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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
author bgruening
date Mon, 02 May 2016 16:14:36 -0400
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children e61a463751e6
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f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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1 <macros>
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2 <token name="@VERSION@">0.9</token>
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3
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4 <xml name="python_requirements">
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5 <requirements>
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6 <requirement type="package" version="0.2.1b">eden</requirement>
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7 <yield />
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8 </requirements>
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9 </xml>
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10
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11 <xml name="macro_stdio">
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12 <stdio>
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13 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
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14 </stdio>
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15 </xml>
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16
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17 <xml name="train_loadConditional" token_train="tabular" token_data="tabular" token_model="txt">
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18 <conditional name="selected_tasks">
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19 <param name="selected_task" type="select" label="Select a Classification Task">
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20 <option value="load">Load a model and predict</option>
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21 <option value="train" selected="true">Train a model</option>
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22 </param>
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23 <when value="load">
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24 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file." />
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25 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
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26 <conditional name="prediction_options">
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27 <param name="prediction_option" type="select" label="Select the type of prediction">
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28 <option value="predict">Predict class labels</option>
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29 <option value="advanced">Include advanced options</option>
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30 </param>
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31 <when value="predict">
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32 </when>
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33 <when value="advanced">
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34 </when>
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35 </conditional>
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36 </when>
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37 <when value="train">
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38 <param name="infile_train" type="data" format="@TRAIN@" label="Training samples (tabular)" />
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39 <conditional name="selected_algorithms">
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40 <yield />
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41 </conditional>
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42 </when>
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43 </conditional>
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44 </xml>
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45
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46 <xml name="advanced_section">
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47 <section name="options" title="Advanced Options" expanded="False">
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48 <yield />
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49 </section>
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50 </xml>
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51
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52 <xml name="tabular_input">
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53 <param name="infile" type="data" format="tabular" label="Data file with numeric values"/>
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54 <param name="start_column" type="data_column" data_ref="infile" optional="True" label="Select a subset of data. Start column:" />
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55 <param name="end_column" type="data_column" data_ref="infile" optional="True" label="End column:" />
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56 </xml>
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57
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58 <xml name="tol" token_default_value="0.0" token_help_text="Early stopping heuristics based on the relative center changes. Set to default (0.0) to disable this convergence detection.">
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59 <param argument="tol" type="float" optional="true" value="@DEFAULT_VALUE@" label="Tolerance" help="@HELP_TEXT@"/>
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60 </xml>
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61
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62 <xml name="n_clusters" token_default_value="8">
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63 <param argument="n_clusters" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of clusters" help=" "/>
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64 </xml>
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65
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66 <xml name="fit_intercept" token_checked="true">
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67 <param argument="fit_intercept" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Estimate the intercept" help="If false, the data is assumed to be already centered."/>
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68 </xml>
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69
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70 <xml name="n_iter" token_default_value="5" token_help_text="The number of passes over the training data (aka epochs). ">
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71 <param argument="n_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@"/>
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72 </xml>
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73
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74 <xml name="shuffle" token_checked="true" token_help_text=" " token_label="Shuffle data after each iteration">
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75 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="@LABEL@" help="@HELP_TEXT@"/>
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76 </xml>
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77
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78 <xml name="random_state" token_default_value="" token_help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data. A fixed seed allows reproducible results.">
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79 <param argument="random_state" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Random seed number" help="@HELP_TEXT@"/>
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80 </xml>
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81
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82 <xml name="warm_start" token_checked="true" token_help_text="When set to True, reuse the solution of the previous call to fit as initialization,otherwise, just erase the previous solution.">
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83 <param argument="warm_start" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Perform warm start" help="@HELP_TEXT@"/>
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84 </xml>
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85
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86 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term.">
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87 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
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88 </xml>
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90 <!--xml name="class_weight" token_default_value="" token_help_text="">
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91 <param argument="class_weight" type="" optional="true" value="@DEFAULT_VALUE@" label="" help="@HELP_TEXT@"/>
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92 </xml-->
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93
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94 <xml name="alpha" token_default_value="0.0001" token_help_text="Constant that multiplies the regularization term if regularization is used. ">
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95 <param argument="alpha" type="float" optional="true" value="@DEFAULT_VALUE@" label="Regularization coefficient" help="@HELP_TEXT@"/>
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96 </xml>
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97
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98 <xml name="n_samples" token_default_value="100" token_help_text="The total number of points equally divided among clusters.">
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99 <param argument="n_samples" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of samples" help="@HELP_TEXT@"/>
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100 </xml>
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101
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102 <xml name="n_features" token_default_value="2" token_help_text="Number of different numerical properties produced for each sample.">
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103 <param argument="n_features" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of features" help="@HELP_TEXT@"/>
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104 </xml>
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105
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106 <xml name="noise" token_default_value="0.0" token_help_text="Floating point number. ">
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107 <param argument="noise" type="float" optional="true" value="@DEFAULT_VALUE@" label="Standard deviation of the Gaussian noise added to the data" help="@HELP_TEXT@"/>
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108 </xml>
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109
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110 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term. ">
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111 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
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112 </xml>
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113
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114 <xml name="max_iter" token_default_value="300" token_label="Maximum number of iterations per single run" token_help_text=" ">
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115 <param argument="max_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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116 </xml>
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117
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118 <xml name="n_init" token_default_value="10" >
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119 <param argument="n_init" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of runs with different centroid seeds" help=" "/>
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120 </xml>
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121
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122 <xml name="init">
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123 <param argument="init" type="select" label="Centroid initialization method" help="''k-means++'' selects initial cluster centers that speed up convergence. ''random'' chooses k observations (rows) at random from data as initial centroids.">
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124 <option value="k-means++">k-means++</option>
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125 <option value="random">random</option>
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126 </param>
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127 </xml>
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128
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129 <xml name="multiple_sparse">
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130 <repeat name="sparse_inputs" min="1" max="10" title="Inputs">
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131 <param name="input" type="data" format="txt" label="Sparse matrix file (.mtx, .txt)" help="Specify a sparse matrix file in .txt format."/>
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132 </repeat>
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133 </xml>
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134
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135 <xml name="eden_citation">
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136 <citations>
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137 <citation type="bibtex">
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138 @misc{fabrizio_costa_2015_15094,
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139 author = {Fabrizio Costa and
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140 Björn Grüning and
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141 gigolo},
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142 title = {EDeN: EDeN - Graph Vectorizer},
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143 month = feb,
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144 year = 2015,
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145 doi = {10.5281/zenodo.15094},
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146 url = {http://dx.doi.org/10.5281/zenodo.15094}
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147 }
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148 }
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149 </citation>
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150 </citations>
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151 </xml>
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152
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153 <xml name="sklearn_citation">
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154 <citations>
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155 <citation type="bibtex">
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156 @article{scikit-learn,
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157 title={Scikit-learn: Machine Learning in {P}ython},
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158 author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
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159 and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
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160 and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
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161 Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
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162 journal={Journal of Machine Learning Research},
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163 volume={12},
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164 pages={2825--2830},
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165 year={2011}
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166 url = {https://github.com/scikit-learn/scikit-learn}
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167 }
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168 </citation>
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169 </citations>
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170 </xml>
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171
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172 <xml name="scipy_citation">
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173 <citations>
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174 <citation type="bibtex">
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175 @Misc{,
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176 author = {Eric Jones and Travis Oliphant and Pearu Peterson and others},
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177 title = {{SciPy}: Open source scientific tools for {Python}},
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178 year = {2001--},
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179 url = "http://www.scipy.org/",
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180 note = {[Online; accessed 2016-04-09]}
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181 }
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182 </citation>
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183 </citations>
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184 </xml>
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185
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186
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187 <xml name="nn_advanced_options">
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188 <section name="options" title="Advanced Options" expanded="False">
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189 <yield/>
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190 <param argument="weights" type="select" label="Weight function" help="Used in prediction.">
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191 <option value="uniform" selected="true" help="Uniform weights. All points in each neighborhood are weighted equally.">Uniform</option>
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192 <option value="distance" help="Weight points by the inverse of their distance.">Distance</option>
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193 </param>
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194 <param argument="algorithm" type="select" label="Neighbor selection algorithm" help=" ">
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195 <option value="auto" selected="true">Auto</option>
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196 <option value="ball_tree">BallTree</option>
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197 <option value="kd_tree">KDTree</option>
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198 <option value="brute">Brute-force</option>
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199 </param>
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200 <param argument="leaf_size" type="integer" value="30" label="Leaf size" help="Used with BallTree and KDTree. Affects the time and memory usage of the constructed tree."/>
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201 <!--param name="metric"-->
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202 <!--param name="p"-->
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203 <!--param name="metric_params"-->
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204 </section>
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205 </xml>
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206
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207 <xml name="svc_advanced_options">
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208 <section name="options" title="Advanced Options" expanded="False">
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209 <yield/>
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210 <param argument="kernel" type="select" optional="true" label="Kernel type" help="Kernel type to be used in the algorithm. If none is given, ‘rbf’ will be used.">
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211 <option value="rbf" selected="true">rbf</option>
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212 <option value="linear">linear</option>
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213 <option value="poly">poly</option>
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214 <option value="sigmoid">sigmoid</option>
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215 <option value="precomputed">precomputed</option>
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216 </param>
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217 <param argument="degree" type="integer" optional="true" value="3" label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/>
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218 <!--TODO: param argument="gamma" float, optional (default=’auto’) -->
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219 <param argument="coef0" type="float" optional="true" value="0.0" label="Zero coefficient (polynomial and sigmoid kernels only)" help="Independent term in kernel function. dafault: 0.0 "/>
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220 <param argument="shrinking" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use the shrinking heuristic" help=" "/>
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221 <param argument="probability" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Enable probability estimates. " help="This must be enabled prior to calling fit, and will slow down that method."/>
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222 <!-- param argument="cache_size"-->
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223 <!--expand macro="class_weight"/-->
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224 <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. "/>
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225 <expand macro="max_iter" default_value="-1" label="Solver maximum number of iterations" help_text="Hard limit on iterations within solver, or -1 for no limit."/>
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226 <!--param argument="decision_function_shape"-->
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227 <expand macro="random_state" help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data for probability estimation. A fixed seed allows reproducible results."/>
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228 </section>
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229 </xml>
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230
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231 <xml name="spectral_clustering_advanced_options">
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232 <section name="options" title="Advanced Options" expanded="False">
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233 <expand macro="n_clusters"/>
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234 <param argument="eigen_solver" type="select" value="" label="Eigen solver" help="The eigenvalue decomposition strategy to use.">
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235 <option value="arpack" selected="true">arpack</option>
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236 <option value="lobpcg">lobpcg</option>
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237 <option value="amg">amg</option>
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238 <!--None-->
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239 </param>
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240 <expand macro="random_state"/>
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241 <expand macro="n_init"/>
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242 <param argument="gamma" type="float" optional="true" value="1.0" label="Kernel scaling factor" help="Scaling factor of RBF, polynomial, exponential chi^2 and sigmoid affinity kernel. Ignored for affinity=''nearest_neighbors''."/>
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243 <param argument="affinity" type="select" label="Affinity" help="Affinity kernel to use. ">
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244 <option value="rbf" selected="true">RBF</option>
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245 <option value="precomputed">precomputed</option>
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246 <option value="nearest_neighbors">Nearset neighbors</option>
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247 </param>
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248 <param argument="n_neighbors" type="integer" optional="true" value="10" label="Number of neighbors" help="Number of neighbors to use when constructing the affinity matrix using the nearest neighbors method. Ignored for affinity=''rbf''"/>
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249 <!--param argument="eigen_tol"-->
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250 <param argument="assign_labels" type="select" label="Assign labels" help="The strategy to use to assign labels in the embedding space.">
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251 <option value="kmeans" selected="true">kmeans</option>
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252 <option value="discretize">discretize</option>
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253 </param>
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254 <param argument="degree" type="integer" optional="true" value="3" label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/>
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255 <param argument="coef0" type="integer" optional="true" value="1" label="Zero coefficient (polynomial and sigmoid kernels only)" help="Ignored by other kernels. dafault : 1 "/>
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256 <!--param argument="kernel_params"-->
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257 </section>
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258 </xml>
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259
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260 <xml name="minibatch_kmeans_advanced_options">
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261 <section name="options" title="Advanced Options" expanded="False">
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262 <expand macro="n_clusters"/>
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263 <expand macro="init"/>
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264 <expand macro="n_init" default_value="3"/>
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265 <expand macro="max_iter" default_value="100"/>
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266 <expand macro="tol" help_text="Early stopping heuristics based on normalized center change. To disable set to 0.0 ."/>
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267 <expand macro="random_state"/>
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268 <param argument="batch_size" type="integer" optional="true" value="100" label="Batch size" help="Size of the mini batches."/>
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269 <!--param argument="compute_labels"-->
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270 <param argument="max_no_improvement" type="integer" optional="true" value="10" label="Maximum number of improvement attempts" help="
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271 Convergence detection based on inertia (the consecutive number of mini batches that doe not yield an improvement on the smoothed inertia).
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272 To disable, set max_no_improvement to None. "/>
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273 <param argument="init_size" type="integer" optional="true" value="" label="Number of random initialization samples" help="Number of samples to randomly sample for speeding up the initialization . ( default: 3 * batch_size )"/>
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274 <param argument="reassignment_ratio" type="float" optional="true" value="0.01" label="Re-assignment ratio" help="Controls the fraction of the maximum number of counts for a center to be reassigned. Higher values yield better clustering results."/>
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275 </section>
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276 </xml>
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277
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278 <xml name="kmeans_advanced_options">
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279 <section name="options" title="Advanced Options" expanded="False">
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280 <expand macro="n_clusters"/>
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281 <expand macro="init"/>
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282 <expand macro="n_init"/>
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283 <expand macro="max_iter"/>
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284 <expand macro="tol" default_value="0.0001" help_text="Relative tolerance with regards to inertia to declare convergence."/>
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285 <!--param argument="precompute_distances"/-->
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286 <expand macro="random_state"/>
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287 <param argument="copy_x" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing distances" help="Mofifying the original data introduces small numerical differences caused by subtracting and then adding the data mean."/>
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288 </section>
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289 </xml>
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290
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291 <xml name="birch_advanced_options">
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292 <section name="options" title="Advanced Options" expanded="False">
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293 <param argument="threshold" type="float" optional="true" value="0.5" label="Subcluster radius threshold" help="The radius of the subcluster obtained by merging a new sample; the closest subcluster should be less than the threshold to avoid a new subcluster."/>
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294 <param argument="branching_factor" type="integer" optional="true" value="50" label="Maximum number of subclusters per branch" help="Maximum number of CF subclusters in each node."/>
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295 <expand macro="n_clusters" default_value="3"/>
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296 <!--param argument="compute_labels"/-->
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297 </section>
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298 </xml>
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299
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300 <xml name="dbscan_advanced_options">
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301 <section name="options" title="Advanced Options" expanded="False">
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302 <param argument="eps" type="float" optional="true" value="0.5" label="Maximum neighborhood distance" help="The maximum distance between two samples for them to be considered as in the same neighborhood."/>
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303 <param argument="min_samples" type="integer" optional="true" value="5" label="Minimal core point density" help="The number of samples (or total weight) in a neighborhood for a point (including the point itself) to be considered as a core point."/>
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304 <param argument="metric" type="text" optional="true" value="euclidean" label="Metric" help="The metric to use when calculating distance between instances in a feature array."/>
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305 <param argument="algorithm" type="select" label="Pointwise distance computation algorithm" help="The algorithm to be used by the NearestNeighbors module to compute pointwise distances and find nearest neighbors.">
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306 <option value="auto" selected="true">auto</option>
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307 <option value="ball_tree">ball_tree</option>
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308 <option value="kd_tree">kd_tree</option>
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309 <option value="brute">brute</option>
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310 </param>
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311 <param argument="leaf_size" type="integer" optional="true" value="30" label="Leaf size" help="Leaf size passed to BallTree or cKDTree. Memory and time efficieny factor in tree constrution and querying."/>
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312 </section>
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313 </xml>
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314
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315 <xml name="clustering_algorithms_options">
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316 <conditional name="algorithm_options">
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317 <param name="selected_algorithm" type="select" label="Clustering Algorithm">
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318 <option value="KMeans" selected="true">KMeans</option>
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319 <option value="SpectralClustering">Spectral Clustering</option>
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320 <option value="MiniBatchKMeans">Mini Batch KMeans</option>
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321 <option value="DBSCAN">DBSCAN</option>
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322 <option value="Birch">Birch</option>
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323 </param>
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324 <when value="KMeans">
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325 <expand macro="kmeans_advanced_options"/>
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326 </when>
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327 <when value="DBSCAN">
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328 <expand macro="dbscan_advanced_options"/>
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329 </when>
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330 <when value="Birch">
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331 <expand macro="birch_advanced_options"/>
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332 </when>
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333 <when value="SpectralClustering">
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334 <expand macro="spectral_clustering_advanced_options"/>
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335 </when>
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336 <when value="MiniBatchKMeans">
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337 <expand macro="minibatch_kmeans_advanced_options"/>
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338 </when>
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339 </conditional>
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340 </xml>
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341 </macros>