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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
author bgruening
date Wed, 09 Aug 2023 12:54:37 +0000
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1 Galaxy wrapper for scikit-learn library
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2 ***************************************
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4 Contents
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5 ========
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7 - `What is scikit-learn?`_
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8 - `Scikit-learn main package groups`_
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9 - `Tools offered by this wrapper`_
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11 - `Machine learning workflows`_
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12 - `Supervised learning workflows`_
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13 - `Unsupervised learning workflows`_
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16 ____________________________
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19 .. _What is scikit-learn?:
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21 What is scikit-learn?
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22 =====================
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24 Scikit-learn is an open-source machine learning library for the Python programming language. It offers various algorithms for performing supervised and unsupervised learning as well as data preprocessing and transformation, model selection and evaluation, and dataset utilities. It is built upon SciPy (Scientific Python) library.
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26 Scikit-learn source code can be accessed at https://github.com/scikit-learn/scikit-learn.
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27 Detailed installation instructions can be found at http://scikit-learn.org/stable/install.html
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30 .. _Scikit-learn main package groups:
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32 Scikit-learn main package groups
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33 ================================
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35 Scikit-learn provides the users with several main groups of related operations.
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36 These are:
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38 - Classification
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39 - Identifying to which category an object belongs.
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40 - Regression
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41 - Predicting a continuous-valued attribute associated with an object.
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42 - Clustering
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43 - Automatic grouping of similar objects into sets.
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44 - Preprocessing
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45 - Feature extraction and normalization.
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46 - Model selection and evaluation
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47 - Comparing, validating and choosing parameters and models.
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48 - Dimensionality reduction
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49 - Reducing the number of random variables to consider.
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51 Each group consists of a number of well-known algorithms from the category. For example, one can find hierarchical, spectral, kmeans, and other clustering methods in sklearn.cluster package.
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54 .. _Tools offered by this wrapper:
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56 Available tools in the current wrapper
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57 ======================================
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59 The current release of the wrapper offers a subset of the packages from scikit-learn library. You can find:
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61 - A subset of classification metric functions
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62 - Linear and quadratic discriminant classifiers
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63 - Random forest and Ada boost classifiers and regressors
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64 - All the clustering methods
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65 - All support vector machine classifiers
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66 - A subset of data preprocessing estimator classes
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67 - Pairwise metric measurement functions
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69 In addition, several tools for performing matrix operations, generating problem-specific datasets, and encoding text and extracting features have been prepared to help the user with more advanced operations.
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71 .. _Machine learning workflows:
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73 Machine learning workflows
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74 ==========================
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76 Machine learning is about processes. No matter what machine learning algorithm we use, we can apply typical workflows and dataflows to produce more robust models and better predictions.
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77 Here we discuss supervised and unsupervised learning workflows.
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79 .. _Supervised learning workflows:
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81 Supervised machine learning workflows
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82 =====================================
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84 **What is supervised learning?**
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86 In this machine learning task, given sample data which are labeled, the aim is to build a model which can predict the labels for new observations.
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87 In practice, there are five steps which we can go through to start from raw input data and end up getting reasonable predictions for new samples:
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89 1. Preprocess the data::
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90
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91 * Change the collected data into the proper format and datatype.
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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92 * Adjust the data quality by filling the missing values, performing
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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93 required scaling and normalizations, etc.
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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94 * Extract features which are the most meaningfull for the learning task.
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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95 * Split the ready dataset into training and test samples.
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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96
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97 2. Choose an algorithm::
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98
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99 * These factors help one to choose a learning algorithm:
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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100 - Nature of the data (e.g. linear vs. nonlinear data)
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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101 - Structure of the predicted output (e.g. binary vs. multilabel classification)
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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102 - Memory and time usage of the training
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103 - Predictive accuracy on new data
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104 - Interpretability of the predictions
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105
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106 3. Choose a validation method
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107
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108 Every machine learning model should be evaluated before being put into practicical use.
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109 There are numerous performance metrics to evaluate machine learning models.
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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110 For supervised learning, usually classification or regression metrics are used.
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111
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112 A validation method helps to evaluate the performance metrics of a trained model in order
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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113 to optimize its performance or ultimately switch to a more efficient model.
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114 Cross-validation is a known validation method.
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115
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116 4. Fit a model
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117
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118 Given the learning algorithm, validation method, and performance metric(s)
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119 repeat the following steps::
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120
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121 * Train the model.
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122 * Evaluate based on metrics.
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123 * Optimize unitl satisfied.
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124
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125 5. Use fitted model for prediction::
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126
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127 This is a final evaluation in which, the optimized model is used to make predictions
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128 on unseen (here test) samples. After this, the model is put into production.
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129
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130 .. _Unsupervised learning workflows:
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131
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132 Unsupervised machine learning workflows
10
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133 =======================================
0
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134
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135 **What is unsupervised learning?**
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136
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137 Unlike supervised learning and more liklely in real life, here the initial data is not labeled.
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138 The task is to extract the structure from the data and group the samples based on their similarities.
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139 Clustering and dimensionality reduction are two famous examples of unsupervised learning tasks.
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140
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141 In this case, the workflow is as follows::
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142
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143 * Preprocess the data (without splitting to train and test).
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144 * Train a model.
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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145 * Evaluate and tune parameters.
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146 * Analyse the model and test on real data.