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Morten Hjorth-Jensen
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@@ -55,7 +55,6 @@ const thebe_selector_output = ".output, .cell_output"
<script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
<link rel="index" title="Index" href="genindex.html" />
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<link rel="next" title="Exercises week 36" href="exercisesweek36.html" />
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@@ -268,123 +267,6 @@ const thebe_selector_output = ".output, .cell_output"
Week 35: From Ordinary Linear Regression to Ridge and Lasso Regression
</a>
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<li class="toctree-l1">
<a class="reference internal" href="exercisesweek36.html">
Exercises week 36
</a>
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<li class="toctree-l1">
<a class="reference internal" href="week36.html">
Week 36: Statistical interpretation of Linear Regression and Resampling techniques
</a>
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<li class="toctree-l1">
<a class="reference internal" href="exercisesweek37.html">
Exercises week 37
</a>
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<a class="reference internal" href="week37.html">
Week 37: Statistical interpretations and Resampling Methods
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<a class="reference internal" href="exercisesweek38.html">
Exercises week 38
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<a class="reference internal" href="week38.html">
Week 38: Logistic Regression and Optimization
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<a class="reference internal" href="exercisesweek39.html">
Exercises week 39
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Week 39: Optimization and Gradient Methods
</a>
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<a class="reference internal" href="week40.html">
Week 40: Gradient descent methods (continued) and start Neural networks
</a>
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<a class="reference internal" href="exercisesweek41.html">
Exercises week 41
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Week 41 Neural networks and constructing a neural network code
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Exercises week 42
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<a class="reference internal" href="week42.html">
Week 42 Constructing a Neural Network code with introduction to Tensor flow
</a>
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<a class="reference internal" href="exercisesweek43.html">
Exercises weeks 43 and 44
</a>
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<a class="reference internal" href="week43.html">
Week 43: Deep Learning: Constructing a Neural Network code and solving differential equations
</a>
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<a class="reference internal" href="week44.html">
Week 44, Convolutional Neural Networks (CNN)
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<a class="reference internal" href="week45.html">
Week 45, Recurrent Neural Networks
</a>
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<li class="toctree-l1">
<a class="reference internal" href="week46.html">
Week 46: Decision Trees, Ensemble methods and Random Forests
</a>
</li>
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<a class="reference internal" href="week47.html">
Week 47: From Decision Trees to Ensemble Methods, Random Forests and Boosting Methods and Summary of Course
</a>
</li>
<li class="toctree-l1">
<a class="reference internal" href="exercisesweek47.html">
Exercise week 47
</a>
</li>
</ul>
<p aria-level="2" class="caption" role="heading">
<span class="caption-text">
Projects
</span>
</p>
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<li class="toctree-l1">
<a class="reference internal" href="project1.html">
Project 1 on Machine Learning, deadline October 9 (midnight), 2023
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<a class="reference internal" href="project2.html">
Project 2 on Machine Learning, deadline November 17 (Midnight)
</a>
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</ul>
</div>
@@ -1240,7 +1122,7 @@ doconce format html week35.do.txt --no_mako -->
<!-- dom:TITLE: Week 35: From Ordinary Linear Regression to Ridge and Lasso Regression --><div class="tex2jax_ignore mathjax_ignore section" id="week-35-from-ordinary-linear-regression-to-ridge-and-lasso-regression">
<h1>Week 35: From Ordinary Linear Regression to Ridge and Lasso Regression<a class="headerlink" href="#week-35-from-ordinary-linear-regression-to-ridge-and-lasso-regression" title="Permalink to this headline"></a></h1>
<p><strong>Morten Hjorth-Jensen</strong>, Department of Physics, University of Oslo and Department of Physics and Astronomy and National Superconducting Cyclotron Laboratory, Michigan State University</p>
<p>Date: <strong>August 28-September 1</strong></p>
<p>Date: <strong>August 26-30</strong></p>
<div class="section" id="plans-for-week-35">
<h2>Plans for week 35<a class="headerlink" href="#plans-for-week-35" title="Permalink to this headline"></a></h2>
<p>The main topics are:</p>
@@ -1248,17 +1130,14 @@ doconce format html week35.do.txt --no_mako -->
<li><p>Brief repetition from last week</p></li>
<li><p>Derivation of the equations for ordinary least squares</p></li>
<li><p>Discussion on how to prepare data and examples of applications of linear regression</p></li>
<li><p>Material for the lecture on Thursday: Mathematical interpretations of linear regression</p></li>
<li><p>Thursday: Ridge and Lasso regression and Singular Value Decomposition</p></li>
<li><p><a class="reference external" href="https://youtu.be/qBNm-HGSxL4">Video of lecture</a></p></li>
<li><p><a class="reference external" href="https://github.com/CompPhysics/MachineLearning/blob/master/doc/HandWrittenNotes/2023/NotesAug31.pdf">Whiteboard notes</a></p></li>
<li><p>Material for the lecture on Monday: Mathematical interpretations of linear regression</p></li>
<li><p>Monday: Ridge and Lasso regression and Singular Value Decomposition</p></li>
</ol>
<div class="section" id="reading-recommendations">
<h3>Reading recommendations:<a class="headerlink" href="#reading-recommendations" title="Permalink to this headline"></a></h3>
<ol class="simple">
<li><p>See lecture notes for week 35 at <a class="reference external" href="https://compphysics.github.io/MachineLearning/doc/web/course.html">https://compphysics.github.io/MachineLearning/doc/web/course.html</a></p></li>
<li><p>Goodfellow, Bengio and Courville, Deep Learning, chapter 2 on linear algebra and sections 3.1-3.10 on elements of statistics (background)</p></li>
<li><p>Hastie, Tibshirani and Friedman, The elements of statistical learning, sections 3.1-3.4 (on relevance for the discussion of linear regression).</p></li>
</ol>
</div>
</div>
@@ -1731,7 +1610,7 @@ Since we are not using <strong>Scikit-Learn</strong> here we can define our own
</div>
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<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>0.9958946686888259
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>0.9952638231265687
</pre></div>
</div>
</div>
@@ -1748,7 +1627,7 @@ Since we are not using <strong>Scikit-Learn</strong> here we can define our own
</div>
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>0.008142188979400687
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>0.011761161707539526
</pre></div>
</div>
</div>
@@ -1763,23 +1642,23 @@ Since we are not using <strong>Scikit-Learn</strong> here we can define our own
</div>
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[0.0476021 0.02689869 0.01088331 0.01783105 0.00544013 0.05110385
0.02900389 0.01629703 0.05594058 0.02527366 0.00657884 0.04127087
0.01925607 0.02221978 0.01212083 0.04919181 0.00745959 0.03110176
0.010203 0.0076995 0.00298213 0.01702968 0.04557362 0.03192124
0.06668218 0.0178392 0.00706728 0.0095239 0.00784983 0.05197707
0.01519861 0.0134093 0.00291822 0.00311528 0.02036289 0.01136976
0.0189559 0.04908155 0.01384493 0.01715895 0.01262581 0.00756465
0.00473818 0.00224783 0.01773579 0.03804636 0.03945128 0.01662346
0.05137822 0.00206124 0.06090176 0.01632212 0.01220987 0.06361921
0.00318122 0.00362359 0.03177421 0.06554078 0.00123144 0.01091059
0.04958045 0.00291334 0.01541622 0.00607264 0.05274561 0.007352
0.06263415 0.01593612 0.00853836 0.01006042 0.00223784 0.02106518
0.02410507 0.08294341 0.0043675 0.06502562 0.03422156 0.00213264
0.02365779 0.01883403 0.00683222 0.01848399 0.02930957 0.02161016
0.02746315 0.02774744 0.03591454 0.04814746 0.00568413 0.00215333
0.03631783 0.02866734 0.01684326 0.00953152 0.01001378 0.00119895
0.02603725 0.00127672 0.04770636 0.028797 ]
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[0.00035753 0.04937621 0.02268114 0.03112297 0.01856502 0.05322899
0.01397927 0.03999935 0.02508836 0.01834042 0.0652633 0.00887114
0.01956921 0.01987248 0.06294313 0.01152476 0.00328431 0.03564082
0.02337045 0.01743586 0.01278035 0.02400968 0.08388138 0.03270341
0.00335956 0.01031903 0.09575469 0.00956774 0.00900879 0.01867985
0.01191227 0.02090296 0.04045671 0.03582958 0.06692165 0.06615863
0.06594872 0.03756493 0.00488992 0.01405237 0.00117071 0.0017567
0.05006306 0.02545639 0.03456485 0.00373984 0.02576476 0.03530741
0.00092902 0.0275742 0.05948007 0.01321652 0.18500705 0.00382166
0.00327313 0.01853877 0.01771317 0.05293662 0.07199977 0.00836148
0.01541649 0.00343257 0.00626797 0.05350297 0.01548272 0.05235058
0.04310698 0.00225189 0.02356396 0.01690512 0.03467756 0.00064364
0.02593596 0.00019607 0.0029508 0.0180194 0.06825695 0.01659559
0.01971341 0.02012338 0.02241311 0.00135736 0.0095653 0.05695438
0.00395659 0.07068033 0.02699873 0.00919237 0.02493299 0.00803115
0.0293055 0.02178063 0.00594353 0.04081883 0.01325225 0.0386443
0.01889695 0.02810253 0.0181166 0.01135924]
</pre></div>
</div>
</div>
@@ -1848,15 +1727,15 @@ but now splitting the data into a training set and a test set.</p>
</div>
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[ 2.02283241 0.15972118 3.84256187 1.89005305 -0.93145755]
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[ 2.00507876 0.39026883 3.20764972 2.73806921 -1.39609089]
Training R2
0.9959044445566834
0.9972493421341901
Training MSE
0.010349061754867921
0.007021475481484069
Test R2
0.9961996615568259
0.9976639055733267
Test MSE
0.008771887357306985
0.00575158411598985
</pre></div>
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</div>
@@ -2903,45 +2782,73 @@ the house using the features (predictors) listed here.</p>
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<div class="cell_output docutils container">
<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/sklearn/utils/deprecation.py:87: FutureWarning: Function load_boston is deprecated; `load_boston` is deprecated in 1.0 and will be removed in 1.2.
<div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span>---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
Cell In[16], line 1
----&gt; 1 from sklearn.datasets import load_boston
3 boston_dataset = load_boston()
5 # boston_dataset is a dictionary
6 # let&#39;s check what it contains
The Boston housing prices dataset has an ethical problem. You can refer to
the documentation of this function for further details.
File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/sklearn/datasets/__init__.py:157, in __getattr__(name)
108 if name == &quot;load_boston&quot;:
109 msg = textwrap.dedent(&quot;&quot;&quot;
110 `load_boston` has been removed from scikit-learn since version 1.2.
111
(...)
155 &lt;https://www.researchgate.net/publication/4974606_Hedonic_housing_prices_and_the_demand_for_clean_air&gt;
156 &quot;&quot;&quot;)
--&gt; 157 raise ImportError(msg)
158 try:
159 return globals()[name]
The scikit-learn maintainers therefore strongly discourage the use of this
dataset unless the purpose of the code is to study and educate about
ethical issues in data science and machine learning.
ImportError:
`load_boston` has been removed from scikit-learn since version 1.2.
In this special case, you can fetch the dataset from the original
source::
The Boston housing prices dataset has an ethical problem: as
investigated in [1], the authors of this dataset engineered a
non-invertible variable &quot;B&quot; assuming that racial self-segregation had a
positive impact on house prices [2]. Furthermore the goal of the
research that led to the creation of this dataset was to study the
impact of air quality but it did not give adequate demonstration of the
validity of this assumption.
import pandas as pd
import numpy as np
The scikit-learn maintainers therefore strongly discourage the use of
this dataset unless the purpose of the code is to study and educate
about ethical issues in data science and machine learning.
In this special case, you can fetch the dataset from the original
source::
data_url = &quot;http://lib.stat.cmu.edu/datasets/boston&quot;
raw_df = pd.read_csv(data_url, sep=&quot;\s+&quot;, skiprows=22, header=None)
data = np.hstack([raw_df.values[::2, :], raw_df.values[1::2, :2]])
target = raw_df.values[1::2, 2]
import pandas as pd
import numpy as np
Alternative datasets include the California housing dataset (i.e.
:func:`~sklearn.datasets.fetch_california_housing`) and the Ames housing
dataset. You can load the datasets as follows::
data_url = &quot;http://lib.stat.cmu.edu/datasets/boston&quot;
raw_df = pd.read_csv(data_url, sep=&quot;\s+&quot;, skiprows=22, header=None)
data = np.hstack([raw_df.values[::2, :], raw_df.values[1::2, :2]])
target = raw_df.values[1::2, 2]
from sklearn.datasets import fetch_california_housing
housing = fetch_california_housing()
Alternative datasets include the California housing dataset and the
Ames housing dataset. You can load the datasets as follows::
for the California housing dataset and::
from sklearn.datasets import fetch_california_housing
housing = fetch_california_housing()
from sklearn.datasets import fetch_openml
housing = fetch_openml(name=&quot;house_prices&quot;, as_frame=True)
for the California housing dataset and::
for the Ames housing dataset.
warnings.warn(msg, category=FutureWarning)
</pre></div>
</div>
<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>dict_keys([&#39;data&#39;, &#39;target&#39;, &#39;feature_names&#39;, &#39;DESCR&#39;, &#39;filename&#39;, &#39;data_module&#39;])
from sklearn.datasets import fetch_openml
housing = fetch_openml(name=&quot;house_prices&quot;, as_frame=True)
for the Ames housing dataset.
[1] M Carlisle.
&quot;Racist data destruction?&quot;
&lt;https://medium.com/@docintangible/racist-data-destruction-113e3eff54a8&gt;
[2] Harrison Jr, David, and Daniel L. Rubinfeld.
&quot;Hedonic housing prices and the demand for clean air.&quot;
Journal of environmental economics and management 5.1 (1978): 81-102.
&lt;https://www.researchgate.net/publication/4974606_Hedonic_housing_prices_and_the_demand_for_clean_air&gt;
</pre></div>
</div>
</div>
@@ -2964,25 +2871,6 @@ the house using the features (predictors) listed here.</p>
</pre></div>
</div>
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<div class="cell_output docutils container">
<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>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
</pre></div>
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<p>We can then visualize the data</p>
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@@ -2996,13 +2884,6 @@ dtype: int64
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<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/seaborn/distributions.py:2619: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `histplot` (an axes-level function for histograms).
warnings.warn(msg, FutureWarning)
</pre></div>
</div>
<img alt="_images/week35_199_1.png" src="_images/week35_199_1.png" />
</div>
</div>
<p>It is now useful to look at the correlation matrix</p>
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@@ -3015,12 +2896,6 @@ dtype: int64
</pre></div>
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<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;AxesSubplot:&gt;
</pre></div>
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<img alt="_images/week35_201_1.png" src="_images/week35_201_1.png" />
</div>
</div>
<p>From the above coorelation plot we can see that <strong>MEDV</strong> is strongly correlated to <strong>LSTAT</strong> and <strong>RM</strong>. We see also that <strong>RAD</strong> and <strong>TAX</strong> are stronly correlated, but we dont include this in our features together to avoid multi-colinearity</p>
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@@ -3041,9 +2916,6 @@ dtype: int64
</pre></div>
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<img alt="_images/week35_203_0.png" src="_images/week35_203_0.png" />
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<p>Now we start training our model</p>
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@@ -3069,14 +2941,6 @@ dtype: int64
</pre></div>
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>(404, 2)
(102, 2)
(404,)
(102,)
</pre></div>
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<p>Then we use the linear regression functionality from <strong>Scikit-Learn</strong></p>
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@@ -3115,20 +2979,6 @@ dtype: int64
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>The model performance for training set
--------------------------------------
RMSE is 5.637129335071195
R2 score is 0.6300745149331701
The model performance for testing set
--------------------------------------
RMSE is 5.137400784702911
R2 score is 0.6628996975186953
</pre></div>
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@@ -3139,9 +2989,6 @@ R2 score is 0.6628996975186953
</pre></div>
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<img alt="_images/week35_210_0.png" src="_images/week35_210_0.png" />
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<div class="section" id="material-for-lecture-thursday-august-31">
@@ -3421,25 +3268,6 @@ In general the economy-size SVD leads to less FLOPS and still conserving the des
</pre></div>
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<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[[ 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]]
</pre></div>
</div>
</div>
</div>
<p>The matrix <span class="math notranslate nohighlight">\(\boldsymbol{X}\)</span> has columns that are linearly dependent. The first
column is the row-wise sum of the other two columns. The rank of a
@@ -3795,14 +3623,6 @@ covariance matrix through the <strong>np.linalg.eig()</strong> function.</p>
</pre></div>
</div>
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>0.10790125813226321
4.340071371496255
[[ 1.04193203 3.08165104]
[ 3.08165104 10.18383522]]
</pre></div>
</div>
</div>
</div>
</div>
<div class="section" id="correlation-matrix">
@@ -3838,14 +3658,6 @@ a more brute force way. Here we scale the mean values for each column of the des
</pre></div>
</div>
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>0.08881497884574564
1.7086067479626619
[[1. 0.66080313]
[0.66080313 1. ]]
</pre></div>
</div>
</div>
</div>
<p>We see that the matrix elements along the diagonal are one as they
should be and that the matrix is symmetric. Furthermore, diagonalizing
@@ -3874,34 +3686,6 @@ this matrix we easily see that it is a positive definite matrix.</p>
</pre></div>
</div>
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<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[[-0.40620066 -2.01265755]
[ 0.01458611 0.37737221]
[-1.0895387 -3.65442354]
[ 0.2338675 1.12044974]
[ 0.4676059 1.54393936]
[-0.65891389 -3.16304863]
[-0.1715252 0.39197698]
[ 0.71142161 2.95511792]
[ 0.39214397 0.13069442]
[ 0.50655336 2.3105791 ]]
0 1
0 -0.406201 -2.012658
1 0.014586 0.377372
2 -1.089539 -3.654424
3 0.233868 1.120450
4 0.467606 1.543939
5 -0.658914 -3.163049
6 -0.171525 0.391977
7 0.711422 2.955118
8 0.392144 0.130694
9 0.506553 2.310579
0 1
0 1.000000 0.952387
1 0.952387 1.000000
</pre></div>
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<p>We expand this model to the Franke function discussed above.</p>
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@@ -3955,43 +3739,6 @@ this matrix we easily see that it is a positive definite matrix.</p>
</pre></div>
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<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> 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 0.078974 0.081276 0.075889 0.077168 0.078540 0.065410 0.066474
2 0.0 0.081276 0.084076 0.078336 0.079946 0.081655 0.067707 0.069028
3 0.0 0.075889 0.078336 0.077460 0.078986 0.080616 0.069452 0.070737
4 0.0 0.077168 0.079946 0.078986 0.080764 0.082653 0.070986 0.072476
5 0.0 0.078540 0.081655 0.080616 0.082653 0.084809 0.072621 0.074323
6 0.0 0.065410 0.067707 0.069452 0.070986 0.072621 0.064074 0.065378
7 0.0 0.066474 0.069028 0.070737 0.072476 0.074323 0.065378 0.066854
8 0.0 0.067637 0.070457 0.072132 0.074084 0.076150 0.066787 0.068441
9 0.0 0.068906 0.072000 0.073644 0.075816 0.078110 0.068307 0.070146
10 0.0 0.055734 0.057835 0.060872 0.062337 0.063894 0.057393 0.058645
11 0.0 0.056683 0.058996 0.062016 0.063653 0.065390 0.058552 0.059951
12 0.0 0.057722 0.060254 0.063260 0.065077 0.066999 0.059807 0.061359
13 0.0 0.058854 0.061614 0.064609 0.066612 0.068727 0.061163 0.062874
14 0.0 0.060083 0.063080 0.066066 0.068264 0.070582 0.062624 0.064501
8 9 10 11 12 13 14
0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1 0.067637 0.068906 0.055734 0.056683 0.057722 0.058854 0.060083
2 0.070457 0.072000 0.057835 0.058996 0.060254 0.061614 0.063080
3 0.072132 0.073644 0.060872 0.062016 0.063260 0.064609 0.066066
4 0.074084 0.075816 0.062337 0.063653 0.065077 0.066612 0.068264
5 0.076150 0.078110 0.063894 0.065390 0.066999 0.068727 0.070582
6 0.066787 0.068307 0.057393 0.058552 0.059807 0.061163 0.062624
7 0.068441 0.070146 0.058645 0.059951 0.061359 0.062874 0.064501
8 0.070213 0.072111 0.059993 0.061452 0.063019 0.064699 0.066500
9 0.072111 0.074210 0.061443 0.063061 0.064793 0.066647 0.068629
10 0.059993 0.061443 0.052305 0.053417 0.054617 0.055910 0.057300
11 0.061452 0.063061 0.053417 0.054655 0.055987 0.057418 0.058952
12 0.063019 0.064793 0.054617 0.055987 0.057457 0.059031 0.060716
13 0.064699 0.066647 0.055910 0.057418 0.059031 0.060756 0.062599
14 0.066500 0.068629 0.057300 0.058952 0.060716 0.062599 0.064606
</pre></div>
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<p>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
@@ -4331,13 +4078,6 @@ C(\boldsymbol{X},\boldsymbol{\beta})=\frac{1}{n}\left\{(\boldsymbol{y}-\boldsymb
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