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@@ -63,8 +73,15 @@ end of tocinfo -->
  • Contents
    • @@ -83,7 +100,7 @@ end of tocinfo -->
    -

    Data Analysis and Machine Learning: Representing data

    +

    Data Analysis and Machine Learning: Introduction and Representing data

    @@ -99,7 +116,7 @@ end of tocinfo -->

    [2] Department of Physics and Astronomy and National Superconducting Cyclotron Laboratory, Michigan State University

    -

    Nov 26, 2017

    +

    Nov 27, 2017


    @@ -115,6 +132,13 @@ end of tocinfo -->

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    • diff --git a/doc/pub/How2ReadData/html/._How2ReadData-bs001.html b/doc/pub/How2ReadData/html/._How2ReadData-bs001.html index 774e3f2ac..01b0e4145 100644 --- a/doc/pub/How2ReadData/html/._How2ReadData-bs001.html +++ b/doc/pub/How2ReadData/html/._How2ReadData-bs001.html @@ -6,9 +6,9 @@ Automatically generated HTML file from DocOnce source - + -Data Analysis and Machine Learning: Representing data +Data Analysis and Machine Learning: Introduction and Representing data @@ -40,8 +40,18 @@ Automatically generated HTML file from DocOnce source @@ -55,7 +65,7 @@ end of tocinfo --> - Data Analysis and Machine Learning: Representing data + Data Analysis and Machine Learning: Introduction and Representing data
    @@ -63,8 +73,15 @@ end of tocinfo -->
  • Contents
    • @@ -80,34 +97,23 @@ end of tocinfo --> -

    Representing data, overarching aims

    -
    -
    -

    -

    +

    What is Machine Learning?

    - -
    import numpy as np
-import matplotlib.pyplot as plt
-from scipy import sparse
-import pandas as pd
-from IPython.display import display
-eye = np.eye(4)
-print(eye)
-sparse_mtx = sparse.csr_matrix(eye)
-print(sparse_mtx)
-x = np.linspace(-10,10,100)
-y = np.sin(x)
-plt.plot(x,y,marker='x')
-plt.show()
-data = {'Name': ["John", "Anna", "Peter", "Linda"], 'Location': ["Roma", "Napoli", "Torino", "Milano"], 'Age':[51, 21, 34, 45]}
-data_pandas = pd.DataFrame(data)
-display(data_pandas)
-

    -

    -
    +Machine learning is the science of giving computers the ability to +learn without being explicitly programmed. The idea is that there +exist generic algorithms which can be used to find patterns in a broad +class of data sets without having to write code specifically for each +problem. The algorithm will build its own logic based on the data. +

    +Machine learning is a subfield of computer science, and is closely +related to computational statistics. It evolved from the study of +pattern recognition in artificial intelligence (AI) research, and has +made contributions to AI tasks like computer vision, natural language +processing and speech recognition. It has also, especially in later +years, found applications in a wide variety of other areas, including +bioinformatics, economy, physics, finance and marketing.

    @@ -117,6 +123,13 @@ display(data_pandas)

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  • Contents
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    -

    Data Analysis and Machine Learning: Representing data

    +

    Data Analysis and Machine Learning: Introduction and Representing data

    @@ -99,7 +116,7 @@ end of tocinfo -->

    [2] Department of Physics and Astronomy and National Superconducting Cyclotron Laboratory, Michigan State University

    -

    Nov 26, 2017

    +

    Nov 27, 2017


    @@ -115,6 +132,13 @@ end of tocinfo -->

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    • diff --git a/doc/pub/How2ReadData/html/How2ReadData-reveal.html b/doc/pub/How2ReadData/html/How2ReadData-reveal.html index 234d4cb92..fe53afa95 100644 --- a/doc/pub/How2ReadData/html/How2ReadData-reveal.html +++ b/doc/pub/How2ReadData/html/How2ReadData-reveal.html @@ -3,9 +3,9 @@ - + -Data Analysis and Machine Learning: Representing data +Data Analysis and Machine Learning: Introduction and Representing data @@ -116,7 +116,7 @@ td.padding { -

    Data Analysis and Machine Learning: Representing data

    +

    Data Analysis and Machine Learning: Introduction and Representing data

    @@ -132,7 +132,7 @@ td.padding {

    [2] Department of Physics and Astronomy and National Superconducting Cyclotron Laboratory, Michigan State University

     
    -

    Nov 26, 2017

    +

    Nov 27, 2017


    @@ -143,7 +143,155 @@ td.padding {

    -

    Representing data, overarching aims

    +

    What is Machine Learning?

    + +

    +Machine learning is the science of giving computers the ability to +learn without being explicitly programmed. The idea is that there +exist generic algorithms which can be used to find patterns in a broad +class of data sets without having to write code specifically for each +problem. The algorithm will build its own logic based on the data. + +

    +Machine learning is a subfield of computer science, and is closely +related to computational statistics. It evolved from the study of +pattern recognition in artificial intelligence (AI) research, and has +made contributions to AI tasks like computer vision, natural language +processing and speech recognition. It has also, especially in later +years, found applications in a wide variety of other areas, including +bioinformatics, economy, physics, finance and marketing. +

    + + +
    +

    Types of Machine Learning

    + +

    +The approaches to machine learning are many, but are often split into two main categories. +In supervised learning we know the answer to a problem, +and let the computer deduce the logic behind it. On the other hand, unsupervised learning +is a method for finding patterns and relationship in data sets without any prior knowledge of the system. +Some authours also operate with a third category, namely reinforcement learning. This is a paradigm +of learning inspired by behavioural psychology, where learning is achieved by trial-and-error, +solely from rewards and punishment. + +

    +Another way to categorize machine learning tasks is to consider the desired output of a system. +Some of the most common tasks are: + +

      + +

    • Classification: Outputs are divided into two or more classes. The goal is to produce a model that assigns inputs into one of these classes. An example is to identify digits based on pictures of hand-written ones. Classification is typically supervised learning.
      • + +

    • Regression: Finding a functional relationship between an input data set and a reference data set. The goal is to construct a function that maps input data to continuous output values.
      • + +

    • Clustering: Data are divided into groups with certain common traits, without knowing the different groups beforehand. It is thus a form of unsupervised learning.
      • +
    +
    + + +
    +

    Different algorithms

    +In this course we will build our machine learning approach on a statistical foundation, with elements +from data analysis, stochastic processes etc before we proceed with the following machine learning algorithms + +
      +

    1. Linear regression and its variants
      2. +

    2. Decision tree algorithms, from simpler to more complex ones
      3. +

    3. Nearest neighbors models
      4. +

    4. Bayesian statistics
      5. +

    5. Support vector machines and finally various variants of
      6. +

    6. Artifical neural networks
      7. +
    +

    + +Before we proceed however, there are several practicalities with data analysis and software tools we would +like to present. These tools will help us in our understanding of various machine learning algorithms. + +

    +Our emphasis here is on understanding the mathematical aspects of different algorithms, however, where possible +we will emphasize the importance of using available software. +

    + + +
    +

    Software and needed installations

    +We will make intensive use of python as programming language and the myriad of available libraries. +Furthermore, you will find IPython/Jupyter notebooks invaluable in your work. +You can run R codes in the Jupyter/IPython notebooks, with the immediate benefit of visualizing your data. + +

    +If you have Python installed (we recommend Python3) and you feel pretty familiar with installing different packages, +we recommend that you install the following Python packages via pip as + +

      +

    1. pip install numpy scipy matplotlib ipython scikit-learn mglearn sympy pandas pillow
      2. +
    +

    + +For Python3, replace pip with pip3. + +

    +For OSX user we recommend also, after having installed Xcode, to install brew. Brew allows +for a seamless installation of additional software via for example + +

      +

    1. brew install python3
      2. +
    +

    + +For Linux users, with its variety of distributions like for example the widely popular Ubuntu distribution +you can use pip as well and simply install Python as + +

      +

    1. sudo apt-get install python3 (or python for pyhton2.7)
      2. +
    +

    + +etc etc. +

    + + +
    +

    Python installers

    +If you don't want to perform these operations separately, we recommend two widely used distrubutions which set up +all relevant dependencies for Python, namely + +
      +

    1. anaconda
      2. +

    2. Enthought canopy
      3. +
    +
    + + +
    +

    Installing R and C++

    + +

    +You will also find it convenient to utilize R. Say more about R. +Jupyter/Ipython notebook allows you run R code interactively in your browser. The software library R is +tuned to statistically analysis and allows for an easy usage of the tools we will discuss in these texts. + +

    +For the C++ affecianodas, Jupyter/IPython notebook allows you also to install C++ and run codes written in this language +interactively in the browser. Since we will emphasize writing many of the algorithms yourself, you can thus opt for +either Python or C++ as programming languages. + +

    +To add more entropy, cython can also be used when running your notebooks. It means that Python with the Jupyter/IPython notebook +setup allows you to integrate widely popular softwares and tools for scientific computing. With its versatility, +including symbolic operations, Python offers a unique computational environment. Your Jupyter/IPython notebook +can easily be converted into a nicely rendered PDF file or a Latex file for further processing. +

    + + +
    +

    Introduction to Jupyter notebook and available tools

    +
    + + +
    +

    Representing data, overarching aims

    @@ -172,7 +320,7 @@ display(data_pandas)

    -

    Representing data, overarching aims

    +

    Representing data, more examples

    diff --git a/doc/pub/How2ReadData/html/How2ReadData-solarized.html b/doc/pub/How2ReadData/html/How2ReadData-solarized.html index 2b0f5ca82..56cfd80c8 100644 --- a/doc/pub/How2ReadData/html/How2ReadData-solarized.html +++ b/doc/pub/How2ReadData/html/How2ReadData-solarized.html @@ -6,9 +6,9 @@ Automatically generated HTML file from DocOnce source - + -Data Analysis and Machine Learning: Representing data +Data Analysis and Machine Learning: Introduction and Representing data @@ -60,8 +60,18 @@ div { text-align: justify; text-justify: inter-word; } @@ -71,7 +81,7 @@ end of tocinfo --> -

    Data Analysis and Machine Learning: Representing data

    +

    Data Analysis and Machine Learning: Introduction and Representing data

    @@ -87,12 +97,151 @@ end of tocinfo -->

    [2] Department of Physics and Astronomy and National Superconducting Cyclotron Laboratory, Michigan State University

    -

    Nov 26, 2017

    +

    Nov 27, 2017












    -

    Representing data, overarching aims

    +

    What is Machine Learning?

    + +

    +Machine learning is the science of giving computers the ability to +learn without being explicitly programmed. The idea is that there +exist generic algorithms which can be used to find patterns in a broad +class of data sets without having to write code specifically for each +problem. The algorithm will build its own logic based on the data. + +

    +Machine learning is a subfield of computer science, and is closely +related to computational statistics. It evolved from the study of +pattern recognition in artificial intelligence (AI) research, and has +made contributions to AI tasks like computer vision, natural language +processing and speech recognition. It has also, especially in later +years, found applications in a wide variety of other areas, including +bioinformatics, economy, physics, finance and marketing. + +

    +









    + +

    Types of Machine Learning

    + +

    +The approaches to machine learning are many, but are often split into two main categories. +In supervised learning we know the answer to a problem, +and let the computer deduce the logic behind it. On the other hand, unsupervised learning +is a method for finding patterns and relationship in data sets without any prior knowledge of the system. +Some authours also operate with a third category, namely reinforcement learning. This is a paradigm +of learning inspired by behavioural psychology, where learning is achieved by trial-and-error, +solely from rewards and punishment. + +

    +Another way to categorize machine learning tasks is to consider the desired output of a system. +Some of the most common tasks are: + +

      +
    • Classification: Outputs are divided into two or more classes. The goal is to produce a model that assigns inputs into one of these classes. An example is to identify digits based on pictures of hand-written ones. Classification is typically supervised learning.
      • +
    • Regression: Finding a functional relationship between an input data set and a reference data set. The goal is to construct a function that maps input data to continuous output values.
      • +
    • Clustering: Data are divided into groups with certain common traits, without knowing the different groups beforehand. It is thus a form of unsupervised learning.
      • +
    + +









    + +

    Different algorithms

    +In this course we will build our machine learning approach on a statistical foundation, with elements +from data analysis, stochastic processes etc before we proceed with the following machine learning algorithms + +
      +
    1. Linear regression and its variants
      2. +
    2. Decision tree algorithms, from simpler to more complex ones
      3. +
    3. Nearest neighbors models
      4. +
    4. Bayesian statistics
      5. +
    5. Support vector machines and finally various variants of
      6. +
    6. Artifical neural networks
      7. +
    + +Before we proceed however, there are several practicalities with data analysis and software tools we would +like to present. These tools will help us in our understanding of various machine learning algorithms. + +

    +Our emphasis here is on understanding the mathematical aspects of different algorithms, however, where possible +we will emphasize the importance of using available software. + +

    +









    + +

    Software and needed installations

    +We will make intensive use of python as programming language and the myriad of available libraries. +Furthermore, you will find IPython/Jupyter notebooks invaluable in your work. +You can run R codes in the Jupyter/IPython notebooks, with the immediate benefit of visualizing your data. + +

    +If you have Python installed (we recommend Python3) and you feel pretty familiar with installing different packages, +we recommend that you install the following Python packages via pip as + +

      +
    1. pip install numpy scipy matplotlib ipython scikit-learn mglearn sympy pandas pillow
      2. +
    + +For Python3, replace pip with pip3. + +

    +For OSX user we recommend also, after having installed Xcode, to install brew. Brew allows +for a seamless installation of additional software via for example + +

      +
    1. brew install python3
      2. +
    + +For Linux users, with its variety of distributions like for example the widely popular Ubuntu distribution +you can use pip as well and simply install Python as + +
      +
    1. sudo apt-get install python3 (or python for pyhton2.7)
      2. +
    + +etc etc. + +

    +









    + +

    Python installers

    +If you don't want to perform these operations separately, we recommend two widely used distrubutions which set up +all relevant dependencies for Python, namely + +
      +
    1. anaconda
      2. +
    2. Enthought canopy
      3. +
    + +









    + +

    Installing R and C++

    + +

    +You will also find it convenient to utilize R. Say more about R. +Jupyter/Ipython notebook allows you run R code interactively in your browser. The software library R is +tuned to statistically analysis and allows for an easy usage of the tools we will discuss in these texts. + +

    +For the C++ affecianodas, Jupyter/IPython notebook allows you also to install C++ and run codes written in this language +interactively in the browser. Since we will emphasize writing many of the algorithms yourself, you can thus opt for +either Python or C++ as programming languages. + +

    +To add more entropy, cython can also be used when running your notebooks. It means that Python with the Jupyter/IPython notebook +setup allows you to integrate widely popular softwares and tools for scientific computing. With its versatility, +including symbolic operations, Python offers a unique computational environment. Your Jupyter/IPython notebook +can easily be converted into a nicely rendered PDF file or a Latex file for further processing. + +

    +









    + +

    Introduction to Jupyter notebook and available tools

    + +

    +









    + +

    Representing data, overarching aims

    @@ -123,7 +272,7 @@ display(data_pandas)











    -

    Representing data, overarching aims

    +

    Representing data, more examples

    @@ -151,6 +300,8 @@ plt.show()

    +

    + diff --git a/doc/pub/How2ReadData/html/How2ReadData.html b/doc/pub/How2ReadData/html/How2ReadData.html index 2688b53b1..eb101e92a 100644 --- a/doc/pub/How2ReadData/html/How2ReadData.html +++ b/doc/pub/How2ReadData/html/How2ReadData.html @@ -6,9 +6,9 @@ Automatically generated HTML file from DocOnce source - + -Data Analysis and Machine Learning: Representing data +Data Analysis and Machine Learning: Introduction and Representing data \n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
    AgeLocationName
    051RomaJohn
    121NapoliAnna
    234TorinoPeter
    345MilanoLinda
    \n", + "

    " + ], + "text/plain": [ + " Age Location Name\n", + "0 51 Roma John\n", + "1 21 Napoli Anna\n", + "2 34 Torino Peter\n", + "3 45 Milano Linda" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "%matplotlib inline\n", + "\n", + "import numpy as np\n", + "import matplotlib.pyplot as plt\n", + "from scipy import sparse\n", + "import pandas as pd\n", + "from IPython.display import display\n", + "eye = np.eye(4)\n", + "print(eye)\n", + "sparse_mtx = sparse.csr_matrix(eye)\n", + "print(sparse_mtx)\n", + "x = np.linspace(-10,10,100)\n", + "y = np.sin(x)\n", + "plt.plot(x,y,marker='x')\n", + "plt.show()\n", + "data = {'Name': [\"John\", \"Anna\", \"Peter\", \"Linda\"], 'Location': [\"Roma\", \"Napoli\", \"Torino\", \"Milano\"], 'Age':[51, 21, 34, 45]}\n", + "data_pandas = pd.DataFrame(data)\n", + "display(data_pandas)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Representing data, overarching aims" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/usr/local/lib/python3.6/site-packages/scipy/linalg/basic.py:1226: RuntimeWarning: internal gelsd driver lwork query error, required iwork dimension not returned. This is likely the result of LAPACK bug 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to 'gelss' driver.\n", + " warnings.warn(mesg, RuntimeWarning)\n" + ] + }, + { + "data": { + "image/png": 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Yl/LUNbuPs+Vga9L24X0bOGfy4KwuH7E0DaES+NhzKALmfPxdESvuhpuOzoiJ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\nRU5ErkJggg==\n", + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "import numpy as np\n", + "import matplotlib.pyplot as plt\n", + "from scipy import sparse\n", + "import pandas as pd\n", + "from IPython.display import display\n", + "import mglearn\n", + "import sklearn\n", + "from sklearn.linear_model import LinearRegression\n", + "from sklearn.tree import DecisionTreeRegressor\n", + "x, y = mglearn.datasets.make_wave(n_samples=100)\n", + "line = np.linspace(-3,3,1000,endpoint=False).reshape(-1,1)\n", + "reg = DecisionTreeRegressor(min_samples_split=3).fit(x,y)\n", + "plt.plot(line, reg.predict(line), label=\"decision tree\")\n", + "regline = LinearRegression().fit(x,y)\n", + "plt.plot(line, regline.predict(line), label= \"Linear Rgression\")\n", + "plt.show()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.3" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/doc/pub/How2ReadData/ipynb/How2ReadData.ipynb b/doc/pub/How2ReadData/ipynb/How2ReadData.ipynb index bd86ecf96..c658f51e7 100644 --- a/doc/pub/How2ReadData/ipynb/How2ReadData.ipynb +++ b/doc/pub/How2ReadData/ipynb/How2ReadData.ipynb @@ -4,19 +4,127 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "\n", - "# Data Analysis and Machine Learning: Representing data\n", + "\n", + "# Data Analysis and Machine Learning: Introduction and Representing data\n", "\n", " \n", "**Morten Hjorth-Jensen**, Department of Physics, University of Oslo and Department of Physics and Astronomy and National Superconducting Cyclotron Laboratory, Michigan State University\n", "\n", - "Date: **Nov 26, 2017**\n", + "Date: **Nov 27, 2017**\n", "\n", "Copyright 1999-2017, Morten Hjorth-Jensen. Released under CC Attribution-NonCommercial 4.0 license\n", "\n", "\n", "\n", "\n", + "## What is Machine Learning?\n", + "\n", + "Machine learning is the science of giving computers the ability to\n", + "learn without being explicitly programmed. The idea is that there\n", + "exist generic algorithms which can be used to find patterns in a broad\n", + "class of data sets without having to write code specifically for each\n", + "problem. The algorithm will build its own logic based on the data.\n", + "\n", + "Machine learning is a subfield of computer science, and is closely\n", + "related to computational statistics. It evolved from the study of\n", + "pattern recognition in artificial intelligence (AI) research, and has\n", + "made contributions to AI tasks like computer vision, natural language\n", + "processing and speech recognition. It has also, especially in later\n", + "years, found applications in a wide variety of other areas, including\n", + "bioinformatics, economy, physics, finance and marketing.\n", + "\n", + "## Types of Machine Learning\n", + "\n", + "\n", + "The approaches to machine learning are many, but are often split into two main categories. \n", + "In *supervised learning* we know the answer to a problem,\n", + "and let the computer deduce the logic behind it. On the other hand, *unsupervised learning*\n", + "is a method for finding patterns and relationship in data sets without any prior knowledge of the system.\n", + "Some authours also operate with a third category, namely *reinforcement learning*. This is a paradigm \n", + "of learning inspired by behavioural psychology, where learning is achieved by trial-and-error, \n", + "solely from rewards and punishment.\n", + "\n", + "Another way to categorize machine learning tasks is to consider the desired output of a system.\n", + "Some of the most common tasks are:\n", + "\n", + " * Classification: Outputs are divided into two or more classes. The goal is to produce a model that assigns inputs into one of these classes. An example is to identify digits based on pictures of hand-written ones. Classification is typically supervised learning.\n", + "\n", + " * Regression: Finding a functional relationship between an input data set and a reference data set. The goal is to construct a function that maps input data to continuous output values.\n", + "\n", + " * Clustering: Data are divided into groups with certain common traits, without knowing the different groups beforehand. It is thus a form of unsupervised learning.\n", + "\n", + "## Different algorithms\n", + "In this course we will build our machine learning approach on a statistical foundation, with elements \n", + "from data analysis, stochastic processes etc before we proceed with the following machine learning algorithms\n", + "\n", + "1. Linear regression and its variants\n", + "\n", + "2. Decision tree algorithms, from simpler to more complex ones\n", + "\n", + "3. Nearest neighbors models\n", + "\n", + "4. Bayesian statistics \n", + "\n", + "5. Support vector machines and finally various variants of\n", + "\n", + "6. Artifical neural networks\n", + "\n", + "Before we proceed however, there are several practicalities with data analysis and software tools we would \n", + "like to present. These tools will help us in our understanding of various machine learning algorithms. \n", + "\n", + "Our emphasis here is on understanding the mathematical aspects of different algorithms, however, where possible \n", + "we will emphasize the importance of using available software. \n", + "\n", + "\n", + "## Software and needed installations\n", + "We will make intensive use of python as programming language and the myriad of available libraries. \n", + "Furthermore, you will find IPython/Jupyter notebooks invaluable in your work. \n", + "You can run **R** codes in the Jupyter/IPython notebooks, with the immediate benefit of visualizing your data.\n", + "\n", + "\n", + "If you have Python installed (we recommend Python3) and you feel pretty familiar with installing different packages, \n", + "we recommend that you install the following Python packages via **pip** as\n", + "1. pip install numpy scipy matplotlib ipython scikit-learn mglearn sympy pandas pillow\n", + "\n", + "For Python3, replace **pip** with **pip3**.\n", + "\n", + "For OSX user we recommend also, after having installed Xcode, to install **brew**. Brew allows \n", + "for a seamless installation of additional software via for example\n", + "1. brew install python3\n", + "\n", + "For Linux users, with its variety of distributions like for example the widely popular Ubuntu distribution\n", + "you can use **pip** as well and simply install Python as \n", + "1. sudo apt-get install python3 (or python for pyhton2.7)\n", + "\n", + "etc etc. \n", + "\n", + "## Python installers\n", + "If you don't want to perform these operations separately, we recommend two widely used distrubutions which set up \n", + "all relevant dependencies for Python, namely\n", + "1. anaconda\n", + "\n", + "2. Enthought canopy\n", + "\n", + "## Installing R and C++\n", + "\n", + "You will also find it convenient to utilize R. Say more about R. \n", + "Jupyter/Ipython notebook allows you run **R** code interactively in your browser. The software library **R** is \n", + "tuned to statistically analysis and allows for an easy usage of the tools we will discuss in these texts.\n", + "\n", + "For the C++ affecianodas, Jupyter/IPython notebook allows you also to install C++ and run codes written in this language \n", + "interactively in the browser. Since we will emphasize writing many of the algorithms yourself, you can thus opt for\n", + "either Python or C++ as programming languages. \n", + "\n", + "To add more entropy, **cython** can also be used when running your notebooks. It means that Python with the Jupyter/IPython notebook \n", + "setup allows you to integrate widely popular softwares and tools for scientific computing. With its versatility, \n", + "including symbolic operations, Python offers a unique computational environment. Your Jupyter/IPython notebook \n", + "can easily be converted into a nicely rendered **PDF** file or a Latex file for further processing.\n", + "\n", + "\n", + "## Introduction to Jupyter notebook and available tools\n", + "\n", + "\n", + "\n", "## Representing data, overarching aims" ] }, @@ -52,7 +160,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Representing data, overarching aims" + "## Representing data, more examples" ] }, { diff --git a/doc/pub/How2ReadData/ipynb/ipynb-How2ReadData-src.tar.gz b/doc/pub/How2ReadData/ipynb/ipynb-How2ReadData-src.tar.gz index 52374d85e..152d5a1b3 100644 Binary files a/doc/pub/How2ReadData/ipynb/ipynb-How2ReadData-src.tar.gz and b/doc/pub/How2ReadData/ipynb/ipynb-How2ReadData-src.tar.gz differ diff --git a/doc/pub/How2ReadData/pdf/How2ReadData-beamer-handouts2x3.pdf b/doc/pub/How2ReadData/pdf/How2ReadData-beamer-handouts2x3.pdf index 9e3bf4188..e40bd1f11 100644 Binary files a/doc/pub/How2ReadData/pdf/How2ReadData-beamer-handouts2x3.pdf and b/doc/pub/How2ReadData/pdf/How2ReadData-beamer-handouts2x3.pdf differ diff --git a/doc/pub/How2ReadData/pdf/How2ReadData-beamer.pdf b/doc/pub/How2ReadData/pdf/How2ReadData-beamer.pdf index e449058b6..c9a67f747 100644 Binary files a/doc/pub/How2ReadData/pdf/How2ReadData-beamer.pdf and b/doc/pub/How2ReadData/pdf/How2ReadData-beamer.pdf differ diff --git a/doc/pub/How2ReadData/pdf/How2ReadData-minted.pdf b/doc/pub/How2ReadData/pdf/How2ReadData-minted.pdf index 05b3cb5b2..41487143a 100644 Binary files a/doc/pub/How2ReadData/pdf/How2ReadData-minted.pdf and b/doc/pub/How2ReadData/pdf/How2ReadData-minted.pdf differ diff --git a/doc/src/How2ReadData/How2ReadData.do.txt b/doc/src/How2ReadData/How2ReadData.do.txt index f5594dfa2..b4bd94a87 100644 --- a/doc/src/How2ReadData/How2ReadData.do.txt +++ b/doc/src/How2ReadData/How2ReadData.do.txt @@ -1,8 +1,117 @@ -TITLE: Data Analysis and Machine Learning: Representing data +TITLE: Data Analysis and Machine Learning: Introduction and Representing data AUTHOR: Morten Hjorth-Jensen {copyright, 1999-present|CC BY-NC} at Department of Physics, University of Oslo & Department of Physics and Astronomy and National Superconducting Cyclotron Laboratory, Michigan State University DATE: today +!split +===== What is Machine Learning? ===== + +Machine learning is the science of giving computers the ability to +learn without being explicitly programmed. The idea is that there +exist generic algorithms which can be used to find patterns in a broad +class of data sets without having to write code specifically for each +problem. The algorithm will build its own logic based on the data. + +Machine learning is a subfield of computer science, and is closely +related to computational statistics. It evolved from the study of +pattern recognition in artificial intelligence (AI) research, and has +made contributions to AI tasks like computer vision, natural language +processing and speech recognition. It has also, especially in later +years, found applications in a wide variety of other areas, including +bioinformatics, economy, physics, finance and marketing. + +!split +===== Types of Machine Learning ===== + + +The approaches to machine learning are many, but are often split into two main categories. +In *supervised learning* we know the answer to a problem, +and let the computer deduce the logic behind it. On the other hand, *unsupervised learning* +is a method for finding patterns and relationship in data sets without any prior knowledge of the system. +Some authours also operate with a third category, namely *reinforcement learning*. This is a paradigm +of learning inspired by behavioural psychology, where learning is achieved by trial-and-error, +solely from rewards and punishment. + +Another way to categorize machine learning tasks is to consider the desired output of a system. +Some of the most common tasks are: + + * Classification: Outputs are divided into two or more classes. The goal is to produce a model that assigns inputs into one of these classes. An example is to identify digits based on pictures of hand-written ones. Classification is typically supervised learning. + + * Regression: Finding a functional relationship between an input data set and a reference data set. The goal is to construct a function that maps input data to continuous output values. + + * Clustering: Data are divided into groups with certain common traits, without knowing the different groups beforehand. It is thus a form of unsupervised learning. + + +!split +===== Different algorithms ===== +In this course we will build our machine learning approach on a statistical foundation, with elements +from data analysis, stochastic processes etc before we proceed with the following machine learning algorithms + +o Linear regression and its variants +o Decision tree algorithms, from simpler to more complex ones +o Nearest neighbors models +o Bayesian statistics +o Support vector machines and finally various variants of +o Artifical neural networks + +Before we proceed however, there are several practicalities with data analysis and software tools we would +like to present. These tools will help us in our understanding of various machine learning algorithms. + +Our emphasis here is on understanding the mathematical aspects of different algorithms, however, where possible +we will emphasize the importance of using available software. + + +!split +===== Software and needed installations ===== +We will make intensive use of python as programming language and the myriad of available libraries. +Furthermore, you will find IPython/Jupyter notebooks invaluable in your work. +You can run _R_ codes in the Jupyter/IPython notebooks, with the immediate benefit of visualizing your data. + + +If you have Python installed (we recommend Python3) and you feel pretty familiar with installing different packages, +we recommend that you install the following Python packages via _pip_ as +o pip install numpy scipy matplotlib ipython scikit-learn mglearn sympy pandas pillow +For Python3, replace _pip_ with _pip3_. + +For OSX user we recommend also, after having installed Xcode, to install _brew_. Brew allows +for a seamless installation of additional software via for example +o brew install python3 + +For Linux users, with its variety of distributions like for example the widely popular Ubuntu distribution +you can use _pip_ as well and simply install Python as +o sudo apt-get install python3 (or python for pyhton2.7) +etc etc. + +!split +===== Python installers ===== +If you don't want to perform these operations separately, we recommend two widely used distrubutions which set up +all relevant dependencies for Python, namely +o anaconda +o Enthought canopy + + +!split +===== Installing R and C++ ===== + +You will also find it convenient to utilize R. Say more about R. +Jupyter/Ipython notebook allows you run _R_ code interactively in your browser. The software library _R_ is +tuned to statistically analysis and allows for an easy usage of the tools we will discuss in these texts. + +For the C++ affecianodas, Jupyter/IPython notebook allows you also to install C++ and run codes written in this language +interactively in the browser. Since we will emphasize writing many of the algorithms yourself, you can thus opt for +either Python or C++ as programming languages. + +To add more entropy, _cython_ can also be used when running your notebooks. It means that Python with the Jupyter/IPython notebook +setup allows you to integrate widely popular softwares and tools for scientific computing. With its versatility, +including symbolic operations, Python offers a unique computational environment. Your Jupyter/IPython notebook +can easily be converted into a nicely rendered _PDF_ file or a Latex file for further processing. + + +!split +===== Introduction to Jupyter notebook and available tools ===== + + + !split ===== Representing data, overarching aims ===== !bblock @@ -29,7 +138,7 @@ display(data_pandas) !split -===== Representing data, overarching aims ===== +===== Representing data, more examples ===== !bblock !bc pycod import numpy as np @@ -51,3 +160,7 @@ plt.show() !ec !eblock + + + +