 0 & \beta =0\\-1 & \beta < 0, \end{array}\right.
$$

we have that the derivative of the cost function is

$$
\frac{\partial C(\boldsymbol{X},\boldsymbol{\beta})}{\partial \boldsymbol{\beta}}=-2\boldsymbol{X}^T(\boldsymbol{y}-\boldsymbol{X}\boldsymbol{\beta})+\lambda sgn(\boldsymbol{\beta})=0,
$$

and reordering we have

$$
\boldsymbol{X}^T\boldsymbol{X}\boldsymbol{\beta})+\lambda sgn(\boldsymbol{\beta})=2\boldsymbol{X}^T(\boldsymbol{y}.
$$

This equation does not lead to a nice analytical equation as in either Ridge regression or ordinary least squares. This equation can however be solved by using standard convex optimization algorithms using for example the Python package [CVXOPT](https://cvxopt.org/). We will discuss this later.

## Exercises for week 36, September 6-10

The exercises here are meant to prepare you for work with project 1. The first exercise is a follow-up of exercise 2 from week 35 August 30-September 3).

<!-- --- begin exercise --- -->

## Exercise 1: Adding Ridge and Lasso Regression

This exercise is a continuation of exercise 2 from exercise set 1
(week 35, August 30-September 3). We will use the same function to
generate our data set, still staying with a simple function $y(x)$
which we want to fit using linear regression, but now extending the
analysis to include the Ridge and the Lasso regression methods.

We will thus again generate our own dataset for a function $y(x)$ where
$x \in [0,1]$ and defined by random numbers computed with the uniform
distribution. The function $y$ is a quadratic polynomial in $x$ with
added stochastic noise according to the normal distribution $\cal{N}(0,1)$.

The following simple Python instructions define our $x$ and $y$ values (with 100 data points).

```python
x = np.random.rand(100)
y = 2.0+5*x*x+0.1*np.random.randn(100)
```

Write your own code for the Ridge method (see chapter 3.4 of Hastie *et al.*, equations (3.43) and (3.44)) and compute the parametrization for different values of $\lambda$. Compare and analyze your results with those from exercise 3. Study the dependence on $\lambda$ while also varying the strength of the noise in your expression for $y(x)$.

The code here allows you to perform your own Ridge calculation and
perform calculations for various values of the regularization
parameter $\lambda$. This program can easily be extended upon.

```python
import os
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import StandardScaler

def R2(y_data, y_model):
    return 1 - np.sum((y_data - y_model) ** 2) / np.sum((y_data - np.mean(y_data)) ** 2)
def MSE(y_data,y_model):
    n = np.size(y_model)
    return np.sum((y_data-y_model)**2)/n

# A seed just to ensure that the random numbers are the same for every run.
# Useful for eventual debugging.
np.random.seed(3155)

x = np.random.rand(100)
y = 2.0+5*x*x+0.1*np.random.randn(100)

# number of features p (here degree of polynomial
p = 3
#  The design matrix now as function of a given polynomial
X = np.zeros((len(x),p))
X[:,0] = 1.0
X[:,1] = x
X[:,2] = x*x
# We split the data in test and training data
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2)
scaler = StandardScaler()
scaler.fit(X_train)
X_train_scaled = scaler.transform(X_train)
X_test_scaled = scaler.transform(X_test)

# matrix inversion to find beta
OLSbeta = np.linalg.inv(X_train.T @ X_train) @ X_train.T @ y_train
print(OLSbeta)
# and then make the prediction
ytildeOLS = X_train @ OLSbeta
print("Training R2 for OLS")
print(R2(y_train,ytildeOLS))
print("Training MSE for OLS")
print(MSE(y_train,ytildeOLS))
ypredictOLS = X_test @ OLSbeta
print("Test R2 for OLS")
print(R2(y_test,ypredictOLS))
print("Test MSE OLS")
print(MSE(y_test,ypredictOLS))

# Repeat now for Ridge regression and various values of the regularization parameter
I = np.eye(p,p)
# Decide which values of lambda to use
nlambdas = 20
MSEPredict = np.zeros(nlambdas)
MSETrain = np.zeros(nlambdas)
lambdas = np.logspace(-4, 1, nlambdas)
for i in range(nlambdas):
    lmb = lambdas[i]
    Ridgebeta = np.linalg.inv(X_train.T @ X_train+lmb*I) @ X_train.T @ y_train
    # and then make the prediction
    ytildeRidge = X_train @ Ridgebeta
    ypredictRidge = X_test @ Ridgebeta
    MSEPredict[i] = MSE(y_test,ypredictRidge)
    MSETrain[i] = MSE(y_train,ytildeRidge)
# Now plot the results
plt.figure()
plt.plot(np.log10(lambdas), MSETrain, label = 'MSE Ridge train')
plt.plot(np.log10(lambdas), MSEPredict, 'r--', label = 'MSE Ridge Test')
plt.xlabel('log10(lambda)')
plt.ylabel('MSE')
plt.legend()
plt.show()
```

Repeat the above but using the functionality of
**Scikit-Learn**. Compare your code with the results from
**Scikit-Learn**. Remember to run with the same random numbers for
generating $x$ and $y$.  Observe also that when you compare with **Scikit-Learn**, you need to pay attention to how the intercept is dealt with.

Finally, using **Scikit-Learn** or your own code, compute also the mean square error, a risk metric corresponding to the expected value of the squared (quadratic) error defined as

$$
MSE(\hat{y},\hat{\tilde{y}}) = \frac{1}{n}
\sum_{i=0}^{n-1}(y_i-\tilde{y}_i)^2,
$$

and the $R^2$ score function.
If $\tilde{\hat{y}}_i$ is the predicted value of the $i-th$ sample and $y_i$ is the corresponding true value, then the score $R^2$ is defined as

$$
R^2(\hat{y}, \tilde{\hat{y}}) = 1 - \frac{\sum_{i=0}^{n - 1} (y_i - \tilde{y}_i)^2}{\sum_{i=0}^{n - 1} (y_i - \bar{y})^2},
$$

where we have defined the mean value  of $\hat{y}$ as

$$
\bar{y} =  \frac{1}{n} \sum_{i=0}^{n - 1} y_i.
$$

Discuss these quantities as functions of the variable $\lambda$ in the Ridge and Lasso regression methods.

### Exercise: Linear Regression for  a two-dimensional function

This is a longer  exercise and the aim is to study in more detail various
regression methods, including the Ordinary Least Squares (OLS) method,
Ridge regression and finally Lasso regression.
This exercise forms a part of project 1.

We will study how to fit polynomials to a specific
two-dimensional function called [Franke's
function](http://www.dtic.mil/dtic/tr/fulltext/u2/a081688.pdf).  This
is a function which has been widely used when testing various
interpolation and fitting algorithms.

The Franke function, which is a weighted sum of four exponentials  reads as follows

$$
\begin{align*}
f(x,y) &= \frac{3}{4}\exp{\left(-\frac{(9x-2)^2}{4} - \frac{(9y-2)^2}{4}\right)}+\frac{3}{4}\exp{\left(-\frac{(9x+1)^2}{49}- \frac{(9y+1)}{10}\right)} \\
&+\frac{1}{2}\exp{\left(-\frac{(9x-7)^2}{4} - \frac{(9y-3)^2}{4}\right)} -\frac{1}{5}\exp{\left(-(9x-4)^2 - (9y-7)^2\right) }.
\end{align*}
$$

The function will be defined for $x,y\in [0,1]$.  Our first step will
be to perform an OLS regression analysis of this function, trying out
a polynomial fit with an $x$ and $y$ dependence of the form $[x, y,
x^2, y^2, xy, \dots]$.   We will fit a
function (for example a polynomial) of $x$ and $y$.  Thereafter we
will repeat much of the same procedure using the Ridge and Lasso
regression methods, introducing thus a dependence on the bias
(penalty) $\lambda$.

The Python fucntion for the Franke function is included here (it performs also a three-dimensional plot of it)

```python
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
from matplotlib import cm
from matplotlib.ticker import LinearLocator, FormatStrFormatter
import numpy as np
from random import random, seed

fig = plt.figure()
ax = fig.gca(projection='3d')

# Make data.
x = np.arange(0, 1, 0.05)
y = np.arange(0, 1, 0.05)
x, y = np.meshgrid(x,y)

def FrankeFunction(x,y):
    term1 = 0.75*np.exp(-(0.25*(9*x-2)**2) - 0.25*((9*y-2)**2))
    term2 = 0.75*np.exp(-((9*x+1)**2)/49.0 - 0.1*(9*y+1))
    term3 = 0.5*np.exp(-(9*x-7)**2/4.0 - 0.25*((9*y-3)**2))
    term4 = -0.2*np.exp(-(9*x-4)**2 - (9*y-7)**2)
    return term1 + term2 + term3 + term4

z = FrankeFunction(x, y)

# Plot the surface.
surf = ax.plot_surface(x, y, z, cmap=cm.coolwarm,
                       linewidth=0, antialiased=False)

# Customize the z axis.
ax.set_zlim(-0.10, 1.40)
ax.zaxis.set_major_locator(LinearLocator(10))
ax.zaxis.set_major_formatter(FormatStrFormatter('%.02f'))

# Add a color bar which maps values to colors.
fig.colorbar(surf, shrink=0.5, aspect=5)

plt.show()
```

We will generate our own dataset for a function
$\mathrm{FrankeFunction}(x,y)$ with $x,y \in [0,1]$. The function
$f(x,y)$ is the Franke function. You should explore also the addition
an added stochastic noise to this function using the normal
distribution $\cal{N}(0,1)$.

Write your own code (using either a matrix inversion or a singular
value decomposition from e.g., **numpy** ) or use your code and perform a standard least square regression
analysis using polynomials in $x$ and $y$ up to fifth order. You can use **scikit-learn** as well.

Evaluate the Mean Squared error (MSE)

$$
MSE(\hat{y},\hat{\tilde{y}}) = \frac{1}{n}
\sum_{i=0}^{n-1}(y_i-\tilde{y}_i)^2,
$$

and the $R^2$ score function.  If $\tilde{\hat{y}}_i$ is the predicted
value of the $i-th$ sample and $y_i$ is the corresponding true value,
then the score $R^2$ is defined as

$$
R^2(\hat{y}, \tilde{\hat{y}}) = 1 - \frac{\sum_{i=0}^{n - 1} (y_i - \tilde{y}_i)^2}{\sum_{i=0}^{n - 1} (y_i - \bar{y})^2},
$$

where we have defined the mean value  of $\hat{y}$ as

$$
\bar{y} =  \frac{1}{n} \sum_{i=0}^{n - 1} y_i.
$$

You should split your data in train and test and also consider scaling the data.

To set up the design matrix, the following code can be used

```python
def FrankeFunction(x,y):
	term1 = 0.75*np.exp(-(0.25*(9*x-2)**2) - 0.25*((9*y-2)**2))
	term2 = 0.75*np.exp(-((9*x+1)**2)/49.0 - 0.1*(9*y+1))
	term3 = 0.5*np.exp(-(9*x-7)**2/4.0 - 0.25*((9*y-3)**2))
	term4 = -0.2*np.exp(-(9*x-4)**2 - (9*y-7)**2)
	return term1 + term2 + term3 + term4

def create_X(x, y, n ):
	if len(x.shape) > 1:
		x = np.ravel(x)
		y = np.ravel(y)

	N = len(x)
	l = int((n+1)*(n+2)/2)		# Number of elements in beta
	X = np.ones((N,l))

	for i in range(1,n+1):
		q = int((i)*(i+1)/2)
		for k in range(i+1):
			X[:,q+k] = (x**(i-k))*(y**k)

	return X

# Making meshgrid of datapoints and compute Franke's function
n = 5
N = 1000
x = np.sort(np.random.uniform(0, 1, N))
y = np.sort(np.random.uniform(0, 1, N))
z = FrankeFunction(x, y)
X = create_X(x, y, n=n)
```

Write then your own code for the Ridge method or use **Scikit-Learn**.
Perform the same analysis as you did for ordinary Least Squares (for the same polynomials) but now for different values of $\lambda$. Compare and
analyze your results with those obtained with ordinary Least Squares. Study the
dependence on $\lambda$.

This part is essentially a repeat of the previous ones, but now
with Lasso regression. Write either your own code or
use the functionalities of **Scikit-Learn** (recommended).
Give a
critical discussion of the three methods and a judgement of which
model fits the data best.

<!-- --- end exercise --- -->