Mercurial > repos > bgruening > sklearn_stacking_ensemble_models
comparison main_macros.xml @ 10:ac40a2fe5750 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
author | bgruening |
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date | Tue, 13 Apr 2021 17:21:05 +0000 |
parents | b78007bf1cb8 |
children | d25127d5f4e0 |
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9:b78007bf1cb8 | 10:ac40a2fe5750 |
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1 <macros> | 1 <macros> |
2 <token name="@VERSION@">1.0.8.2</token> | 2 <token name="@VERSION@">1.0.8.3</token> |
3 | 3 |
4 <xml name="python_requirements"> | 4 <xml name="python_requirements"> |
5 <requirements> | 5 <requirements> |
6 <requirement type="package" version="3.6">python</requirement> | 6 <requirement type="package" version="0.8.3">Galaxy-ML</requirement> |
7 <requirement type="package" version="0.8.1">Galaxy-ML</requirement> | 7 <yield /> |
8 <yield/> | 8 </requirements> |
9 </requirements> | 9 </xml> |
10 </xml> | 10 |
11 | 11 <xml name="macro_stdio"> |
12 <xml name="macro_stdio"> | 12 <stdio> |
13 <stdio> | 13 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> |
14 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/> | 14 </stdio> |
15 </stdio> | 15 </xml> |
16 </xml> | 16 |
17 | 17 |
18 | 18 <!--Generic interface--> |
19 <!--Generic interface--> | 19 |
20 | 20 <xml name="sl_Conditional" token_train="tabular" token_data="tabular" token_model="txt"> |
21 <xml name="sl_Conditional" token_train="tabular" token_data="tabular" token_model="txt"> | 21 <conditional name="selected_tasks"> |
22 <conditional name="selected_tasks"> | 22 <param name="selected_task" type="select" label="Select a Classification Task"> |
23 <param name="selected_task" type="select" label="Select a Classification Task"> | 23 <option value="train" selected="true">Train a model</option> |
24 <option value="train" selected="true">Train a model</option> | 24 <option value="load">Load a model and predict</option> |
25 <option value="load">Load a model and predict</option> | 25 </param> |
26 <when value="load"> | |
27 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file." /> | |
28 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify." /> | |
29 <param name="header" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | |
30 <conditional name="prediction_options"> | |
31 <param name="prediction_option" type="select" label="Select the type of prediction"> | |
32 <option value="predict">Predict class labels</option> | |
33 <option value="advanced">Include advanced options</option> | |
34 </param> | |
35 <when value="predict"> | |
36 </when> | |
37 <when value="advanced"> | |
38 </when> | |
39 </conditional> | |
40 </when> | |
41 <when value="train"> | |
42 <conditional name="selected_algorithms"> | |
43 <yield /> | |
44 </conditional> | |
45 </when> | |
46 </conditional> | |
47 </xml> | |
48 | |
49 <xml name="advanced_section"> | |
50 <section name="options" title="Advanced Options" expanded="False"> | |
51 <yield /> | |
52 </section> | |
53 </xml> | |
54 | |
55 | |
56 <!--Generalized Linear Models--> | |
57 <xml name="loss" token_help=" " token_select="false"> | |
58 <param argument="loss" type="select" label="Loss function" help="@HELP@"> | |
59 <option value="squared_loss" selected="@SELECT@">squared loss</option> | |
60 <option value="huber">huber</option> | |
61 <option value="epsilon_insensitive">epsilon insensitive</option> | |
62 <option value="squared_epsilon_insensitive">squared epsilon insensitive</option> | |
63 <yield /> | |
26 </param> | 64 </param> |
27 <when value="load"> | 65 </xml> |
28 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/> | 66 |
29 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/> | 67 <xml name="penalty" token_help=" "> |
30 <param name="header" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | 68 <param argument="penalty" type="select" label="Penalty (regularization term)" help="@HELP@"> |
31 <conditional name="prediction_options"> | 69 <option value="l2" selected="true">l2</option> |
32 <param name="prediction_option" type="select" label="Select the type of prediction"> | 70 <option value="l1">l1</option> |
33 <option value="predict">Predict class labels</option> | 71 <option value="elasticnet">elastic net</option> |
34 <option value="advanced">Include advanced options</option> | 72 <option value="none">none</option> |
73 <yield /> | |
74 </param> | |
75 </xml> | |
76 | |
77 <xml name="l1_ratio" token_default_value="0.15" token_help=" "> | |
78 <param argument="l1_ratio" type="float" value="@DEFAULT_VALUE@" label="Elastic Net mixing parameter" help="@HELP@" /> | |
79 </xml> | |
80 | |
81 <xml name="epsilon" token_default_value="0.1" token_help="Used if loss is ‘huber’, ‘epsilon_insensitive’, or ‘squared_epsilon_insensitive’. "> | |
82 <param argument="epsilon" type="float" value="@DEFAULT_VALUE@" label="Epsilon (epsilon-sensitive loss functions only)" help="@HELP@" /> | |
83 </xml> | |
84 | |
85 <xml name="learning_rate_s" token_help=" " token_selected1="false" token_selected2="false"> | |
86 <param argument="learning_rate" type="select" optional="true" label="Learning rate schedule" help="@HELP@"> | |
87 <option value="optimal" selected="@SELECTED1@">optimal</option> | |
88 <option value="constant">constant</option> | |
89 <option value="invscaling" selected="@SELECTED2@">inverse scaling</option> | |
90 <yield /> | |
91 </param> | |
92 </xml> | |
93 | |
94 <xml name="eta0" token_default_value="0.0" token_help="Used with ‘constant’ or ‘invscaling’ schedules. "> | |
95 <param argument="eta0" type="float" value="@DEFAULT_VALUE@" label="Initial learning rate" help="@HELP@" /> | |
96 </xml> | |
97 | |
98 <xml name="power_t" token_default_value="0.5" token_help=" "> | |
99 <param argument="power_t" type="float" value="@DEFAULT_VALUE@" label="Exponent for inverse scaling learning rate" help="@HELP@" /> | |
100 </xml> | |
101 | |
102 <xml name="normalize" token_checked="false" token_help=" "> | |
103 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Normalize samples before training" help=" " /> | |
104 </xml> | |
105 | |
106 <xml name="copy_X" token_checked="true" token_help=" "> | |
107 <param argument="copy_X" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Use a copy of samples" help="If false, samples would be overwritten. " /> | |
108 </xml> | |
109 | |
110 <xml name="ridge_params"> | |
111 <expand macro="normalize" /> | |
112 <expand macro="alpha" default_value="1.0" /> | |
113 <expand macro="fit_intercept" /> | |
114 <expand macro="max_iter" default_value="" /> | |
115 <expand macro="tol" default_value="0.001" help_text="Precision of the solution. " /> | |
116 <!--class_weight--> | |
117 <expand macro="copy_X" /> | |
118 <param argument="solver" type="select" value="" label="Solver to use in the computational routines" help=" "> | |
119 <option value="auto" selected="true">auto</option> | |
120 <option value="svd">svd</option> | |
121 <option value="cholesky">cholesky</option> | |
122 <option value="lsqr">lsqr</option> | |
123 <option value="sparse_cg">sparse_cg</option> | |
124 <option value="sag">sag</option> | |
125 </param> | |
126 <expand macro="random_state" /> | |
127 </xml> | |
128 | |
129 <!--Ensemble methods--> | |
130 <xml name="n_estimators" token_default_value="10" token_help=" "> | |
131 <param argument="n_estimators" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of trees in the forest" help="@HELP@" /> | |
132 </xml> | |
133 | |
134 <xml name="max_depth" token_default_value="" token_help=" "> | |
135 <param argument="max_depth" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum depth of the tree" help="@HELP@" /> | |
136 </xml> | |
137 | |
138 <xml name="min_samples_split" token_type="integer" token_default_value="2" token_help=" "> | |
139 <param argument="min_samples_split" type="@TYPE@" optional="true" value="@DEFAULT_VALUE@" label="Minimum number of samples required to split an internal node" help="@HELP@" /> | |
140 </xml> | |
141 | |
142 <xml name="min_samples_leaf" token_type="integer" token_default_value="1" token_label="Minimum number of samples in newly created leaves" token_help=" "> | |
143 <param argument="min_samples_leaf" type="@TYPE@" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP@" /> | |
144 </xml> | |
145 | |
146 <xml name="min_weight_fraction_leaf" token_default_value="0.0" token_help=" "> | |
147 <param argument="min_weight_fraction_leaf" type="float" optional="true" value="@DEFAULT_VALUE@" label="Minimum weighted fraction of the input samples required to be at a leaf node" help="@HELP@" /> | |
148 </xml> | |
149 | |
150 <xml name="max_leaf_nodes" token_default_value="" token_help=" "> | |
151 <param argument="max_leaf_nodes" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum number of leaf nodes in best-first method" help="@HELP@" /> | |
152 </xml> | |
153 | |
154 <xml name="min_impurity_decrease" token_default_value="0" token_help=" "> | |
155 <param argument="min_impurity_decrease" type="float" value="@DEFAULT_VALUE@" optional="true" label="The threshold value of impurity for stopping node splitting" help="@HELP@" /> | |
156 </xml> | |
157 | |
158 <xml name="bootstrap" token_checked="true" token_help=" "> | |
159 <param argument="bootstrap" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Use bootstrap samples for building trees." help="@HELP@" /> | |
160 </xml> | |
161 | |
162 <xml name="criterion" token_help=" "> | |
163 <param argument="criterion" type="select" label="Function to measure the quality of a split" help=" "> | |
164 <option value="gini" selected="true">Gini impurity</option> | |
165 <option value="entropy">Information gain</option> | |
166 <yield /> | |
167 </param> | |
168 </xml> | |
169 | |
170 <xml name="criterion2" token_help=""> | |
171 <param argument="criterion" type="select" label="Function to measure the quality of a split"> | |
172 <option value="mse">mse - mean squared error</option> | |
173 <option value="mae">mae - mean absolute error</option> | |
174 <yield /> | |
175 </param> | |
176 </xml> | |
177 | |
178 <xml name="oob_score" token_checked="false" token_help=" "> | |
179 <param argument="oob_score" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Use out-of-bag samples to estimate the generalization error" help="@HELP@" /> | |
180 </xml> | |
181 | |
182 <xml name="max_features"> | |
183 <conditional name="select_max_features"> | |
184 <param argument="max_features" type="select" label="max_features"> | |
185 <option value="auto" selected="true">auto - max_features=n_features</option> | |
186 <option value="sqrt">sqrt - max_features=sqrt(n_features)</option> | |
187 <option value="log2">log2 - max_features=log2(n_features)</option> | |
188 <option value="number_input">I want to type the number in or input None type</option> | |
189 </param> | |
190 <when value="auto"> | |
191 </when> | |
192 <when value="sqrt"> | |
193 </when> | |
194 <when value="log2"> | |
195 </when> | |
196 <when value="number_input"> | |
197 <param name="num_max_features" type="float" value="" optional="true" label="Input max_features number:" help="If int, consider the number of features at each split; If float, then max_features is a percentage and int(max_features * n_features) features are considered at each split." /> | |
198 </when> | |
199 </conditional> | |
200 </xml> | |
201 | |
202 <xml name="verbose" token_default_value="0" token_help="If 1 then it prints progress and performance once in a while. If greater than 1 then it prints progress and performance for every tree."> | |
203 <param argument="verbose" type="integer" value="@DEFAULT_VALUE@" optional="true" label="Enable verbose output" help="@HELP@" /> | |
204 </xml> | |
205 | |
206 <xml name="learning_rate" token_default_value="1.0" token_help=" "> | |
207 <param argument="learning_rate" type="float" optional="true" value="@DEFAULT_VALUE@" label="Learning rate" help="@HELP@" /> | |
208 </xml> | |
209 | |
210 <xml name="subsample" token_help=" "> | |
211 <param argument="subsample" type="float" value="1.0" optional="true" label="The fraction of samples to be used for fitting the individual base learners" help="@HELP@" /> | |
212 </xml> | |
213 | |
214 <xml name="presort"> | |
215 <param argument="presort" type="select" label="Whether to presort the data to speed up the finding of best splits in fitting"> | |
216 <option value="auto" selected="true">auto</option> | |
217 <option value="true">true</option> | |
218 <option value="false">false</option> | |
219 </param> | |
220 </xml> | |
221 | |
222 <!-- LightGBM --> | |
223 <xml name="feature_fraction" token_help="LightGBM will randomly select part of the features for each iteration (tree) if feature_fraction is smaller than 1.0. For example, if you set it to 0.8, LightGBM will select 80% of features before training each tree."> | |
224 <param argument="feature_fraction" type="float" value="1.0" label="Proportion of features to train each tree" help="@HELP@" /> | |
225 </xml> | |
226 | |
227 <xml name="lambda_l1" token_help=" "> | |
228 <param argument="lambda_l1" type="float" value="0.0" label="L1 regularization" help="@HELP@" /> | |
229 </xml> | |
230 | |
231 <xml name="lambda_l2" token_help=" "> | |
232 <param argument="lambda_l2" type="float" value="0.0" label="L1 regularization" help="@HELP@" /> | |
233 </xml> | |
234 | |
235 <xml name="min_gain_to_split" token_help=" "> | |
236 <param argument="min_gain_to_split" type="float" value="0.0" label="Minimal gain to perform split" help="@HELP@" /> | |
237 </xml> | |
238 | |
239 <xml name="min_child_weight" token_help="Minimal sum hessian in one leaf. It can be used to deal with over-fitting."> | |
240 <param argument="min_child_weight" type="float" value="0.0" label="Minimal sum hessian in one leaf" help="@HELP@" /> | |
241 </xml> | |
242 | |
243 | |
244 <!--Parameters--> | |
245 <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."> | |
246 <param argument="tol" type="float" optional="true" value="@DEFAULT_VALUE@" label="Tolerance" help="@HELP_TEXT@" /> | |
247 </xml> | |
248 | |
249 <xml name="n_clusters" token_default_value="8"> | |
250 <param argument="n_clusters" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of clusters" help=" " /> | |
251 </xml> | |
252 | |
253 <xml name="fit_intercept" token_checked="true"> | |
254 <param argument="fit_intercept" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Estimate the intercept" help="If false, the data is assumed to be already centered." /> | |
255 </xml> | |
256 | |
257 <xml name="n_iter_no_change" token_default_value="5" token_help_text="Number of iterations with no improvement to wait before early stopping. "> | |
258 <param argument="n_iter_no_change" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@" /> | |
259 </xml> | |
260 | |
261 <xml name="shuffle" token_checked="true" token_help_text=" " token_label="Shuffle data after each iteration"> | |
262 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="@LABEL@" help="@HELP_TEXT@" /> | |
263 </xml> | |
264 | |
265 <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. default=None."> | |
266 <param argument="random_state" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Random seed number" help="@HELP_TEXT@" /> | |
267 </xml> | |
268 | |
269 <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."> | |
270 <param argument="warm_start" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Perform warm start" help="@HELP_TEXT@" /> | |
271 </xml> | |
272 | |
273 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term."> | |
274 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@" /> | |
275 </xml> | |
276 | |
277 <!--xml name="class_weight" token_default_value="" token_help_text=""> | |
278 <param argument="class_weight" type="" optional="true" value="@DEFAULT_VALUE@" label="" help="@HELP_TEXT@"/> | |
279 </xml--> | |
280 | |
281 <xml name="alpha" token_default_value="0.0001" token_help_text="Constant that multiplies the regularization term if regularization is used. "> | |
282 <param argument="alpha" type="float" optional="true" value="@DEFAULT_VALUE@" label="Regularization coefficient" help="@HELP_TEXT@" /> | |
283 </xml> | |
284 | |
285 <xml name="n_samples" token_default_value="100" token_help_text="The total number of points equally divided among clusters."> | |
286 <param argument="n_samples" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of samples" help="@HELP_TEXT@" /> | |
287 </xml> | |
288 | |
289 <xml name="n_features" token_default_value="2" token_help_text="Number of different numerical properties produced for each sample."> | |
290 <param argument="n_features" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of features" help="@HELP_TEXT@" /> | |
291 </xml> | |
292 | |
293 <xml name="noise" token_default_value="0.0" token_help_text="Floating point number. "> | |
294 <param argument="noise" type="float" optional="true" value="@DEFAULT_VALUE@" label="Standard deviation of the Gaussian noise added to the data" help="@HELP_TEXT@" /> | |
295 </xml> | |
296 | |
297 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term. "> | |
298 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@" /> | |
299 </xml> | |
300 | |
301 <xml name="max_iter" token_default_value="300" token_label="Maximum number of iterations per single run" token_help_text=" "> | |
302 <param argument="max_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@" /> | |
303 </xml> | |
304 | |
305 <xml name="n_init" token_default_value="10"> | |
306 <param argument="n_init" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of runs with different centroid seeds" help=" " /> | |
307 </xml> | |
308 | |
309 <xml name="init"> | |
310 <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."> | |
311 <option value="k-means++">k-means++</option> | |
312 <option value="random">random</option> | |
313 </param> | |
314 </xml> | |
315 | |
316 <xml name="gamma" token_default_value="1.0" token_label="Scaling parameter" token_help_text=" "> | |
317 <param argument="gamma" type="float" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@" /> | |
318 </xml> | |
319 | |
320 <xml name="degree" token_default_value="3" token_label="Degree of the polynomial" token_help_text=" "> | |
321 <param argument="degree" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@" /> | |
322 </xml> | |
323 | |
324 <xml name="coef0" token_default_value="1" token_label="Zero coefficient" token_help_text=" "> | |
325 <param argument="coef0" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@" /> | |
326 </xml> | |
327 | |
328 <xml name="pos_label" token_default_value=""> | |
329 <param argument="pos_label" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Label of the positive class" help=" " /> | |
330 </xml> | |
331 | |
332 <xml name="average"> | |
333 <param argument="average" type="select" optional="true" label="Averaging type" help=" "> | |
334 <option value="micro">Calculate metrics globally by counting the total true positives, false negatives and false positives. (micro)</option> | |
335 <option value="samples">Calculate metrics for each instance, and find their average. Only meaningful for multilabel. (samples)</option> | |
336 <option value="macro">Calculate metrics for each label, and find their unweighted mean. This does not take label imbalance into account. (macro)</option> | |
337 <option value="weighted">Calculate metrics for each label, and find their average, weighted by support (the number of true instances for each label). This alters ‘macro’ to account for label imbalance; it can result in an F-score that is not between precision and recall. (weighted)</option> | |
338 <option value="None">None</option> | |
339 <yield /> | |
340 </param> | |
341 </xml> | |
342 | |
343 <xml name="beta"> | |
344 <param argument="beta" type="float" value="1.0" label="The strength of recall versus precision in the F-score" help=" " /> | |
345 </xml> | |
346 | |
347 | |
348 <!--Data interface--> | |
349 | |
350 <xml name="samples_tabular" token_label1="Training samples dataset:" token_multiple1="false" token_multiple2="false"> | |
351 <param name="infile1" type="data" format="tabular" label="@LABEL1@" /> | |
352 <param name="header1" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | |
353 <conditional name="column_selector_options_1"> | |
354 <expand macro="samples_column_selector_options" multiple="@MULTIPLE1@" /> | |
355 </conditional> | |
356 <param name="infile2" type="data" format="tabular" label="Dataset containing class labels or target values:" /> | |
357 <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | |
358 <conditional name="column_selector_options_2"> | |
359 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="@MULTIPLE2@" infile="infile2" /> | |
360 </conditional> | |
361 <yield /> | |
362 </xml> | |
363 | |
364 <xml name="samples_column_selector_options" token_column_option="selected_column_selector_option" token_col_name="col1" token_multiple="False" token_infile="infile1"> | |
365 <param name="@COLUMN_OPTION@" type="select" label="Choose how to select data by column:"> | |
366 <option value="by_index_number" selected="true">Select columns by column index number(s)</option> | |
367 <option value="all_but_by_index_number">All columns EXCLUDING some by column index number(s)</option> | |
368 <option value="by_header_name">Select columns by column header name(s)</option> | |
369 <option value="all_but_by_header_name">All columns EXCLUDING some by column header name(s)</option> | |
370 <option value="all_columns">All columns</option> | |
371 </param> | |
372 <when value="by_index_number"> | |
373 <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" use_header_names="true" data_ref="@INFILE@" label="Select target column(s):" /> | |
374 </when> | |
375 <when value="all_but_by_index_number"> | |
376 <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" use_header_names="true" data_ref="@INFILE@" label="Select target column(s):" /> | |
377 </when> | |
378 <when value="by_header_name"> | |
379 <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="Comma-separated string. For example: target1,target2" /> | |
380 </when> | |
381 <when value="all_but_by_header_name"> | |
382 <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="Comma-separated string. For example: target1,target2" /> | |
383 </when> | |
384 <when value="all_columns"> | |
385 </when> | |
386 </xml> | |
387 | |
388 <xml name="clf_inputs_extended" token_label1=" " token_label2=" " token_multiple="False"> | |
389 <conditional name="true_columns"> | |
390 <param name="selected_input1" type="select" label="Select the input type of true labels dataset:"> | |
391 <option value="tabular" selected="true">Tabular</option> | |
392 <option value="sparse">Sparse</option> | |
393 </param> | |
394 <when value="tabular"> | |
395 <param name="infile1" type="data" label="@LABEL1@" /> | |
396 <param name="col1" type="data_column" data_ref="infile1" label="Select the target column:" /> | |
397 </when> | |
398 <when value="sparse"> | |
399 <param name="infile1" type="data" format="txt" label="@LABEL1@" /> | |
400 </when> | |
401 </conditional> | |
402 <conditional name="predicted_columns"> | |
403 <param name="selected_input2" type="select" label="Select the input type of predicted labels dataset:"> | |
404 <option value="tabular" selected="true">Tabular</option> | |
405 <option value="sparse">Sparse</option> | |
406 </param> | |
407 <when value="tabular"> | |
408 <param name="infile2" type="data" label="@LABEL2@" /> | |
409 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):" /> | |
410 </when> | |
411 <when value="sparse"> | |
412 <param name="infile2" type="data" format="txt" label="@LABEL1@" /> | |
413 </when> | |
414 </conditional> | |
415 </xml> | |
416 | |
417 <xml name="clf_inputs" token_label1="Dataset containing true labels (tabular):" token_label2="Dataset containing predicted values (tabular):" token_multiple1="False" token_multiple="False"> | |
418 <param name="infile1" type="data" format="tabular" label="@LABEL1@" /> | |
419 <param name="header1" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | |
420 <conditional name="column_selector_options_1"> | |
421 <expand macro="samples_column_selector_options" multiple="@MULTIPLE1@" /> | |
422 </conditional> | |
423 <param name="infile2" type="data" format="tabular" label="@LABEL2@" /> | |
424 <param name="header2" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | |
425 <conditional name="column_selector_options_2"> | |
426 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="@MULTIPLE@" infile="infile2" /> | |
427 </conditional> | |
428 </xml> | |
429 | |
430 <xml name="multiple_input" token_name="input_files" token_max_num="10" token_format="txt" token_label="Sparse matrix file (.mtx, .txt)" token_help_text="Specify a sparse matrix file in .txt format."> | |
431 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):"> | |
432 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@" /> | |
433 </repeat> | |
434 </xml> | |
435 | |
436 <xml name="sparse_target" token_label1="Select a sparse matrix:" token_label2="Select the tabular containing true labels:" token_multiple="False" token_format1="txt" token_format2="tabular" token_help1="" token_help2=""> | |
437 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@" /> | |
438 <expand macro="input_tabular_target" /> | |
439 </xml> | |
440 | |
441 <xml name="sl_mixed_input"> | |
442 <conditional name="input_options"> | |
443 <expand macro="data_input_options" /> | |
444 <expand macro="data_input_whens" /> | |
445 </conditional> | |
446 </xml> | |
447 | |
448 <xml name="sl_mixed_input_plus_sequence"> | |
449 <conditional name="input_options"> | |
450 <expand macro="data_input_options"> | |
451 <option value="seq_fasta">sequnences in a fasta file</option> | |
452 <option value="refseq_and_interval">reference genome and intervals</option> | |
453 </expand> | |
454 <expand macro="data_input_whens"> | |
455 <when value="seq_fasta"> | |
456 <expand macro="inputs_seq_fasta" /> | |
457 </when> | |
458 <when value="refseq_and_interval"> | |
459 <expand macro="inputs_refseq_and_interval" /> | |
460 </when> | |
461 </expand> | |
462 </conditional> | |
463 </xml> | |
464 | |
465 <xml name="data_input_options"> | |
466 <param name="selected_input" type="select" label="Select input type:"> | |
467 <option value="tabular" selected="true">tabular data</option> | |
468 <option value="sparse">sparse matrix</option> | |
469 <yield /> | |
470 </param> | |
471 </xml> | |
472 | |
473 <xml name="data_input_whens"> | |
474 <when value="tabular"> | |
475 <expand macro="samples_tabular" multiple1="true" multiple2="false" /> | |
476 </when> | |
477 <when value="sparse"> | |
478 <expand macro="sparse_target" /> | |
479 </when> | |
480 <yield /> | |
481 </xml> | |
482 | |
483 <xml name="input_tabular_target"> | |
484 <param name="infile2" type="data" format="tabular" label="Dataset containing class labels or target values:" /> | |
485 <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" /> | |
486 <conditional name="column_selector_options_2"> | |
487 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="false" infile="infile2" /> | |
488 </conditional> | |
489 </xml> | |
490 | |
491 <xml name="inputs_seq_fasta"> | |
492 <param name="fasta_path" type="data" format="fasta" label="Dataset containing fasta genomic/protein sequences" help="Sequences will be one-hot encoded to arrays." /> | |
493 <expand macro="input_tabular_target" /> | |
494 </xml> | |
495 | |
496 <xml name="inputs_refseq_and_interval"> | |
497 <param name="ref_genome_file" type="data" format="fasta" label="Dataset containing reference genomic sequence" /> | |
498 <param name="interval_file" type="data" format="interval" label="Dataset containing sequence intervals for training" help="interval. Sequences will be retrieved from the reference genome and one-hot encoded to training arrays." /> | |
499 <param name="target_file" type="data" format="bed" label="Dataset containing positions and features for target values." help="bed. The file will be compressed with `bgzip` and then indexed using `tabix`." /> | |
500 <param name="infile2" type="data" format="tabular" label="Dataset containing the feature list for prediction" /> | |
501 <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" /> | |
502 <conditional name="column_selector_options_2"> | |
503 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="true" infile="infile2" /> | |
504 </conditional> | |
505 </xml> | |
506 | |
507 <!--Advanced options--> | |
508 <xml name="nn_advanced_options"> | |
509 <section name="options" title="Advanced Options" expanded="False"> | |
510 <yield /> | |
511 <param argument="weights" type="select" label="Weight function" help="Used in prediction."> | |
512 <option value="uniform" selected="true">Uniform weights. All points in each neighborhood are weighted equally. (Uniform)</option> | |
513 <option value="distance">Weight points by the inverse of their distance. (Distance)</option> | |
514 </param> | |
515 <param argument="algorithm" type="select" label="Neighbor selection algorithm" help=" "> | |
516 <option value="auto" selected="true">Auto</option> | |
517 <option value="ball_tree">BallTree</option> | |
518 <option value="kd_tree">KDTree</option> | |
519 <option value="brute">Brute-force</option> | |
520 </param> | |
521 <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." /> | |
522 <!--param name="metric"--> | |
523 <!--param name="p"--> | |
524 <!--param name="metric_params"--> | |
525 </section> | |
526 </xml> | |
527 | |
528 <xml name="svc_advanced_options"> | |
529 <section name="options" title="Advanced Options" expanded="False"> | |
530 <yield /> | |
531 <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."> | |
532 <option value="rbf" selected="true">rbf</option> | |
533 <option value="linear">linear</option> | |
534 <option value="poly">poly</option> | |
535 <option value="sigmoid">sigmoid</option> | |
536 <option value="precomputed">precomputed</option> | |
537 </param> | |
538 <param argument="degree" type="integer" optional="true" value="3" label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 " /> | |
539 <!--TODO: param argument="gamma" float, optional (default=’auto’) --> | |
540 <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 " /> | |
541 <param argument="shrinking" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Use the shrinking heuristic" help=" " /> | |
542 <param argument="probability" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Enable probability estimates. " help="This must be enabled prior to calling fit, and will slow down that method." /> | |
543 <!-- param argument="cache_size"--> | |
544 <!--expand macro="class_weight"/--> | |
545 <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. " /> | |
546 <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." /> | |
547 <!--param argument="decision_function_shape"--> | |
548 <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." /> | |
549 </section> | |
550 </xml> | |
551 | |
552 <xml name="spectral_clustering_advanced_options"> | |
553 <section name="options" title="Advanced Options" expanded="False"> | |
554 <expand macro="n_clusters" /> | |
555 <param argument="eigen_solver" type="select" value="" label="Eigen solver" help="The eigenvalue decomposition strategy to use."> | |
556 <option value="arpack" selected="true">arpack</option> | |
557 <option value="lobpcg">lobpcg</option> | |
558 <option value="amg">amg</option> | |
559 <!--None--> | |
560 </param> | |
561 <expand macro="random_state" /> | |
562 <expand macro="n_init" /> | |
563 <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''." /> | |
564 <param argument="affinity" type="select" label="Affinity" help="Affinity kernel to use. "> | |
565 <option value="rbf" selected="true">RBF</option> | |
566 <option value="precomputed">precomputed</option> | |
567 <option value="nearest_neighbors">Nearset neighbors</option> | |
568 </param> | |
569 <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''" /> | |
570 <!--param argument="eigen_tol"--> | |
571 <param argument="assign_labels" type="select" label="Assign labels" help="The strategy to use to assign labels in the embedding space."> | |
572 <option value="kmeans" selected="true">kmeans</option> | |
573 <option value="discretize">discretize</option> | |
574 </param> | |
575 <param argument="degree" type="integer" optional="true" value="3" label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 " /> | |
576 <param argument="coef0" type="integer" optional="true" value="1" label="Zero coefficient (polynomial and sigmoid kernels only)" help="Ignored by other kernels. dafault : 1 " /> | |
577 <!--param argument="kernel_params"--> | |
578 </section> | |
579 </xml> | |
580 | |
581 <xml name="minibatch_kmeans_advanced_options"> | |
582 <section name="options" title="Advanced Options" expanded="False"> | |
583 <expand macro="n_clusters" /> | |
584 <expand macro="init" /> | |
585 <expand macro="n_init" default_value="3" /> | |
586 <expand macro="max_iter" default_value="100" /> | |
587 <expand macro="tol" help_text="Early stopping heuristics based on normalized center change. To disable set to 0.0 ." /> | |
588 <expand macro="random_state" /> | |
589 <param argument="batch_size" type="integer" optional="true" value="100" label="Batch size" help="Size of the mini batches." /> | |
590 <!--param argument="compute_labels"--> | |
591 <param argument="max_no_improvement" type="integer" optional="true" value="10" label="Maximum number of improvement attempts" help=" | |
592 Convergence detection based on inertia (the consecutive number of mini batches that doe not yield an improvement on the smoothed inertia). | |
593 To disable, set max_no_improvement to None. " /> | |
594 <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 )" /> | |
595 <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." /> | |
596 </section> | |
597 </xml> | |
598 | |
599 <xml name="kmeans_advanced_options"> | |
600 <section name="options" title="Advanced Options" expanded="False"> | |
601 <expand macro="n_clusters" /> | |
602 <expand macro="init" /> | |
603 <expand macro="n_init" /> | |
604 <expand macro="max_iter" /> | |
605 <expand macro="tol" default_value="0.0001" help_text="Relative tolerance with regards to inertia to declare convergence." /> | |
606 <!--param argument="precompute_distances"/--> | |
607 <expand macro="random_state" /> | |
608 <param argument="copy_x" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" 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." /> | |
609 <expand macro="kmeans_algorithm" /> | |
610 </section> | |
611 </xml> | |
612 | |
613 <xml name="kmeans_algorithm"> | |
614 <param argument="algorithm" type="select" label="K-means algorithm to use:"> | |
615 <option value="auto" selected="true">auto</option> | |
616 <option value="full">full</option> | |
617 <option value="elkan">elkan</option> | |
618 </param> | |
619 </xml> | |
620 | |
621 <xml name="birch_advanced_options"> | |
622 <section name="options" title="Advanced Options" expanded="False"> | |
623 <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." /> | |
624 <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." /> | |
625 <expand macro="n_clusters" default_value="3" /> | |
626 <!--param argument="compute_labels"/--> | |
627 </section> | |
628 </xml> | |
629 | |
630 <xml name="dbscan_advanced_options"> | |
631 <section name="options" title="Advanced Options" expanded="False"> | |
632 <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." /> | |
633 <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." /> | |
634 <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." /> | |
635 <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."> | |
636 <option value="auto" selected="true">auto</option> | |
637 <option value="ball_tree">ball_tree</option> | |
638 <option value="kd_tree">kd_tree</option> | |
639 <option value="brute">brute</option> | |
640 </param> | |
641 <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." /> | |
642 </section> | |
643 </xml> | |
644 | |
645 <xml name="clustering_algorithms_options"> | |
646 <conditional name="algorithm_options"> | |
647 <param name="selected_algorithm" type="select" label="Clustering Algorithm"> | |
648 <option value="KMeans" selected="true">KMeans</option> | |
649 <option value="SpectralClustering">Spectral Clustering</option> | |
650 <option value="MiniBatchKMeans">Mini Batch KMeans</option> | |
651 <option value="DBSCAN">DBSCAN</option> | |
652 <option value="Birch">Birch</option> | |
653 </param> | |
654 <when value="KMeans"> | |
655 <expand macro="kmeans_advanced_options" /> | |
656 </when> | |
657 <when value="DBSCAN"> | |
658 <expand macro="dbscan_advanced_options" /> | |
659 </when> | |
660 <when value="Birch"> | |
661 <expand macro="birch_advanced_options" /> | |
662 </when> | |
663 <when value="SpectralClustering"> | |
664 <expand macro="spectral_clustering_advanced_options" /> | |
665 </when> | |
666 <when value="MiniBatchKMeans"> | |
667 <expand macro="minibatch_kmeans_advanced_options" /> | |
668 </when> | |
669 </conditional> | |
670 </xml> | |
671 | |
672 <xml name="distance_metrics"> | |
673 <param argument="metric" type="select" label="Distance metric" help=" "> | |
674 <option value="euclidean" selected="true">euclidean</option> | |
675 <option value="cityblock">cityblock</option> | |
676 <option value="cosine">cosine</option> | |
677 <option value="l1">l1</option> | |
678 <option value="l2">l2</option> | |
679 <option value="manhattan">manhattan</option> | |
680 <yield /> | |
681 </param> | |
682 </xml> | |
683 | |
684 <xml name="distance_nonsparse_metrics"> | |
685 <option value="braycurtis">braycurtis</option> | |
686 <option value="canberra">canberra</option> | |
687 <option value="chebyshev">chebyshev</option> | |
688 <option value="correlation">correlation</option> | |
689 <option value="dice">dice</option> | |
690 <option value="hamming">hamming</option> | |
691 <option value="jaccard">jaccard</option> | |
692 <option value="kulsinski">kulsinski</option> | |
693 <option value="mahalanobis">mahalanobis</option> | |
694 <option value="matching">matching</option> | |
695 <option value="minkowski">minkowski</option> | |
696 <option value="rogerstanimoto">rogerstanimoto</option> | |
697 <option value="russellrao">russellrao</option> | |
698 <option value="seuclidean">seuclidean</option> | |
699 <option value="sokalmichener">sokalmichener</option> | |
700 <option value="sokalsneath">sokalsneath</option> | |
701 <option value="sqeuclidean">sqeuclidean</option> | |
702 <option value="yule">yule</option> | |
703 </xml> | |
704 | |
705 <xml name="pairwise_kernel_metrics"> | |
706 <param argument="metric" type="select" label="Pirwise Kernel metric" help=" "> | |
707 <option value="rbf" selected="true">rbf</option> | |
708 <option value="sigmoid">sigmoid</option> | |
709 <option value="polynomial">polynomial</option> | |
710 <option value="linear" selected="true">linear</option> | |
711 <option value="chi2">chi2</option> | |
712 <option value="additive_chi2">additive_chi2</option> | |
713 </param> | |
714 </xml> | |
715 | |
716 <xml name="sparse_pairwise_metric_functions"> | |
717 <param name="selected_metric_function" type="select" label="Select the pairwise metric you want to compute:"> | |
718 <option value="euclidean_distances" selected="true">Euclidean distance matrix</option> | |
719 <option value="pairwise_distances">Distance matrix</option> | |
720 <option value="pairwise_distances_argmin">Minimum distances between one point and a set of points</option> | |
721 <yield /> | |
722 </param> | |
723 </xml> | |
724 | |
725 <xml name="pairwise_metric_functions"> | |
726 <option value="additive_chi2_kernel">Additive chi-squared kernel</option> | |
727 <option value="chi2_kernel">Exponential chi-squared kernel</option> | |
728 <option value="linear_kernel">Linear kernel</option> | |
729 <option value="manhattan_distances">L1 distances</option> | |
730 <option value="pairwise_kernels">Kernel</option> | |
731 <option value="polynomial_kernel">Polynomial kernel</option> | |
732 <option value="rbf_kernel">Gaussian (rbf) kernel</option> | |
733 <option value="laplacian_kernel">Laplacian kernel</option> | |
734 </xml> | |
735 | |
736 <xml name="sparse_pairwise_condition"> | |
737 <when value="pairwise_distances"> | |
738 <section name="options" title="Advanced Options" expanded="False"> | |
739 <expand macro="distance_metrics"> | |
740 <yield /> | |
741 </expand> | |
742 </section> | |
743 </when> | |
744 <when value="euclidean_distances"> | |
745 <section name="options" title="Advanced Options" expanded="False"> | |
746 <param argument="squared" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Return squared Euclidean distances" help=" " /> | |
747 </section> | |
748 </when> | |
749 </xml> | |
750 | |
751 <xml name="argmin_distance_condition"> | |
752 <when value="pairwise_distances_argmin"> | |
753 <section name="options" title="Advanced Options" expanded="False"> | |
754 <param argument="axis" type="integer" optional="true" value="1" label="Axis" help="Axis along which the argmin and distances are to be computed." /> | |
755 <expand macro="distance_metrics"> | |
756 <yield /> | |
757 </expand> | |
758 <param argument="batch_size" type="integer" optional="true" value="500" label="Batch size" help="Number of rows to be processed in each batch run." /> | |
759 </section> | |
760 </when> | |
761 </xml> | |
762 | |
763 <xml name="sparse_preprocessors"> | |
764 <param name="selected_pre_processor" type="select" label="Select a preprocessor:"> | |
765 <option value="StandardScaler" selected="true">Standard Scaler (Standardizes features by removing the mean and scaling to unit variance)</option> | |
766 <option value="Binarizer">Binarizer (Binarizes data)</option> | |
767 <option value="MaxAbsScaler">Max Abs Scaler (Scales features by their maximum absolute value)</option> | |
768 <option value="Normalizer">Normalizer (Normalizes samples individually to unit norm)</option> | |
769 <yield /> | |
770 </param> | |
771 </xml> | |
772 | |
773 <xml name="sparse_preprocessors_ext"> | |
774 <expand macro="sparse_preprocessors"> | |
775 <option value="KernelCenterer">Kernel Centerer (Centers a kernel matrix)</option> | |
776 <option value="MinMaxScaler">Minmax Scaler (Scales features to a range)</option> | |
777 <option value="PolynomialFeatures">Polynomial Features (Generates polynomial and interaction features)</option> | |
778 <option value="RobustScaler">Robust Scaler (Scales features using outlier-invariance statistics)</option> | |
779 <option value="QuantileTransformer">QuantileTransformer (Transform features using quantiles information)</option> | |
780 <option value="PowerTransformer">PowerTransformer (Apply a power transform featurewise to make data more Gaussian-like)</option> | |
781 <option value="KBinsDiscretizer">KBinsDiscretizer (Bin continuous data into intervals.)</option> | |
782 </expand> | |
783 </xml> | |
784 | |
785 <xml name="sparse_preprocessor_options"> | |
786 <when value="Binarizer"> | |
787 <section name="options" title="Advanced Options" expanded="False"> | |
788 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Use a copy of data for precomputing binarization" help=" " /> | |
789 <param argument="threshold" type="float" optional="true" value="0.0" label="Threshold" help="Feature values below or equal to this are replaced by 0, above it by 1. Threshold may not be less than 0 for operations on sparse matrices. " /> | |
790 </section> | |
791 </when> | |
792 <when value="StandardScaler"> | |
793 <section name="options" title="Advanced Options" expanded="False"> | |
794 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Use a copy of data for performing inplace scaling" help=" " /> | |
795 <param argument="with_mean" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Center the data before scaling" help=" " /> | |
796 <param argument="with_std" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Scale the data to unit variance (or unit standard deviation)" help=" " /> | |
797 </section> | |
798 </when> | |
799 <when value="MaxAbsScaler"> | |
800 <section name="options" title="Advanced Options" expanded="False"> | |
801 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Use a copy of data for precomputing scaling" help=" " /> | |
802 </section> | |
803 </when> | |
804 <when value="Normalizer"> | |
805 <section name="options" title="Advanced Options" expanded="False"> | |
806 <param argument="norm" type="select" optional="true" label="The norm to use to normalize non zero samples" help=" "> | |
807 <option value="l1" selected="true">l1</option> | |
808 <option value="l2">l2</option> | |
809 <option value="max">max</option> | |
35 </param> | 810 </param> |
36 <when value="predict"> | 811 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Use a copy of data for precomputing row normalization" help=" " /> |
812 </section> | |
813 </when> | |
814 <yield /> | |
815 </xml> | |
816 | |
817 <xml name="sparse_preprocessor_options_ext"> | |
818 <expand macro="sparse_preprocessor_options"> | |
819 <when value="KernelCenterer"> | |
820 <section name="options" title="Advanced Options" expanded="False"> | |
821 </section> | |
822 </when> | |
823 <when value="MinMaxScaler"> | |
824 <section name="options" title="Advanced Options" expanded="False"> | |
825 <param argument="feature_range" type="text" value="(0, 1)" optional="true" help="Desired range of transformed data. None or tuple (min, max). None equals to (0, 1)" /> | |
826 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing normalization" help=" " /> | |
827 </section> | |
828 </when> | |
829 <when value="PolynomialFeatures"> | |
830 <section name="options" title="Advanced Options" expanded="False"> | |
831 <param argument="degree" type="integer" optional="true" value="2" label="The degree of the polynomial features " help="" /> | |
832 <param argument="interaction_only" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Produce interaction features only" help="(Features that are products of at most degree distinct input features) " /> | |
833 <param argument="include_bias" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Include a bias column" help="Feature in which all polynomial powers are zero " /> | |
834 </section> | |
835 </when> | |
836 <when value="RobustScaler"> | |
837 <section name="options" title="Advanced Options" expanded="False"> | |
838 <!--=True, =True, copy=True--> | |
839 <param argument="with_centering" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Center the data before scaling" help=" " /> | |
840 <param argument="with_scaling" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Scale the data to interquartile range" help=" " /> | |
841 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for inplace scaling" help=" " /> | |
842 </section> | |
843 </when> | |
844 <when value="QuantileTransformer"> | |
845 <section name="options" title="Advanced Options" expanded="False"> | |
846 <param name="n_quantiles" type="integer" value="1000" min="0" label="Number of quantiles to be computed" /> | |
847 <param name="output_distribution" type="select" label="Marginal distribution for the transformed data"> | |
848 <option value="uniform" selected="true">uniform</option> | |
849 <option value="normal">normal</option> | |
850 </param> | |
851 <param name="ignore_implicit_zeros" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Whether to discard sparse entries" help="Only applies to sparse matrices. If False, sparse entries are treated as zeros" /> | |
852 <param name="subsample" type="integer" value="100000" label="Maximum number of samples used to estimate the quantiles for computational efficiency" help="Note that the subsampling procedure may differ for value-identical sparse and dense matrices." /> | |
853 <expand macro="random_state" help_text="This is used by subsampling and smoothing noise" /> | |
854 </section> | |
855 </when> | |
856 <when value="PowerTransformer"> | |
857 <section name="options" title="Advanced Options" expanded="False"> | |
858 <param name="method" type="select" label="The power transform method"> | |
859 <option value="yeo-johnson" selected="true">yeo-johnson (works with positive and negative values)</option> | |
860 <option value="box-cox">box-cox (might perform better, but only works with strictly positive values)</option> | |
861 </param> | |
862 <param name="standardize" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Whether to apply zero-mean, unit-variance normalization to the transformed output." /> | |
863 </section> | |
864 </when> | |
865 <when value="KBinsDiscretizer"> | |
866 <section name="options" title="Advanced Options" expanded="False"> | |
867 <param name="n_bins" type="integer" value="5" min="2" label="The number of bins to produce" /> | |
868 <param name="encode" type="select" label="Method used to encode the transformed result"> | |
869 <option value="onehot" selected="true">onehot (encode the transformed result with one-hot encoding and return a sparse matrix)</option> | |
870 <option value="onehot-dense">onehot-dense (encode the transformed result with one-hot encoding and return a dense array)</option> | |
871 <option value="ordinal">ordinal (return the bin identifier encoded as an integer value)</option> | |
872 </param> | |
873 <param name="strategy" type="select" label="Strategy used to define the widths of the bins"> | |
874 <option value="uniform">uniform (all bins in each feature have identical widths)</option> | |
875 <option value="quantile" selected="true">quantile (all bins in each feature have the same number of points)</option> | |
876 <option value="kmeans">kmeans (values in each bin have the same nearest center of a 1D k-means cluster)</option> | |
877 </param> | |
878 </section> | |
879 </when> | |
880 </expand> | |
881 </xml> | |
882 | |
883 <xml name="cv_splitter"> | |
884 <option value="default" selected="true">default splitter</option> | |
885 <option value="KFold">KFold</option> | |
886 <option value="StratifiedKFold">StratifiedKFold</option> | |
887 <option value="LeaveOneOut">LeaveOneOut</option> | |
888 <option value="LeavePOut">LeavePOut</option> | |
889 <option value="RepeatedKFold">RepeatedKFold</option> | |
890 <option value="RepeatedStratifiedKFold">RepeatedStratifiedKFold</option> | |
891 <option value="ShuffleSplit">ShuffleSplit</option> | |
892 <option value="StratifiedShuffleSplit">StratifiedShuffleSplit</option> | |
893 <option value="TimeSeriesSplit">TimeSeriesSplit</option> | |
894 <option value="PredefinedSplit">PredefinedSplit</option> | |
895 <option value="OrderedKFold">OrderedKFold</option> | |
896 <option value="RepeatedOrderedKFold">RepeatedOrderedKFold</option> | |
897 <yield /> | |
898 </xml> | |
899 | |
900 <xml name="cv_splitter_options"> | |
901 <when value="default"> | |
902 <expand macro="cv_n_splits" /> | |
903 </when> | |
904 <when value="KFold"> | |
905 <expand macro="cv_n_splits" /> | |
906 <expand macro="cv_shuffle" /> | |
907 <expand macro="random_state" /> | |
908 </when> | |
909 <when value="StratifiedKFold"> | |
910 <expand macro="cv_n_splits" /> | |
911 <expand macro="cv_shuffle" /> | |
912 <expand macro="random_state" /> | |
913 </when> | |
914 <when value="LeaveOneOut"> | |
915 </when> | |
916 <when value="LeavePOut"> | |
917 <param argument="p" type="integer" value="" label="p" help="Integer. Size of the test sets." /> | |
918 </when> | |
919 <when value="RepeatedKFold"> | |
920 <expand macro="cv_n_splits" value="5" /> | |
921 <param argument="n_repeats" type="integer" value="10" label="n_repeats" help="Number of times cross-validator needs to be repeated." /> | |
922 <expand macro="random_state" /> | |
923 </when> | |
924 <when value="RepeatedStratifiedKFold"> | |
925 <expand macro="cv_n_splits" value="5" /> | |
926 <param argument="n_repeats" type="integer" value="10" label="n_repeats" help="Number of times cross-validator needs to be repeated." /> | |
927 <expand macro="random_state" /> | |
928 </when> | |
929 <when value="ShuffleSplit"> | |
930 <expand macro="cv_n_splits" value="10" help="Number of re-shuffling and splitting iterations." /> | |
931 <expand macro="cv_test_size" value="0.1" /> | |
932 <expand macro="random_state" /> | |
933 </when> | |
934 <when value="StratifiedShuffleSplit"> | |
935 <expand macro="cv_n_splits" value="10" help="Number of re-shuffling and splitting iterations." /> | |
936 <expand macro="cv_test_size" value="0.1" /> | |
937 <expand macro="random_state" /> | |
938 </when> | |
939 <when value="TimeSeriesSplit"> | |
940 <expand macro="cv_n_splits" /> | |
941 <param argument="max_train_size" type="integer" value="" optional="true" label="Maximum size of the training set" help="Maximum size for a single training set." /> | |
942 </when> | |
943 <when value="PredefinedSplit"> | |
944 <param argument="test_fold" type="text" value="" area="true" label="test_fold" help="List, e.g., [0, 1, -1, 1], represents two test sets, [X[0]] and [X[1], X[3]], X[2] is excluded from any test set due to '-1'." /> | |
945 </when> | |
946 <when value="OrderedKFold"> | |
947 <expand macro="cv_n_splits" /> | |
948 <expand macro="cv_shuffle" /> | |
949 <expand macro="random_state" /> | |
950 </when> | |
951 <when value="RepeatedOrderedKFold"> | |
952 <expand macro="cv_n_splits" /> | |
953 <param argument="n_repeats" type="integer" value="5" /> | |
954 <expand macro="random_state" /> | |
955 </when> | |
956 <yield /> | |
957 </xml> | |
958 | |
959 <xml name="cv"> | |
960 <conditional name="cv_selector"> | |
961 <param name="selected_cv" type="select" label="Select the cv splitter:"> | |
962 <expand macro="cv_splitter"> | |
963 <option value="GroupKFold">GroupKFold</option> | |
964 <option value="GroupShuffleSplit">GroupShuffleSplit</option> | |
965 <option value="LeaveOneGroupOut">LeaveOneGroupOut</option> | |
966 <option value="LeavePGroupsOut">LeavePGroupsOut</option> | |
967 </expand> | |
968 </param> | |
969 <expand macro="cv_splitter_options"> | |
970 <when value="GroupKFold"> | |
971 <expand macro="cv_n_splits" /> | |
972 <expand macro="cv_groups" /> | |
37 </when> | 973 </when> |
38 <when value="advanced"> | 974 <when value="GroupShuffleSplit"> |
975 <expand macro="cv_n_splits" value="5" /> | |
976 <expand macro="cv_test_size" /> | |
977 <expand macro="random_state" /> | |
978 <expand macro="cv_groups" /> | |
979 </when> | |
980 <when value="LeaveOneGroupOut"> | |
981 <expand macro="cv_groups" /> | |
982 </when> | |
983 <when value="LeavePGroupsOut"> | |
984 <param argument="n_groups" type="integer" value="" label="n_groups" help="Number of groups (p) to leave out in the test split." /> | |
985 <expand macro="cv_groups" /> | |
986 </when> | |
987 </expand> | |
988 </conditional> | |
989 </xml> | |
990 | |
991 <xml name="cv_reduced" token_label="Select the cv splitter"> | |
992 <conditional name="cv_selector"> | |
993 <param name="selected_cv" type="select" label="@LABEL@"> | |
994 <expand macro="cv_splitter" /> | |
995 </param> | |
996 <expand macro="cv_splitter_options" /> | |
997 </conditional> | |
998 </xml> | |
999 | |
1000 <xml name="cv_n_splits" token_value="3" token_help="Number of folds. Must be at least 2."> | |
1001 <param argument="n_splits" type="integer" value="@VALUE@" min="1" label="n_splits" help="@HELP@" /> | |
1002 </xml> | |
1003 | |
1004 <xml name="cv_shuffle"> | |
1005 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Whether to shuffle data before splitting" /> | |
1006 </xml> | |
1007 | |
1008 <xml name="cv_test_size" token_value="0.2"> | |
1009 <param argument="test_size" type="float" value="@VALUE@" min="0.0" label="Portion or number of the test set" help="0.0-1.0, proportion of the dataset to include in the test split; >1, integer only, the absolute number of test samples " /> | |
1010 </xml> | |
1011 | |
1012 <xml name="cv_groups"> | |
1013 <section name="groups_selector" title="Groups column selector" expanded="true"> | |
1014 <param name="infile_g" type="data" format="tabular" label="Choose dataset containing groups info:" /> | |
1015 <param name="header_g" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | |
1016 <conditional name="column_selector_options_g"> | |
1017 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option_g" col_name="col_g" multiple="False" infile="infile_g" /> | |
1018 </conditional> | |
1019 </section> | |
1020 </xml> | |
1021 | |
1022 <xml name="train_test_split_params"> | |
1023 <conditional name="split_algos"> | |
1024 <param name="shuffle" type="select" label="Select the splitting method"> | |
1025 <option value="None">No shuffle</option> | |
1026 <option value="simple" selected="true">ShuffleSplit</option> | |
1027 <option value="stratified">StratifiedShuffleSplit -- target values serve as class labels</option> | |
1028 <option value="group">GroupShuffleSplit or split by group names</option> | |
1029 </param> | |
1030 <when value="None"> | |
1031 <expand macro="train_test_split_test_size" /> | |
1032 </when> | |
1033 <when value="simple"> | |
1034 <expand macro="train_test_split_test_size" /> | |
1035 <expand macro="random_state" /> | |
1036 </when> | |
1037 <when value="stratified"> | |
1038 <expand macro="train_test_split_test_size" /> | |
1039 <expand macro="random_state" /> | |
1040 </when> | |
1041 <when value="group"> | |
1042 <expand macro="train_test_split_test_size" optional="true" /> | |
1043 <expand macro="random_state" /> | |
1044 <param argument="group_names" type="text" value="" optional="true" label="Type in group names instead" help="For example: chr6, chr7. This parameter is optional. If used, it will override the holdout size and random seed." /> | |
1045 <yield /> | |
1046 </when> | |
1047 </conditional> | |
1048 <!--param argument="train_size" type="float" optional="True" value="" label="Train size:"/>--> | |
1049 </xml> | |
1050 | |
1051 <xml name="train_test_split_test_size" token_optional="false"> | |
1052 <param name="test_size" type="float" value="0.2" optional="@OPTIONAL@" label="Holdout size" help="Leass than 1, for preportion; greater than 1 (integer), for number of samples." /> | |
1053 </xml> | |
1054 | |
1055 <xml name="feature_selection_algorithms"> | |
1056 <option value="SelectKBest" selected="true">SelectKBest - Select features according to the k highest scores</option> | |
1057 <option value="GenericUnivariateSelect">GenericUnivariateSelect - Univariate feature selector with configurable strategy</option> | |
1058 <option value="SelectPercentile">SelectPercentile - Select features according to a percentile of the highest scores</option> | |
1059 <option value="SelectFpr">SelectFpr - Filter: Select the p-values below alpha based on a FPR test</option> | |
1060 <option value="SelectFdr">SelectFdr - Filter: Select the p-values for an estimated false discovery rate</option> | |
1061 <option value="SelectFwe">SelectFwe - Filter: Select the p-values corresponding to Family-wise error rate</option> | |
1062 <option value="VarianceThreshold">VarianceThreshold - Feature selector that removes all low-variance features</option> | |
1063 <option value="SelectFromModel">SelectFromModel - Meta-transformer for selecting features based on importance weights</option> | |
1064 <option value="RFE">RFE - Feature ranking with recursive feature elimination</option> | |
1065 <option value="RFECV">RFECV - Feature ranking with recursive feature elimination and cross-validated selection of the best number of features</option> | |
1066 <yield /> | |
1067 </xml> | |
1068 | |
1069 <xml name="feature_selection_algorithm_details"> | |
1070 <when value="GenericUnivariateSelect"> | |
1071 <expand macro="feature_selection_score_function" /> | |
1072 <section name="options" title="Advanced Options" expanded="False"> | |
1073 <param argument="mode" type="select" label="Feature selection mode"> | |
1074 <option value="percentile">percentile</option> | |
1075 <option value="k_best">k_best</option> | |
1076 <option value="fpr">fpr</option> | |
1077 <option value="fdr">fdr</option> | |
1078 <option value="fwe">fwe</option> | |
1079 </param> | |
1080 <param argument="param" type="float" value="" optional="true" label="Parameter of the corresponding mode" help="float or int depending on the feature selection mode" /> | |
1081 </section> | |
1082 </when> | |
1083 <when value="SelectPercentile"> | |
1084 <expand macro="feature_selection_score_function" /> | |
1085 <section name="options" title="Advanced Options" expanded="False"> | |
1086 <param argument="percentile" type="integer" value="10" optional="True" label="Percent of features to keep" /> | |
1087 </section> | |
1088 </when> | |
1089 <when value="SelectKBest"> | |
1090 <expand macro="feature_selection_score_function" /> | |
1091 <section name="options" title="Advanced Options" expanded="False"> | |
1092 <param argument="k" type="integer" value="10" optional="True" label="Number of top features to select" help="No 'all' option is supported." /> | |
1093 </section> | |
1094 </when> | |
1095 <when value="SelectFpr"> | |
1096 <expand macro="feature_selection_score_function" /> | |
1097 <section name="options" title="Advanced Options" expanded="False"> | |
1098 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest p-value for features to be kept." /> | |
1099 </section> | |
1100 </when> | |
1101 <when value="SelectFdr"> | |
1102 <expand macro="feature_selection_score_function" /> | |
1103 <section name="options" title="Advanced Options" expanded="False"> | |
1104 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest uncorrected p-value for features to keep." /> | |
1105 </section> | |
1106 </when> | |
1107 <when value="SelectFwe"> | |
1108 <expand macro="feature_selection_score_function" /> | |
1109 <section name="options" title="Advanced Options" expanded="False"> | |
1110 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest uncorrected p-value for features to keep." /> | |
1111 </section> | |
1112 </when> | |
1113 <when value="VarianceThreshold"> | |
1114 <section name="options" title="Options" expanded="False"> | |
1115 <param argument="threshold" type="float" value="0.0" optional="True" label="Threshold" help="Features with a training-set variance lower than this threshold will be removed." /> | |
1116 </section> | |
1117 </when> | |
1118 </xml> | |
1119 | |
1120 <xml name="feature_selection_SelectFromModel"> | |
1121 <when value="SelectFromModel"> | |
1122 <conditional name="model_inputter"> | |
1123 <param name="input_mode" type="select" label="Construct a new estimator from a selection list?"> | |
1124 <option value="new" selected="true">Yes</option> | |
1125 <option value="prefitted">No. Load a prefitted estimator</option> | |
1126 </param> | |
1127 <when value="new"> | |
1128 <expand macro="estimator_selector_fs" /> | |
1129 </when> | |
1130 <when value="prefitted"> | |
1131 <param name="fitted_estimator" type="data" format='zip' label="Load a prefitted estimator" /> | |
39 </when> | 1132 </when> |
40 </conditional> | 1133 </conditional> |
41 </when> | 1134 <expand macro="feature_selection_SelectFromModel_options" /> |
42 <when value="train"> | 1135 </when> |
43 <conditional name="selected_algorithms"> | 1136 </xml> |
44 <yield /> | 1137 |
1138 <xml name="feature_selection_SelectFromModel_no_prefitted"> | |
1139 <when value="SelectFromModel"> | |
1140 <conditional name="model_inputter"> | |
1141 <param name="input_mode" type="select" label="Construct a new estimator from a selection list?"> | |
1142 <option value="new" selected="true">Yes</option> | |
1143 </param> | |
1144 <when value="new"> | |
1145 <expand macro="estimator_selector_all" /> | |
1146 </when> | |
45 </conditional> | 1147 </conditional> |
46 </when> | 1148 <expand macro="feature_selection_SelectFromModel_options" /> |
47 </conditional> | 1149 </when> |
48 </xml> | 1150 </xml> |
49 | 1151 |
50 <xml name="advanced_section"> | 1152 <xml name="feature_selection_SelectFromModel_options"> |
51 <section name="options" title="Advanced Options" expanded="False"> | 1153 <section name="options" title="Advanced Options" expanded="False"> |
52 <yield /> | 1154 <param argument="threshold" type="text" value="" optional="true" label="threshold" help="The threshold value to use for feature selection. e.g. 'mean', 'median', '1.25*mean'." /> |
53 </section> | 1155 <param argument="norm_order" type="integer" value="1" label="norm_order" help="Order of the norm used to filter the vectors of coefficients below threshold in the case where the coef_ attribute of the estimator is of dimension 2. " /> |
54 </xml> | 1156 <param argument="max_features" type="integer" value="" optional="true" label="The maximum number of features selected scoring above threshold" help="To disable threshold and only select based on max_features, set threshold=-np.inf." /> |
55 | 1157 </section> |
56 | 1158 </xml> |
57 <!--Generalized Linear Models--> | 1159 |
58 <xml name="loss" token_help=" " token_select="false"> | 1160 <xml name="feature_selection_RFE"> |
59 <param argument="loss" type="select" label="Loss function" help="@HELP@"> | 1161 <when value="RFE"> |
60 <option value="squared_loss" selected="@SELECT@">squared loss</option> | 1162 <yield /> |
61 <option value="huber">huber</option> | 1163 <section name="options" title="Advanced Options" expanded="False"> |
62 <option value="epsilon_insensitive">epsilon insensitive</option> | 1164 <param argument="n_features_to_select" type="integer" value="" optional="true" label="n_features_to_select" help="The number of features to select. If None, half of the features are selected." /> |
63 <option value="squared_epsilon_insensitive">squared epsilon insensitive</option> | 1165 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " /> |
64 <yield/> | 1166 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." /> |
65 </param> | 1167 </section> |
66 </xml> | 1168 </when> |
67 | 1169 </xml> |
68 <xml name="penalty" token_help=" "> | 1170 |
69 <param argument="penalty" type="select" label="Penalty (regularization term)" help="@HELP@"> | 1171 <xml name="feature_selection_RFECV_fs"> |
70 <option value="l2" selected="true">l2</option> | 1172 <when value="RFECV"> |
71 <option value="l1">l1</option> | 1173 <yield /> |
72 <option value="elasticnet">elastic net</option> | 1174 <section name="options" title="Advanced Options" expanded="False"> |
73 <option value="none">none</option> | 1175 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " /> |
74 <yield/> | 1176 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected" /> |
75 </param> | 1177 <expand macro="cv" /> |
76 </xml> | 1178 <expand macro="scoring_selection" /> |
77 | 1179 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." /> |
78 <xml name="l1_ratio" token_default_value="0.15" token_help=" "> | 1180 </section> |
79 <param argument="l1_ratio" type="float" value="@DEFAULT_VALUE@" label="Elastic Net mixing parameter" help="@HELP@"/> | 1181 </when> |
80 </xml> | 1182 </xml> |
81 | 1183 |
82 <xml name="epsilon" token_default_value="0.1" token_help="Used if loss is ‘huber’, ‘epsilon_insensitive’, or ‘squared_epsilon_insensitive’. "> | 1184 <xml name="feature_selection_RFECV_pipeline"> |
83 <param argument="epsilon" type="float" value="@DEFAULT_VALUE@" label="Epsilon (epsilon-sensitive loss functions only)" help="@HELP@"/> | 1185 <when value="RFECV"> |
84 </xml> | 1186 <yield /> |
85 | 1187 <section name="options" title="Advanced Options" expanded="False"> |
86 <xml name="learning_rate_s" token_help=" " token_selected1="false" token_selected2="false"> | 1188 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " /> |
87 <param argument="learning_rate" type="select" optional="true" label="Learning rate schedule" help="@HELP@"> | 1189 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected" /> |
88 <option value="optimal" selected="@SELECTED1@">optimal</option> | 1190 <expand macro="cv_reduced" /> |
89 <option value="constant">constant</option> | 1191 <!-- TODO: group splitter support--> |
90 <option value="invscaling" selected="@SELECTED2@">inverse scaling</option> | 1192 <expand macro="scoring_selection" /> |
91 <yield/> | 1193 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." /> |
92 </param> | 1194 </section> |
93 </xml> | 1195 </when> |
94 | 1196 </xml> |
95 <xml name="eta0" token_default_value="0.0" token_help="Used with ‘constant’ or ‘invscaling’ schedules. "> | 1197 |
96 <param argument="eta0" type="float" value="@DEFAULT_VALUE@" label="Initial learning rate" help="@HELP@"/> | 1198 <xml name="feature_selection_DyRFECV_fs"> |
97 </xml> | 1199 <when value="DyRFECV"> |
98 | 1200 <yield /> |
99 <xml name="power_t" token_default_value="0.5" token_help=" "> | 1201 <section name="options" title="Advanced Options" expanded="False"> |
100 <param argument="power_t" type="float" value="@DEFAULT_VALUE@" label="Exponent for inverse scaling learning rate" help="@HELP@"/> | 1202 <param argument="step" type="text" size="30" value="1" label="step" optional="true" help="Default = 1. Support float, int and list."> |
101 </xml> | 1203 <sanitizer> |
102 | 1204 <valid initial="default"> |
103 <xml name="normalize" token_checked="false" token_help=" "> | 1205 <add value="[" /> |
104 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Normalize samples before training" help=" "/> | 1206 <add value="]" /> |
105 </xml> | 1207 </valid> |
106 | 1208 </sanitizer> |
107 <xml name="copy_X" token_checked="true" token_help=" "> | 1209 </param> |
108 <param argument="copy_X" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Use a copy of samples" help="If false, samples would be overwritten. "/> | 1210 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected" /> |
109 </xml> | 1211 <expand macro="cv" /> |
110 | 1212 <expand macro="scoring_selection" /> |
111 <xml name="ridge_params"> | 1213 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." /> |
112 <expand macro="normalize"/> | 1214 </section> |
113 <expand macro="alpha" default_value="1.0"/> | 1215 </when> |
114 <expand macro="fit_intercept"/> | 1216 </xml> |
115 <expand macro="max_iter" default_value=""/> | 1217 |
116 <expand macro="tol" default_value="0.001" help_text="Precision of the solution. "/> | 1218 <xml name="feature_selection_pipeline"> |
117 <!--class_weight--> | 1219 <!--compare to `feature_selection_fs`, no fitted estimator for SelectFromModel and no custom estimator for RFE and RFECV--> |
118 <expand macro="copy_X"/> | 1220 <conditional name="fs_algorithm_selector"> |
119 <param argument="solver" type="select" value="" label="Solver to use in the computational routines" help=" "> | 1221 <param name="selected_algorithm" type="select" label="Select a feature selection algorithm"> |
120 <option value="auto" selected="true">auto</option> | 1222 <expand macro="feature_selection_algorithms" /> |
121 <option value="svd">svd</option> | 1223 </param> |
122 <option value="cholesky">cholesky</option> | 1224 <expand macro="feature_selection_algorithm_details" /> |
123 <option value="lsqr">lsqr</option> | 1225 <expand macro="feature_selection_SelectFromModel_no_prefitted" /> |
124 <option value="sparse_cg">sparse_cg</option> | 1226 <expand macro="feature_selection_RFE"> |
125 <option value="sag">sag</option> | 1227 <expand macro="estimator_selector_all" /> |
126 </param> | 1228 </expand> |
127 <expand macro="random_state"/> | 1229 <expand macro="feature_selection_RFECV_pipeline"> |
128 </xml> | 1230 <expand macro="estimator_selector_all" /> |
129 | 1231 </expand> |
130 <!--Ensemble methods--> | 1232 <!-- TODO: add DyRFECV to pipeline--> |
131 <xml name="n_estimators" token_default_value="10" token_help=" "> | 1233 </conditional> |
132 <param argument="n_estimators" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of trees in the forest" help="@HELP@"/> | 1234 </xml> |
133 </xml> | 1235 |
134 | 1236 <xml name="feature_selection_fs"> |
135 <xml name="max_depth" token_default_value="" token_help=" "> | 1237 <conditional name="fs_algorithm_selector"> |
136 <param argument="max_depth" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum depth of the tree" help="@HELP@"/> | 1238 <param name="selected_algorithm" type="select" label="Select a feature selection algorithm"> |
137 </xml> | 1239 <expand macro="feature_selection_algorithms"> |
138 | 1240 <option value="DyRFECV">DyRFECV - Extended RFECV with changeable steps</option> |
139 <xml name="min_samples_split" token_type="integer" token_default_value="2" token_help=" "> | 1241 </expand> |
140 <param argument="min_samples_split" type="@TYPE@" optional="true" value="@DEFAULT_VALUE@" label="Minimum number of samples required to split an internal node" help="@HELP@"/> | 1242 </param> |
141 </xml> | 1243 <expand macro="feature_selection_algorithm_details" /> |
142 | 1244 <expand macro="feature_selection_SelectFromModel" /> |
143 <xml name="min_samples_leaf" token_type="integer" token_default_value="1" token_label="Minimum number of samples in newly created leaves" token_help=" "> | 1245 <expand macro="feature_selection_RFE"> |
144 <param argument="min_samples_leaf" type="@TYPE@" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP@"/> | 1246 <expand macro="estimator_selector_fs" /> |
145 </xml> | 1247 </expand> |
146 | 1248 <expand macro="feature_selection_RFECV_fs"> |
147 <xml name="min_weight_fraction_leaf" token_default_value="0.0" token_help=" "> | 1249 <expand macro="estimator_selector_fs" /> |
148 <param argument="min_weight_fraction_leaf" type="float" optional="true" value="@DEFAULT_VALUE@" label="Minimum weighted fraction of the input samples required to be at a leaf node" help="@HELP@"/> | 1250 </expand> |
149 </xml> | 1251 <expand macro="feature_selection_DyRFECV_fs"> |
150 | 1252 <expand macro="estimator_selector_fs" /> |
151 <xml name="max_leaf_nodes" token_default_value="" token_help=" "> | 1253 </expand> |
152 <param argument="max_leaf_nodes" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum number of leaf nodes in best-first method" help="@HELP@"/> | 1254 </conditional> |
153 </xml> | 1255 </xml> |
154 | 1256 |
155 <xml name="min_impurity_decrease" token_default_value="0" token_help=" "> | 1257 <xml name="feature_selection_score_function"> |
156 <param argument="min_impurity_decrease" type="float" value="@DEFAULT_VALUE@" optional="true" label="The threshold value of impurity for stopping node splitting" help="@HELP@"/> | 1258 <param argument="score_func" type="select" label="Select a score function"> |
157 </xml> | 1259 <option value="chi2">chi2 - Compute chi-squared stats between each non-negative feature and class</option> |
158 | 1260 <option value="f_classif">f_classif - Compute the ANOVA F-value for the provided sample</option> |
159 <xml name="bootstrap" token_checked="true" token_help=" "> | 1261 <option value="f_regression">f_regression - Univariate linear regression tests</option> |
160 <param argument="bootstrap" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Use bootstrap samples for building trees." help="@HELP@"/> | 1262 <option value="mutual_info_classif">mutual_info_classif - Estimate mutual information for a discrete target variable</option> |
161 </xml> | 1263 <option value="mutual_info_regression">mutual_info_regression - Estimate mutual information for a continuous target variable</option> |
162 | |
163 <xml name="criterion" token_help=" "> | |
164 <param argument="criterion" type="select" label="Function to measure the quality of a split" help=" "> | |
165 <option value="gini" selected="true">Gini impurity</option> | |
166 <option value="entropy">Information gain</option> | |
167 <yield/> | |
168 </param> | |
169 </xml> | |
170 | |
171 <xml name="criterion2" token_help=""> | |
172 <param argument="criterion" type="select" label="Function to measure the quality of a split" > | |
173 <option value="mse">mse - mean squared error</option> | |
174 <option value="mae">mae - mean absolute error</option> | |
175 <yield/> | |
176 </param> | |
177 </xml> | |
178 | |
179 <xml name="oob_score" token_checked="false" token_help=" "> | |
180 <param argument="oob_score" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Use out-of-bag samples to estimate the generalization error" help="@HELP@"/> | |
181 </xml> | |
182 | |
183 <xml name="max_features"> | |
184 <conditional name="select_max_features"> | |
185 <param argument="max_features" type="select" label="max_features"> | |
186 <option value="auto" selected="true">auto - max_features=n_features</option> | |
187 <option value="sqrt">sqrt - max_features=sqrt(n_features)</option> | |
188 <option value="log2">log2 - max_features=log2(n_features)</option> | |
189 <option value="number_input">I want to type the number in or input None type</option> | |
190 </param> | |
191 <when value="auto"> | |
192 </when> | |
193 <when value="sqrt"> | |
194 </when> | |
195 <when value="log2"> | |
196 </when> | |
197 <when value="number_input"> | |
198 <param name="num_max_features" type="float" value="" optional="true" label="Input max_features number:" help="If int, consider the number of features at each split; If float, then max_features is a percentage and int(max_features * n_features) features are considered at each split."/> | |
199 </when> | |
200 </conditional> | |
201 </xml> | |
202 | |
203 <xml name="verbose" token_default_value="0" token_help="If 1 then it prints progress and performance once in a while. If greater than 1 then it prints progress and performance for every tree."> | |
204 <param argument="verbose" type="integer" value="@DEFAULT_VALUE@" optional="true" label="Enable verbose output" help="@HELP@"/> | |
205 </xml> | |
206 | |
207 <xml name="learning_rate" token_default_value="1.0" token_help=" "> | |
208 <param argument="learning_rate" type="float" optional="true" value="@DEFAULT_VALUE@" label="Learning rate" help="@HELP@"/> | |
209 </xml> | |
210 | |
211 <xml name="subsample" token_help=" "> | |
212 <param argument="subsample" type="float" value="1.0" optional="true" label="The fraction of samples to be used for fitting the individual base learners" help="@HELP@"/> | |
213 </xml> | |
214 | |
215 <xml name="presort"> | |
216 <param argument="presort" type="select" label="Whether to presort the data to speed up the finding of best splits in fitting" > | |
217 <option value="auto" selected="true">auto</option> | |
218 <option value="true">true</option> | |
219 <option value="false">false</option> | |
220 </param> | |
221 </xml> | |
222 | |
223 <!-- LightGBM --> | |
224 <xml name="feature_fraction" token_help="LightGBM will randomly select part of the features for each iteration (tree) if feature_fraction is smaller than 1.0. For example, if you set it to 0.8, LightGBM will select 80% of features before training each tree."> | |
225 <param argument="feature_fraction" type="float" value="1.0" label="Proportion of features to train each tree" help="@HELP@"/> | |
226 </xml> | |
227 | |
228 <xml name="lambda_l1" token_help=" "> | |
229 <param argument="lambda_l1" type="float" value="0.0" label="L1 regularization" help="@HELP@"/> | |
230 </xml> | |
231 | |
232 <xml name="lambda_l2" token_help=" "> | |
233 <param argument="lambda_l2" type="float" value="0.0" label="L1 regularization" help="@HELP@"/> | |
234 </xml> | |
235 | |
236 <xml name="min_gain_to_split" token_help=" "> | |
237 <param argument="min_gain_to_split" type="float" value="0.0" label="Minimal gain to perform split" help="@HELP@"/> | |
238 </xml> | |
239 | |
240 <xml name="min_child_weight" token_help="Minimal sum hessian in one leaf. It can be used to deal with over-fitting."> | |
241 <param argument="min_child_weight" type="float" value="0.0" label="Minimal sum hessian in one leaf" help="@HELP@"/> | |
242 </xml> | |
243 | |
244 | |
245 <!--Parameters--> | |
246 <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."> | |
247 <param argument="tol" type="float" optional="true" value="@DEFAULT_VALUE@" label="Tolerance" help="@HELP_TEXT@"/> | |
248 </xml> | |
249 | |
250 <xml name="n_clusters" token_default_value="8"> | |
251 <param argument="n_clusters" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of clusters" help=" "/> | |
252 </xml> | |
253 | |
254 <xml name="fit_intercept" token_checked="true"> | |
255 <param argument="fit_intercept" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Estimate the intercept" help="If false, the data is assumed to be already centered."/> | |
256 </xml> | |
257 | |
258 <xml name="n_iter_no_change" token_default_value="5" token_help_text="Number of iterations with no improvement to wait before early stopping. "> | |
259 <param argument="n_iter_no_change" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@"/> | |
260 </xml> | |
261 | |
262 <xml name="shuffle" token_checked="true" token_help_text=" " token_label="Shuffle data after each iteration"> | |
263 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="@LABEL@" help="@HELP_TEXT@"/> | |
264 </xml> | |
265 | |
266 <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. default=None."> | |
267 <param argument="random_state" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Random seed number" help="@HELP_TEXT@"/> | |
268 </xml> | |
269 | |
270 <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."> | |
271 <param argument="warm_start" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Perform warm start" help="@HELP_TEXT@"/> | |
272 </xml> | |
273 | |
274 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term."> | |
275 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/> | |
276 </xml> | |
277 | |
278 <!--xml name="class_weight" token_default_value="" token_help_text=""> | |
279 <param argument="class_weight" type="" optional="true" value="@DEFAULT_VALUE@" label="" help="@HELP_TEXT@"/> | |
280 </xml--> | |
281 | |
282 <xml name="alpha" token_default_value="0.0001" token_help_text="Constant that multiplies the regularization term if regularization is used. "> | |
283 <param argument="alpha" type="float" optional="true" value="@DEFAULT_VALUE@" label="Regularization coefficient" help="@HELP_TEXT@"/> | |
284 </xml> | |
285 | |
286 <xml name="n_samples" token_default_value="100" token_help_text="The total number of points equally divided among clusters."> | |
287 <param argument="n_samples" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of samples" help="@HELP_TEXT@"/> | |
288 </xml> | |
289 | |
290 <xml name="n_features" token_default_value="2" token_help_text="Number of different numerical properties produced for each sample."> | |
291 <param argument="n_features" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of features" help="@HELP_TEXT@"/> | |
292 </xml> | |
293 | |
294 <xml name="noise" token_default_value="0.0" token_help_text="Floating point number. "> | |
295 <param argument="noise" type="float" optional="true" value="@DEFAULT_VALUE@" label="Standard deviation of the Gaussian noise added to the data" help="@HELP_TEXT@"/> | |
296 </xml> | |
297 | |
298 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term. "> | |
299 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/> | |
300 </xml> | |
301 | |
302 <xml name="max_iter" token_default_value="300" token_label="Maximum number of iterations per single run" token_help_text=" "> | |
303 <param argument="max_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/> | |
304 </xml> | |
305 | |
306 <xml name="n_init" token_default_value="10" > | |
307 <param argument="n_init" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of runs with different centroid seeds" help=" "/> | |
308 </xml> | |
309 | |
310 <xml name="init"> | |
311 <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."> | |
312 <option value="k-means++">k-means++</option> | |
313 <option value="random">random</option> | |
314 </param> | |
315 </xml> | |
316 | |
317 <xml name="gamma" token_default_value="1.0" token_label="Scaling parameter" token_help_text=" "> | |
318 <param argument="gamma" type="float" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/> | |
319 </xml> | |
320 | |
321 <xml name="degree" token_default_value="3" token_label="Degree of the polynomial" token_help_text=" "> | |
322 <param argument="degree" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/> | |
323 </xml> | |
324 | |
325 <xml name="coef0" token_default_value="1" token_label="Zero coefficient" token_help_text=" "> | |
326 <param argument="coef0" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/> | |
327 </xml> | |
328 | |
329 <xml name="pos_label" token_default_value=""> | |
330 <param argument="pos_label" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Label of the positive class" help=" "/> | |
331 </xml> | |
332 | |
333 <xml name="average"> | |
334 <param argument="average" type="select" optional="true" label="Averaging type" help=" "> | |
335 <option value="micro">Calculate metrics globally by counting the total true positives, false negatives and false positives. (micro)</option> | |
336 <option value="samples">Calculate metrics for each instance, and find their average. Only meaningful for multilabel. (samples)</option> | |
337 <option value="macro">Calculate metrics for each label, and find their unweighted mean. This does not take label imbalance into account. (macro)</option> | |
338 <option value="weighted">Calculate metrics for each label, and find their average, weighted by support (the number of true instances for each label). This alters ‘macro’ to account for label imbalance; it can result in an F-score that is not between precision and recall. (weighted)</option> | |
339 <option value="None">None</option> | |
340 <yield/> | |
341 </param> | |
342 </xml> | |
343 | |
344 <xml name="beta"> | |
345 <param argument="beta" type="float" value="1.0" label="The strength of recall versus precision in the F-score" help=" "/> | |
346 </xml> | |
347 | |
348 | |
349 <!--Data interface--> | |
350 | |
351 <xml name="samples_tabular" token_label1="Training samples dataset:" token_multiple1="false" token_multiple2="false"> | |
352 <param name="infile1" type="data" format="tabular" label="@LABEL1@"/> | |
353 <param name="header1" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | |
354 <conditional name="column_selector_options_1"> | |
355 <expand macro="samples_column_selector_options" multiple="@MULTIPLE1@"/> | |
356 </conditional> | |
357 <param name="infile2" type="data" format="tabular" label="Dataset containing class labels or target values:"/> | |
358 <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | |
359 <conditional name="column_selector_options_2"> | |
360 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="@MULTIPLE2@" infile="infile2"/> | |
361 </conditional> | |
362 <yield/> | |
363 </xml> | |
364 | |
365 <xml name="samples_column_selector_options" token_column_option="selected_column_selector_option" token_col_name="col1" token_multiple="False" token_infile="infile1"> | |
366 <param name="@COLUMN_OPTION@" type="select" label="Choose how to select data by column:"> | |
367 <option value="by_index_number" selected="true">Select columns by column index number(s)</option> | |
368 <option value="all_but_by_index_number">All columns EXCLUDING some by column index number(s)</option> | |
369 <option value="by_header_name">Select columns by column header name(s)</option> | |
370 <option value="all_but_by_header_name">All columns EXCLUDING some by column header name(s)</option> | |
371 <option value="all_columns">All columns</option> | |
372 </param> | |
373 <when value="by_index_number"> | |
374 <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" use_header_names="true" data_ref="@INFILE@" label="Select target column(s):"/> | |
375 </when> | |
376 <when value="all_but_by_index_number"> | |
377 <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" use_header_names="true" data_ref="@INFILE@" label="Select target column(s):"/> | |
378 </when> | |
379 <when value="by_header_name"> | |
380 <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="Comma-separated string. For example: target1,target2"/> | |
381 </when> | |
382 <when value="all_but_by_header_name"> | |
383 <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="Comma-separated string. For example: target1,target2"/> | |
384 </when> | |
385 <when value="all_columns"> | |
386 </when> | |
387 </xml> | |
388 | |
389 <xml name="clf_inputs_extended" token_label1=" " token_label2=" " token_multiple="False"> | |
390 <conditional name="true_columns"> | |
391 <param name="selected_input1" type="select" label="Select the input type of true labels dataset:"> | |
392 <option value="tabular" selected="true">Tabular</option> | |
393 <option value="sparse">Sparse</option> | |
394 </param> | |
395 <when value="tabular"> | |
396 <param name="infile1" type="data" label="@LABEL1@"/> | |
397 <param name="col1" type="data_column" data_ref="infile1" label="Select the target column:"/> | |
398 </when> | |
399 <when value="sparse"> | |
400 <param name="infile1" type="data" format="txt" label="@LABEL1@"/> | |
401 </when> | |
402 </conditional> | |
403 <conditional name="predicted_columns"> | |
404 <param name="selected_input2" type="select" label="Select the input type of predicted labels dataset:"> | |
405 <option value="tabular" selected="true">Tabular</option> | |
406 <option value="sparse">Sparse</option> | |
407 </param> | |
408 <when value="tabular"> | |
409 <param name="infile2" type="data" label="@LABEL2@"/> | |
410 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/> | |
411 </when> | |
412 <when value="sparse"> | |
413 <param name="infile2" type="data" format="txt" label="@LABEL1@"/> | |
414 </when> | |
415 </conditional> | |
416 </xml> | |
417 | |
418 <xml name="clf_inputs" token_label1="Dataset containing true labels (tabular):" token_label2="Dataset containing predicted values (tabular):" token_multiple1="False" token_multiple="False"> | |
419 <param name="infile1" type="data" format="tabular" label="@LABEL1@"/> | |
420 <param name="header1" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | |
421 <conditional name="column_selector_options_1"> | |
422 <expand macro="samples_column_selector_options" multiple="@MULTIPLE1@"/> | |
423 </conditional> | |
424 <param name="infile2" type="data" format="tabular" label="@LABEL2@"/> | |
425 <param name="header2" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | |
426 <conditional name="column_selector_options_2"> | |
427 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="@MULTIPLE@" infile="infile2"/> | |
428 </conditional> | |
429 </xml> | |
430 | |
431 <xml name="multiple_input" token_name="input_files" token_max_num="10" token_format="txt" token_label="Sparse matrix file (.mtx, .txt)" token_help_text="Specify a sparse matrix file in .txt format."> | |
432 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):"> | |
433 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/> | |
434 </repeat> | |
435 </xml> | |
436 | |
437 <xml name="sparse_target" token_label1="Select a sparse matrix:" token_label2="Select the tabular containing true labels:" token_multiple="False" token_format1="txt" token_format2="tabular" token_help1="" token_help2=""> | |
438 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/> | |
439 <expand macro="input_tabular_target"/> | |
440 </xml> | |
441 | |
442 <xml name="sl_mixed_input"> | |
443 <conditional name="input_options"> | |
444 <expand macro="data_input_options"/> | |
445 <expand macro="data_input_whens"/> | |
446 </conditional> | |
447 </xml> | |
448 | |
449 <xml name="sl_mixed_input_plus_sequence"> | |
450 <conditional name="input_options"> | |
451 <expand macro="data_input_options"> | |
452 <option value="seq_fasta">sequnences in a fasta file</option> | |
453 <option value="refseq_and_interval">reference genome and intervals</option> | |
454 </expand> | |
455 <expand macro="data_input_whens"> | |
456 <when value="seq_fasta"> | |
457 <expand macro="inputs_seq_fasta"/> | |
458 </when> | |
459 <when value="refseq_and_interval"> | |
460 <expand macro="inputs_refseq_and_interval"/> | |
461 </when> | |
462 </expand> | |
463 </conditional> | |
464 </xml> | |
465 | |
466 <xml name="data_input_options"> | |
467 <param name="selected_input" type="select" label="Select input type:"> | |
468 <option value="tabular" selected="true">tabular data</option> | |
469 <option value="sparse">sparse matrix</option> | |
470 <yield/> | |
471 </param> | |
472 </xml> | |
473 | |
474 <xml name="data_input_whens"> | |
475 <when value="tabular"> | |
476 <expand macro="samples_tabular" multiple1="true" multiple2="false"/> | |
477 </when> | |
478 <when value="sparse"> | |
479 <expand macro="sparse_target"/> | |
480 </when> | |
481 <yield/> | |
482 </xml> | |
483 | |
484 <xml name="input_tabular_target"> | |
485 <param name="infile2" type="data" format="tabular" label="Dataset containing class labels or target values:"/> | |
486 <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" /> | |
487 <conditional name="column_selector_options_2"> | |
488 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="false" infile="infile2"/> | |
489 </conditional> | |
490 </xml> | |
491 | |
492 <xml name="inputs_seq_fasta"> | |
493 <param name="fasta_path" type="data" format="fasta" label="Dataset containing fasta genomic/protein sequences" help="Sequences will be one-hot encoded to arrays."/> | |
494 <expand macro="input_tabular_target"/> | |
495 </xml> | |
496 | |
497 <xml name="inputs_refseq_and_interval"> | |
498 <param name="ref_genome_file" type="data" format="fasta" label="Dataset containing reference genomic sequence"/> | |
499 <param name="interval_file" type="data" format="interval" label="Dataset containing sequence intervals for training" help="interval. Sequences will be retrieved from the reference genome and one-hot encoded to training arrays."/> | |
500 <param name="target_file" type="data" format="bed" label="Dataset containing positions and features for target values." help="bed. The file will be compressed with `bgzip` and then indexed using `tabix`."/> | |
501 <param name="infile2" type="data" format="tabular" label="Dataset containing the feature list for prediction"/> | |
502 <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" /> | |
503 <conditional name="column_selector_options_2"> | |
504 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="true" infile="infile2"/> | |
505 </conditional> | |
506 </xml> | |
507 | |
508 <!--Advanced options--> | |
509 <xml name="nn_advanced_options"> | |
510 <section name="options" title="Advanced Options" expanded="False"> | |
511 <yield/> | |
512 <param argument="weights" type="select" label="Weight function" help="Used in prediction."> | |
513 <option value="uniform" selected="true">Uniform weights. All points in each neighborhood are weighted equally. (Uniform)</option> | |
514 <option value="distance">Weight points by the inverse of their distance. (Distance)</option> | |
515 </param> | |
516 <param argument="algorithm" type="select" label="Neighbor selection algorithm" help=" "> | |
517 <option value="auto" selected="true">Auto</option> | |
518 <option value="ball_tree">BallTree</option> | |
519 <option value="kd_tree">KDTree</option> | |
520 <option value="brute">Brute-force</option> | |
521 </param> | |
522 <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."/> | |
523 <!--param name="metric"--> | |
524 <!--param name="p"--> | |
525 <!--param name="metric_params"--> | |
526 </section> | |
527 </xml> | |
528 | |
529 <xml name="svc_advanced_options"> | |
530 <section name="options" title="Advanced Options" expanded="False"> | |
531 <yield/> | |
532 <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."> | |
533 <option value="rbf" selected="true">rbf</option> | |
534 <option value="linear">linear</option> | |
535 <option value="poly">poly</option> | |
536 <option value="sigmoid">sigmoid</option> | |
537 <option value="precomputed">precomputed</option> | |
538 </param> | 1264 </param> |
539 <param argument="degree" type="integer" optional="true" value="3" label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/> | 1265 </xml> |
540 <!--TODO: param argument="gamma" float, optional (default=’auto’) --> | 1266 |
541 <param argument="coef0" type="float" optional="true" value="0.0" label="Zero coefficient (polynomial and sigmoid kernels only)" | 1267 <xml name="model_validation_common_options"> |
542 help="Independent term in kernel function. dafault: 0.0 "/> | 1268 <expand macro="cv" /> |
543 <param argument="shrinking" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" | 1269 <expand macro="verbose" /> |
544 label="Use the shrinking heuristic" help=" "/> | 1270 <yield /> |
545 <param argument="probability" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" | 1271 </xml> |
546 label="Enable probability estimates. " help="This must be enabled prior to calling fit, and will slow down that method."/> | 1272 |
547 <!-- param argument="cache_size"--> | 1273 <xml name="scoring_selection"> |
548 <!--expand macro="class_weight"/--> | 1274 <conditional name="scoring"> |
549 <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. "/> | 1275 <param name="primary_scoring" type="select" multiple="false" label="Select the primary metric (scoring):" help="Metric to refit the best estimator."> |
550 <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."/> | 1276 <option value="default" selected="true">default with estimator</option> |
551 <!--param argument="decision_function_shape"--> | 1277 <option value="accuracy">Classification -- 'accuracy'</option> |
552 <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."/> | 1278 <option value="balanced_accuracy">Classification -- 'balanced_accuracy'</option> |
553 </section> | 1279 <option value="average_precision">Classification -- 'average_precision'</option> |
554 </xml> | 1280 <option value="f1">Classification -- 'f1'</option> |
555 | 1281 <option value="f1_micro">Classification -- 'f1_micro'</option> |
556 <xml name="spectral_clustering_advanced_options"> | 1282 <option value="f1_macro">Classification -- 'f1_macro'</option> |
557 <section name="options" title="Advanced Options" expanded="False"> | 1283 <option value="f1_weighted">Classification -- 'f1_weighted'</option> |
558 <expand macro="n_clusters"/> | 1284 <option value="f1_samples">Classification -- 'f1_samples'</option> |
559 <param argument="eigen_solver" type="select" value="" label="Eigen solver" help="The eigenvalue decomposition strategy to use."> | 1285 <option value="neg_log_loss">Classification -- 'neg_log_loss'</option> |
560 <option value="arpack" selected="true">arpack</option> | 1286 <option value="precision">Classification -- 'precision'</option> |
561 <option value="lobpcg">lobpcg</option> | 1287 <option value="precision_micro">Classification -- 'precision_micro'</option> |
562 <option value="amg">amg</option> | 1288 <option value="precision_macro">Classification -- 'precision_macro'</option> |
563 <!--None--> | 1289 <option value="precision_wighted">Classification -- 'precision_wighted'</option> |
1290 <option value="precision_samples">Classification -- 'precision_samples'</option> | |
1291 <option value="recall">Classification -- 'recall'</option> | |
1292 <option value="recall_micro">Classification -- 'recall_micro'</option> | |
1293 <option value="recall_macro">Classification -- 'recall_macro'</option> | |
1294 <option value="recall_wighted">Classification -- 'recall_wighted'</option> | |
1295 <option value="recall_samples">Classification -- 'recall_samples'</option> | |
1296 <option value="roc_auc">Classification -- 'roc_auc'</option> | |
1297 <option value="explained_variance">Regression -- 'explained_variance'</option> | |
1298 <option value="neg_mean_absolute_error">Regression -- 'neg_mean_absolute_error'</option> | |
1299 <option value="neg_mean_squared_error">Regression -- 'neg_mean_squared_error'</option> | |
1300 <option value="neg_mean_squared_log_error">Regression -- 'neg_mean_squared_log_error'</option> | |
1301 <option value="neg_median_absolute_error">Regression -- 'neg_median_absolute_error'</option> | |
1302 <option value="r2">Regression -- 'r2'</option> | |
1303 <option value="max_error">Regression -- 'max_error'</option> | |
1304 <option value="binarize_auc_scorer">anomaly detection -- binarize_auc_scorer</option> | |
1305 <option value="binarize_average_precision_scorer">anomaly detection -- binarize_average_precision_scorer</option> | |
1306 </param> | |
1307 <when value="default" /> | |
1308 <when value="accuracy"> | |
1309 <expand macro="secondary_scoring_selection_classification" /> | |
1310 </when> | |
1311 <when value="balanced_accuracy"> | |
1312 <expand macro="secondary_scoring_selection_classification" /> | |
1313 </when> | |
1314 <when value="average_precision"> | |
1315 <expand macro="secondary_scoring_selection_classification" /> | |
1316 </when> | |
1317 <when value="f1"> | |
1318 <expand macro="secondary_scoring_selection_classification" /> | |
1319 </when> | |
1320 <when value="f1_micro"> | |
1321 <expand macro="secondary_scoring_selection_classification" /> | |
1322 </when> | |
1323 <when value="f1_macro"> | |
1324 <expand macro="secondary_scoring_selection_classification" /> | |
1325 </when> | |
1326 <when value="f1_weighted"> | |
1327 <expand macro="secondary_scoring_selection_classification" /> | |
1328 </when> | |
1329 <when value="f1_samples"> | |
1330 <expand macro="secondary_scoring_selection_classification" /> | |
1331 </when> | |
1332 <when value="neg_log_loss"> | |
1333 <expand macro="secondary_scoring_selection_classification" /> | |
1334 </when> | |
1335 <when value="precision"> | |
1336 <expand macro="secondary_scoring_selection_classification" /> | |
1337 </when> | |
1338 <when value="precision_micro"> | |
1339 <expand macro="secondary_scoring_selection_classification" /> | |
1340 </when> | |
1341 <when value="precision_macro"> | |
1342 <expand macro="secondary_scoring_selection_classification" /> | |
1343 </when> | |
1344 <when value="precision_wighted"> | |
1345 <expand macro="secondary_scoring_selection_classification" /> | |
1346 </when> | |
1347 <when value="precision_samples"> | |
1348 <expand macro="secondary_scoring_selection_classification" /> | |
1349 </when> | |
1350 <when value="recall"> | |
1351 <expand macro="secondary_scoring_selection_classification" /> | |
1352 </when> | |
1353 <when value="recall_micro"> | |
1354 <expand macro="secondary_scoring_selection_classification" /> | |
1355 </when> | |
1356 <when value="recall_macro"> | |
1357 <expand macro="secondary_scoring_selection_classification" /> | |
1358 </when> | |
1359 <when value="recall_wighted"> | |
1360 <expand macro="secondary_scoring_selection_classification" /> | |
1361 </when> | |
1362 <when value="recall_samples"> | |
1363 <expand macro="secondary_scoring_selection_classification" /> | |
1364 </when> | |
1365 <when value="roc_auc"> | |
1366 <expand macro="secondary_scoring_selection_classification" /> | |
1367 </when> | |
1368 <when value="explained_variance"> | |
1369 <expand macro="secondary_scoring_selection_regression" /> | |
1370 </when> | |
1371 <when value="neg_mean_absolute_error"> | |
1372 <expand macro="secondary_scoring_selection_regression" /> | |
1373 </when> | |
1374 <when value="neg_mean_squared_error"> | |
1375 <expand macro="secondary_scoring_selection_regression" /> | |
1376 </when> | |
1377 <when value="neg_mean_squared_log_error"> | |
1378 <expand macro="secondary_scoring_selection_regression" /> | |
1379 </when> | |
1380 <when value="neg_median_absolute_error"> | |
1381 <expand macro="secondary_scoring_selection_regression" /> | |
1382 </when> | |
1383 <when value="r2"> | |
1384 <expand macro="secondary_scoring_selection_regression" /> | |
1385 </when> | |
1386 <when value="max_error"> | |
1387 <expand macro="secondary_scoring_selection_regression" /> | |
1388 </when> | |
1389 <when value="binarize_auc_scorer"> | |
1390 <expand macro="secondary_scoring_selection_anormaly" /> | |
1391 </when> | |
1392 <when value="binarize_average_precision_scorer"> | |
1393 <expand macro="secondary_scoring_selection_anormaly" /> | |
1394 </when> | |
1395 </conditional> | |
1396 </xml> | |
1397 | |
1398 <xml name="secondary_scoring_selection_classification"> | |
1399 <param name="secondary_scoring" type="select" multiple="true" label="Additional scoring used in multi-metric mode:" help="If the same metric with the primary is chosen, the metric will be ignored."> | |
1400 <option value="accuracy">Classification -- 'accuracy'</option> | |
1401 <option value="balanced_accuracy">Classification -- 'balanced_accuracy'</option> | |
1402 <option value="average_precision">Classification -- 'average_precision'</option> | |
1403 <option value="f1">Classification -- 'f1'</option> | |
1404 <option value="f1_micro">Classification -- 'f1_micro'</option> | |
1405 <option value="f1_macro">Classification -- 'f1_macro'</option> | |
1406 <option value="f1_weighted">Classification -- 'f1_weighted'</option> | |
1407 <option value="f1_samples">Classification -- 'f1_samples'</option> | |
1408 <option value="neg_log_loss">Classification -- 'neg_log_loss'</option> | |
1409 <option value="precision">Classification -- 'precision'</option> | |
1410 <option value="precision_micro">Classification -- 'precision_micro'</option> | |
1411 <option value="precision_macro">Classification -- 'precision_macro'</option> | |
1412 <option value="precision_wighted">Classification -- 'precision_wighted'</option> | |
1413 <option value="precision_samples">Classification -- 'precision_samples'</option> | |
1414 <option value="recall">Classification -- 'recall'</option> | |
1415 <option value="recall_micro">Classification -- 'recall_micro'</option> | |
1416 <option value="recall_macro">Classification -- 'recall_macro'</option> | |
1417 <option value="recall_wighted">Classification -- 'recall_wighted'</option> | |
1418 <option value="recall_samples">Classification -- 'recall_samples'</option> | |
1419 <option value="roc_auc">Classification -- 'roc_auc'</option> | |
564 </param> | 1420 </param> |
565 <expand macro="random_state"/> | 1421 </xml> |
566 <expand macro="n_init"/> | 1422 |
567 <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''."/> | 1423 <xml name="secondary_scoring_selection_regression"> |
568 <param argument="affinity" type="select" label="Affinity" help="Affinity kernel to use. "> | 1424 <param name="secondary_scoring" type="select" multiple="true" label="Additional scoring used in multi-metric mode:" help="If the same metric with the primary is chosen, the metric will be ignored."> |
569 <option value="rbf" selected="true">RBF</option> | 1425 <option value="explained_variance">Regression -- 'explained_variance'</option> |
570 <option value="precomputed">precomputed</option> | 1426 <option value="neg_mean_absolute_error">Regression -- 'neg_mean_absolute_error'</option> |
571 <option value="nearest_neighbors">Nearset neighbors</option> | 1427 <option value="neg_mean_squared_error">Regression -- 'neg_mean_squared_error'</option> |
1428 <option value="neg_mean_squared_log_error">Regression -- 'neg_mean_squared_log_error'</option> | |
1429 <option value="neg_median_absolute_error">Regression -- 'neg_median_absolute_error'</option> | |
1430 <option value="r2">Regression -- 'r2'</option> | |
1431 <option value="max_error">Regression -- 'max_error'</option> | |
572 </param> | 1432 </param> |
573 <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''"/> | 1433 </xml> |
574 <!--param argument="eigen_tol"--> | 1434 |
575 <param argument="assign_labels" type="select" label="Assign labels" help="The strategy to use to assign labels in the embedding space."> | 1435 <xml name="secondary_scoring_selection_anormaly"> |
576 <option value="kmeans" selected="true">kmeans</option> | 1436 <param name="secondary_scoring" type="select" multiple="true" label="Additional scoring used in multi-metric mode:" help="If the same metric with the primary is chosen, the metric will be ignored."> |
577 <option value="discretize">discretize</option> | 1437 <option value="binarize_auc_scorer">anomaly detection -- binarize_auc_scorer</option> |
1438 <option value="binarize_average_precision_scorer">anomaly detection -- binarize_average_precision_scorer</option> | |
578 </param> | 1439 </param> |
579 <param argument="degree" type="integer" optional="true" value="3" | 1440 </xml> |
580 label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/> | 1441 |
581 <param argument="coef0" type="integer" optional="true" value="1" | 1442 <xml name="pre_dispatch" token_type="hidden" token_default_value="all" token_help="Number of predispatched jobs for parallel execution"> |
582 label="Zero coefficient (polynomial and sigmoid kernels only)" help="Ignored by other kernels. dafault : 1 "/> | 1443 <param argument="pre_dispatch" type="@TYPE@" value="@DEFAULT_VALUE@" optional="true" label="pre_dispatch" help="@HELP@" /> |
583 <!--param argument="kernel_params"--> | 1444 </xml> |
584 </section> | 1445 |
585 </xml> | 1446 <xml name="estimator_and_hyperparameter"> |
586 | 1447 <param name="infile_estimator" type="data" format="zip" label="Choose the dataset containing pipeline/estimator object" /> |
587 <xml name="minibatch_kmeans_advanced_options"> | 1448 <section name="hyperparams_swapping" title="Hyperparameter Swapping" expanded="false"> |
588 <section name="options" title="Advanced Options" expanded="False"> | 1449 <param name="infile_params" type="data" format="tabular" optional="true" label="Choose the dataset containing hyperparameters for the pipeline/estimator above" help="This dataset could be the output of `get_params` in the `Estimator Attributes` tool." /> |
589 <expand macro="n_clusters"/> | 1450 <repeat name="param_set" min="1" max="30" title="New hyperparameter setting"> |
590 <expand macro="init"/> | 1451 <param name="sp_name" type="select" optional="true" label="Choose a parameter name (with current value)"> |
591 <expand macro="n_init" default_value="3"/> | 1452 <options from_dataset="infile_params" startswith="@"> |
592 <expand macro="max_iter" default_value="100"/> | 1453 <column name="name" index="2" /> |
593 <expand macro="tol" help_text="Early stopping heuristics based on normalized center change. To disable set to 0.0 ."/> | 1454 <column name="value" index="1" /> |
594 <expand macro="random_state"/> | 1455 <filter type="unique_value" name="unique_param" column="1" /> |
595 <param argument="batch_size" type="integer" optional="true" value="100" label="Batch size" help="Size of the mini batches."/> | 1456 </options> |
596 <!--param argument="compute_labels"--> | 1457 </param> |
597 <param argument="max_no_improvement" type="integer" optional="true" value="10" label="Maximum number of improvement attempts" help=" | 1458 <param name="sp_value" type="text" value="" optional="true" label="New value" help="Supports int, float, boolean, single quoted string, and selected object constructor. Similar to the `Parameter settings for search` section in `searchcv` tool except that only single value is expected here."> |
598 Convergence detection based on inertia (the consecutive number of mini batches that doe not yield an improvement on the smoothed inertia). | 1459 <sanitizer> |
599 To disable, set max_no_improvement to None. "/> | 1460 <valid initial="default"> |
600 <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 )"/> | 1461 <add value="'" /> |
601 <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."/> | 1462 <add value=""" /> |
602 </section> | 1463 </valid> |
603 </xml> | 1464 </sanitizer> |
604 | 1465 </param> |
605 <xml name="kmeans_advanced_options"> | 1466 </repeat> |
606 <section name="options" title="Advanced Options" expanded="False"> | |
607 <expand macro="n_clusters"/> | |
608 <expand macro="init"/> | |
609 <expand macro="n_init"/> | |
610 <expand macro="max_iter"/> | |
611 <expand macro="tol" default_value="0.0001" help_text="Relative tolerance with regards to inertia to declare convergence."/> | |
612 <!--param argument="precompute_distances"/--> | |
613 <expand macro="random_state"/> | |
614 <param argument="copy_x" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" 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."/> | |
615 <expand macro="kmeans_algorithm"/> | |
616 </section> | |
617 </xml> | |
618 | |
619 <xml name="kmeans_algorithm"> | |
620 <param argument="algorithm" type="select" label="K-means algorithm to use:"> | |
621 <option value="auto" selected="true">auto</option> | |
622 <option value="full">full</option> | |
623 <option value="elkan">elkan</option> | |
624 </param> | |
625 </xml> | |
626 | |
627 <xml name="birch_advanced_options"> | |
628 <section name="options" title="Advanced Options" expanded="False"> | |
629 <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."/> | |
630 <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."/> | |
631 <expand macro="n_clusters" default_value="3"/> | |
632 <!--param argument="compute_labels"/--> | |
633 </section> | |
634 </xml> | |
635 | |
636 <xml name="dbscan_advanced_options"> | |
637 <section name="options" title="Advanced Options" expanded="False"> | |
638 <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."/> | |
639 <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."/> | |
640 <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."/> | |
641 <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."> | |
642 <option value="auto" selected="true">auto</option> | |
643 <option value="ball_tree">ball_tree</option> | |
644 <option value="kd_tree">kd_tree</option> | |
645 <option value="brute">brute</option> | |
646 </param> | |
647 <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."/> | |
648 </section> | |
649 </xml> | |
650 | |
651 <xml name="clustering_algorithms_options"> | |
652 <conditional name="algorithm_options"> | |
653 <param name="selected_algorithm" type="select" label="Clustering Algorithm"> | |
654 <option value="KMeans" selected="true">KMeans</option> | |
655 <option value="SpectralClustering">Spectral Clustering</option> | |
656 <option value="MiniBatchKMeans">Mini Batch KMeans</option> | |
657 <option value="DBSCAN">DBSCAN</option> | |
658 <option value="Birch">Birch</option> | |
659 </param> | |
660 <when value="KMeans"> | |
661 <expand macro="kmeans_advanced_options"/> | |
662 </when> | |
663 <when value="DBSCAN"> | |
664 <expand macro="dbscan_advanced_options"/> | |
665 </when> | |
666 <when value="Birch"> | |
667 <expand macro="birch_advanced_options"/> | |
668 </when> | |
669 <when value="SpectralClustering"> | |
670 <expand macro="spectral_clustering_advanced_options"/> | |
671 </when> | |
672 <when value="MiniBatchKMeans"> | |
673 <expand macro="minibatch_kmeans_advanced_options"/> | |
674 </when> | |
675 </conditional> | |
676 </xml> | |
677 | |
678 <xml name="distance_metrics"> | |
679 <param argument="metric" type="select" label="Distance metric" help=" "> | |
680 <option value="euclidean" selected="true">euclidean</option> | |
681 <option value="cityblock">cityblock</option> | |
682 <option value="cosine">cosine</option> | |
683 <option value="l1">l1</option> | |
684 <option value="l2">l2</option> | |
685 <option value="manhattan">manhattan</option> | |
686 <yield/> | |
687 </param> | |
688 </xml> | |
689 | |
690 <xml name="distance_nonsparse_metrics"> | |
691 <option value="braycurtis">braycurtis</option> | |
692 <option value="canberra">canberra</option> | |
693 <option value="chebyshev">chebyshev</option> | |
694 <option value="correlation">correlation</option> | |
695 <option value="dice">dice</option> | |
696 <option value="hamming">hamming</option> | |
697 <option value="jaccard">jaccard</option> | |
698 <option value="kulsinski">kulsinski</option> | |
699 <option value="mahalanobis">mahalanobis</option> | |
700 <option value="matching">matching</option> | |
701 <option value="minkowski">minkowski</option> | |
702 <option value="rogerstanimoto">rogerstanimoto</option> | |
703 <option value="russellrao">russellrao</option> | |
704 <option value="seuclidean">seuclidean</option> | |
705 <option value="sokalmichener">sokalmichener</option> | |
706 <option value="sokalsneath">sokalsneath</option> | |
707 <option value="sqeuclidean">sqeuclidean</option> | |
708 <option value="yule">yule</option> | |
709 </xml> | |
710 | |
711 <xml name="pairwise_kernel_metrics"> | |
712 <param argument="metric" type="select" label="Pirwise Kernel metric" help=" "> | |
713 <option value="rbf" selected="true">rbf</option> | |
714 <option value="sigmoid">sigmoid</option> | |
715 <option value="polynomial">polynomial</option> | |
716 <option value="linear" selected="true">linear</option> | |
717 <option value="chi2">chi2</option> | |
718 <option value="additive_chi2">additive_chi2</option> | |
719 </param> | |
720 </xml> | |
721 | |
722 <xml name="sparse_pairwise_metric_functions"> | |
723 <param name="selected_metric_function" type="select" label="Select the pairwise metric you want to compute:"> | |
724 <option value="euclidean_distances" selected="true">Euclidean distance matrix</option> | |
725 <option value="pairwise_distances">Distance matrix</option> | |
726 <option value="pairwise_distances_argmin">Minimum distances between one point and a set of points</option> | |
727 <yield/> | |
728 </param> | |
729 </xml> | |
730 | |
731 <xml name="pairwise_metric_functions"> | |
732 <option value="additive_chi2_kernel" >Additive chi-squared kernel</option> | |
733 <option value="chi2_kernel">Exponential chi-squared kernel</option> | |
734 <option value="linear_kernel">Linear kernel</option> | |
735 <option value="manhattan_distances">L1 distances</option> | |
736 <option value="pairwise_kernels">Kernel</option> | |
737 <option value="polynomial_kernel">Polynomial kernel</option> | |
738 <option value="rbf_kernel">Gaussian (rbf) kernel</option> | |
739 <option value="laplacian_kernel">Laplacian kernel</option> | |
740 </xml> | |
741 | |
742 <xml name="sparse_pairwise_condition"> | |
743 <when value="pairwise_distances"> | |
744 <section name="options" title="Advanced Options" expanded="False"> | |
745 <expand macro="distance_metrics"> | |
746 <yield/> | |
747 </expand> | |
748 </section> | |
749 </when> | |
750 <when value="euclidean_distances"> | |
751 <section name="options" title="Advanced Options" expanded="False"> | |
752 <param argument="squared" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" | |
753 label="Return squared Euclidean distances" help=" "/> | |
754 </section> | |
755 </when> | |
756 </xml> | |
757 | |
758 <xml name="argmin_distance_condition"> | |
759 <when value="pairwise_distances_argmin"> | |
760 <section name="options" title="Advanced Options" expanded="False"> | |
761 <param argument="axis" type="integer" optional="true" value="1" label="Axis" help="Axis along which the argmin and distances are to be computed."/> | |
762 <expand macro="distance_metrics"> | |
763 <yield/> | |
764 </expand> | |
765 <param argument="batch_size" type="integer" optional="true" value="500" label="Batch size" help="Number of rows to be processed in each batch run."/> | |
766 </section> | |
767 </when> | |
768 </xml> | |
769 | |
770 <xml name="sparse_preprocessors"> | |
771 <param name="selected_pre_processor" type="select" label="Select a preprocessor:"> | |
772 <option value="StandardScaler" selected="true">Standard Scaler (Standardizes features by removing the mean and scaling to unit variance)</option> | |
773 <option value="Binarizer">Binarizer (Binarizes data)</option> | |
774 <option value="MaxAbsScaler">Max Abs Scaler (Scales features by their maximum absolute value)</option> | |
775 <option value="Normalizer">Normalizer (Normalizes samples individually to unit norm)</option> | |
776 <yield/> | |
777 </param> | |
778 </xml> | |
779 | |
780 <xml name="sparse_preprocessors_ext"> | |
781 <expand macro="sparse_preprocessors"> | |
782 <option value="KernelCenterer">Kernel Centerer (Centers a kernel matrix)</option> | |
783 <option value="MinMaxScaler">Minmax Scaler (Scales features to a range)</option> | |
784 <option value="PolynomialFeatures">Polynomial Features (Generates polynomial and interaction features)</option> | |
785 <option value="RobustScaler">Robust Scaler (Scales features using outlier-invariance statistics)</option> | |
786 <option value="QuantileTransformer">QuantileTransformer (Transform features using quantiles information)</option> | |
787 <option value="PowerTransformer">PowerTransformer (Apply a power transform featurewise to make data more Gaussian-like)</option> | |
788 <option value="KBinsDiscretizer">KBinsDiscretizer (Bin continuous data into intervals.)</option> | |
789 </expand> | |
790 </xml> | |
791 | |
792 <xml name="sparse_preprocessor_options"> | |
793 <when value="Binarizer"> | |
794 <section name="options" title="Advanced Options" expanded="False"> | |
795 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" | |
796 label="Use a copy of data for precomputing binarization" help=" "/> | |
797 <param argument="threshold" type="float" optional="true" value="0.0" | |
798 label="Threshold" | |
799 help="Feature values below or equal to this are replaced by 0, above it by 1. Threshold may not be less than 0 for operations on sparse matrices. "/> | |
800 </section> | 1467 </section> |
801 </when> | 1468 </xml> |
802 <when value="StandardScaler"> | 1469 |
803 <section name="options" title="Advanced Options" expanded="False"> | 1470 <xml name="search_cv_options"> |
804 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" | 1471 <expand macro="scoring_selection" /> |
805 label="Use a copy of data for performing inplace scaling" help=" "/> | 1472 <expand macro="model_validation_common_options" /> |
806 <param argument="with_mean" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" | 1473 <!--expand macro="pre_dispatch" default_value="2*n_jobs" help="Controls the number of jobs that get dispatched during parallel execution"/--> |
807 label="Center the data before scaling" help=" "/> | 1474 <param argument="iid" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="iid" help="If True, data is identically distributed across the folds" /> |
808 <param argument="with_std" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" | 1475 <!--param argument="refit" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="refit" help="Refit an estimator using the best found parameters on the whole dataset. Be aware that `refit=True` invokes extra computation, but it's REQUIRED for outputting the best estimator!"/> --> |
809 label="Scale the data to unit variance (or unit standard deviation)" help=" "/> | 1476 <param argument="error_score" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Raise fit error:" help="If false, the metric score is assigned to NaN if an error occurs in estimator fitting and FitFailedWarning is raised." /> |
810 </section> | 1477 <param argument="return_train_score" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="return_train_score" help="" /> |
811 </when> | 1478 </xml> |
812 <when value="MaxAbsScaler"> | 1479 |
813 <section name="options" title="Advanced Options" expanded="False"> | 1480 <xml name="estimator_module_options"> |
814 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" | 1481 <option value="svm" selected="true">sklearn.svm</option> |
815 label="Use a copy of data for precomputing scaling" help=" "/> | 1482 <option value="linear_model">sklearn.linear_model</option> |
816 </section> | 1483 <option value="ensemble">sklearn.ensemble</option> |
817 </when> | 1484 <option value="naive_bayes">sklearn.naive_bayes</option> |
818 <when value="Normalizer"> | 1485 <option value="tree">sklearn.tree</option> |
819 <section name="options" title="Advanced Options" expanded="False"> | 1486 <option value="neighbors">sklearn.neighbors</option> |
820 <param argument="norm" type="select" optional="true" label="The norm to use to normalize non zero samples" help=" "> | 1487 <option value="xgboost">xgboost</option> |
821 <option value="l1" selected="true">l1</option> | 1488 <yield /> |
822 <option value="l2">l2</option> | 1489 </xml> |
823 <option value="max">max</option> | 1490 |
1491 <xml name="estimator_suboptions"> | |
1492 <when value="svm"> | |
1493 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
1494 <option value="LinearSVC" selected="true">LinearSVC</option> | |
1495 <option value="LinearSVR">LinearSVR</option> | |
1496 <option value="NuSVC">NuSVC</option> | |
1497 <option value="NuSVR">NuSVR</option> | |
1498 <option value="OneClassSVM">OneClassSVM</option> | |
1499 <option value="SVC">SVC</option> | |
1500 <option value="SVR">SVR</option> | |
1501 </param> | |
1502 <expand macro="estimator_params_text" /> | |
1503 </when> | |
1504 <when value="linear_model"> | |
1505 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
1506 <option value="ARDRegression" selected="true">ARDRegression</option> | |
1507 <option value="BayesianRidge">BayesianRidge</option> | |
1508 <option value="ElasticNet">ElasticNet</option> | |
1509 <option value="ElasticNetCV">ElasticNetCV</option> | |
1510 <option value="HuberRegressor">HuberRegressor</option> | |
1511 <option value="Lars">Lars</option> | |
1512 <option value="LarsCV">LarsCV</option> | |
1513 <option value="Lasso">Lasso</option> | |
1514 <option value="LassoCV">LassoCV</option> | |
1515 <option value="LassoLars">LassoLars</option> | |
1516 <option value="LassoLarsCV">LassoLarsCV</option> | |
1517 <option value="LassoLarsIC">LassoLarsIC</option> | |
1518 <option value="LinearRegression">LinearRegression</option> | |
1519 <option value="LogisticRegression">LogisticRegression</option> | |
1520 <option value="LogisticRegressionCV">LogisticRegressionCV</option> | |
1521 <option value="MultiTaskLasso">MultiTaskLasso</option> | |
1522 <option value="MultiTaskElasticNet">MultiTaskElasticNet</option> | |
1523 <option value="MultiTaskLassoCV">MultiTaskLassoCV</option> | |
1524 <option value="MultiTaskElasticNetCV">MultiTaskElasticNetCV</option> | |
1525 <option value="OrthogonalMatchingPursuit">OrthogonalMatchingPursuit</option> | |
1526 <option value="OrthogonalMatchingPursuitCV">OrthogonalMatchingPursuitCV</option> | |
1527 <option value="PassiveAggressiveClassifier">PassiveAggressiveClassifier</option> | |
1528 <option value="PassiveAggressiveRegressor">PassiveAggressiveRegressor</option> | |
1529 <option value="Perceptron">Perceptron</option> | |
1530 <option value="RANSACRegressor">RANSACRegressor</option> | |
1531 <option value="Ridge">Ridge</option> | |
1532 <option value="RidgeClassifier">RidgeClassifier</option> | |
1533 <option value="RidgeClassifierCV">RidgeClassifierCV</option> | |
1534 <option value="RidgeCV">RidgeCV</option> | |
1535 <option value="SGDClassifier">SGDClassifier</option> | |
1536 <option value="SGDRegressor">SGDRegressor</option> | |
1537 <option value="TheilSenRegressor">TheilSenRegressor</option> | |
1538 </param> | |
1539 <expand macro="estimator_params_text" /> | |
1540 </when> | |
1541 <when value="ensemble"> | |
1542 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
1543 <option value="AdaBoostClassifier" selected="true">AdaBoostClassifier</option> | |
1544 <option value="AdaBoostRegressor">AdaBoostRegressor</option> | |
1545 <option value="BaggingClassifier">BaggingClassifier</option> | |
1546 <option value="BaggingRegressor">BaggingRegressor</option> | |
1547 <option value="ExtraTreesClassifier">ExtraTreesClassifier</option> | |
1548 <option value="ExtraTreesRegressor">ExtraTreesRegressor</option> | |
1549 <option value="GradientBoostingClassifier">GradientBoostingClassifier</option> | |
1550 <option value="GradientBoostingRegressor">GradientBoostingRegressor</option> | |
1551 <option value="IsolationForest">IsolationForest</option> | |
1552 <option value="HistGradientBoostingClassifier">HistGradientBoostingClassifier</option> | |
1553 <option value="HistGradientBoostingRegressor">HistGradientBoostingRegressor</option> | |
1554 <option value="RandomForestClassifier">RandomForestClassifier</option> | |
1555 <option value="RandomForestRegressor">RandomForestRegressor</option> | |
1556 <option value="RandomTreesEmbedding">RandomTreesEmbedding</option> | |
1557 <!--option value="VotingClassifier">VotingClassifier</option--> | |
1558 </param> | |
1559 <expand macro="estimator_params_text" /> | |
1560 </when> | |
1561 <when value="naive_bayes"> | |
1562 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
1563 <option value="BernoulliNB" selected="true">BernoulliNB</option> | |
1564 <option value="GaussianNB">GaussianNB</option> | |
1565 <option value="MultinomialNB">MultinomialNB</option> | |
1566 </param> | |
1567 <expand macro="estimator_params_text" /> | |
1568 </when> | |
1569 <when value="tree"> | |
1570 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
1571 <option value="DecisionTreeClassifier" selected="true">DecisionTreeClassifier</option> | |
1572 <option value="DecisionTreeRegressor">DecisionTreeRegressor</option> | |
1573 <option value="ExtraTreeClassifier">ExtraTreeClassifier</option> | |
1574 <option value="ExtraTreeRegressor">ExtraTreeRegressor</option> | |
1575 </param> | |
1576 <expand macro="estimator_params_text" /> | |
1577 </when> | |
1578 <when value="neighbors"> | |
1579 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
1580 <option value="KNeighborsClassifier" selected="true">KNeighborsClassifier</option> | |
1581 <option value="KNeighborsRegressor">KNeighborsRegressor</option> | |
1582 <!--option value="BallTree">BallTree</option--> | |
1583 <!--option value="KDTree">KDTree</option--> | |
1584 <option value="KernelDensity">KernelDensity</option> | |
1585 <option value="LocalOutlierFactor">LocalOutlierFactor</option> | |
1586 <option value="RadiusNeighborsClassifier">RadiusNeighborsClassifier</option> | |
1587 <option value="RadiusNeighborsRegressor">RadiusNeighborsRegressor</option> | |
1588 <option value="NearestCentroid">NearestCentroid</option> | |
1589 <option value="NearestNeighbors">NearestNeighbors</option> | |
1590 </param> | |
1591 <expand macro="estimator_params_text" /> | |
1592 </when> | |
1593 <when value="xgboost"> | |
1594 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
1595 <option value="XGBRegressor" selected="true">XGBRegressor</option> | |
1596 <option value="XGBClassifier">XGBClassifier</option> | |
1597 </param> | |
1598 <expand macro="estimator_params_text" /> | |
1599 </when> | |
1600 <yield /> | |
1601 </xml> | |
1602 | |
1603 <xml name="estimator_selector_all"> | |
1604 <conditional name="estimator_selector"> | |
1605 <param name="selected_module" type="select" label="Choose the module that contains target estimator:"> | |
1606 <expand macro="estimator_module_options" /> | |
1607 </param> | |
1608 <expand macro="estimator_suboptions" /> | |
1609 </conditional> | |
1610 </xml> | |
1611 | |
1612 <xml name="estimator_selector_fs"> | |
1613 <conditional name="estimator_selector"> | |
1614 <param name="selected_module" type="select" label="Choose the module that contains target estimator:"> | |
1615 <expand macro="estimator_module_options"> | |
1616 <option value="custom_estimator">Load a custom estimator</option> | |
1617 </expand> | |
1618 </param> | |
1619 <expand macro="estimator_suboptions"> | |
1620 <when value="custom_estimator"> | |
1621 <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline:" /> | |
1622 </when> | |
1623 </expand> | |
1624 </conditional> | |
1625 </xml> | |
1626 | |
1627 <xml name="estimator_params_text" token_label="Type in parameter settings if different from default:" token_default_value='' token_help="Dictionary-capable, e.g., C=1, kernel='linear'. No double quotes. Leave this box blank for default estimator."> | |
1628 <param name="text_params" type="text" value="@DEFAULT_VALUE@" optional="true" label="@LABEL@" help="@HELP@"> | |
1629 <sanitizer> | |
1630 <valid initial="default"> | |
1631 <add value="'" /> | |
1632 </valid> | |
1633 </sanitizer> | |
824 </param> | 1634 </param> |
825 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" | 1635 </xml> |
826 label="Use a copy of data for precomputing row normalization" help=" "/> | 1636 |
827 </section> | 1637 <xml name="kernel_approximation_all"> |
828 </when> | 1638 <conditional name="kernel_approximation_selector"> |
829 <yield/> | 1639 <param name="select_algorithm" type="select" label="Choose a kernel approximation algorithm:"> |
830 </xml> | 1640 <option value="Nystroem" selected="true">Nystroem</option> |
831 | 1641 <option value="RBFSampler">RBFSampler</option> |
832 <xml name="sparse_preprocessor_options_ext"> | 1642 <option value="AdditiveChi2Sampler">AdditiveChi2Sampler</option> |
833 <expand macro="sparse_preprocessor_options"> | 1643 <option value="SkewedChi2Sampler">SkewedChi2Sampler</option> |
834 <when value="KernelCenterer"> | 1644 </param> |
835 <section name="options" title="Advanced Options" expanded="False"> | 1645 <when value="Nystroem"> |
1646 <expand macro="estimator_params_text" help="Default(=blank): coef0=None, degree=None, gamma=None, kernel='rbf', kernel_params=None, n_components=100, random_state=None. No double quotes" /> | |
1647 </when> | |
1648 <when value="RBFSampler"> | |
1649 <expand macro="estimator_params_text" help="Default(=blank): gamma=1.0, n_components=100, random_state=None." /> | |
1650 </when> | |
1651 <when value="AdditiveChi2Sampler"> | |
1652 <expand macro="estimator_params_text" help="Default(=blank): sample_interval=None, sample_steps=2." /> | |
1653 </when> | |
1654 <when value="SkewedChi2Sampler"> | |
1655 <expand macro="estimator_params_text" help="Default(=blank): n_components=100, random_state=None, skewedness=1.0." /> | |
1656 </when> | |
1657 </conditional> | |
1658 </xml> | |
1659 | |
1660 <xml name="matrix_decomposition_all"> | |
1661 <conditional name="matrix_decomposition_selector"> | |
1662 <param name="select_algorithm" type="select" label="Choose a matrix decomposition algorithm:"> | |
1663 <option value="DictionaryLearning" selected="true">DictionaryLearning</option> | |
1664 <option value="FactorAnalysis">FactorAnalysis</option> | |
1665 <option value="FastICA">FastICA</option> | |
1666 <option value="IncrementalPCA">IncrementalPCA</option> | |
1667 <option value="KernelPCA">KernelPCA</option> | |
1668 <option value="LatentDirichletAllocation">LatentDirichletAllocation</option> | |
1669 <option value="MiniBatchDictionaryLearning">MiniBatchDictionaryLearning</option> | |
1670 <option value="MiniBatchSparsePCA">MiniBatchSparsePCA</option> | |
1671 <option value="NMF">NMF</option> | |
1672 <option value="PCA">PCA</option> | |
1673 <option value="SparsePCA">SparsePCA</option> | |
1674 <!--option value="SparseCoder">SparseCoder</option--> | |
1675 <option value="TruncatedSVD">TruncatedSVD</option> | |
1676 </param> | |
1677 <when value="DictionaryLearning"> | |
1678 <expand macro="estimator_params_text" help="Default(=blank): alpha=1, code_init=None, dict_init=None, fit_algorithm='lars', max_iter=1000, n_components=None, random_state=None, split_sign=False, tol=1e-08, transform_algorithm='omp', transform_alpha=None, transform_n_nonzero_coefs=None, verbose=False." /> | |
1679 </when> | |
1680 <when value="FactorAnalysis"> | |
1681 <expand macro="estimator_params_text" help="Default(=blank): copy=True, iterated_power=3, max_iter=1000, n_components=None, noise_variance_init=None, random_state=0, svd_method='randomized', tol=0.01." /> | |
1682 </when> | |
1683 <when value="FastICA"> | |
1684 <expand macro="estimator_params_text" help="Default(=blank): algorithm='parallel', fun='logcosh', fun_args=None, max_iter=200, n_components=None, random_state=None, tol=0.0001, w_init=None, whiten=True. No double quotes." /> | |
1685 </when> | |
1686 <when value="IncrementalPCA"> | |
1687 <expand macro="estimator_params_text" help="Default(=blank): batch_size=None, copy=True, n_components=None, whiten=False." /> | |
1688 </when> | |
1689 <when value="KernelPCA"> | |
1690 <expand macro="estimator_params_text" help="Default(=blank): alpha=1.0, coef0=1, copy_X=True, degree=3, eigen_solver='auto', fit_inverse_transform=False, gamma=None, kernel='linear', kernel_params=None, max_iter=None, n_components=None, random_state=None, remove_zero_eig=False, tol=0. No double quotes." /> | |
1691 </when> | |
1692 <when value="LatentDirichletAllocation"> | |
1693 <expand macro="estimator_params_text" help="Default(=blank): batch_size=128, doc_topic_prior=None, evaluate_every=-1, learning_decay=0.7, learning_method=None, learning_offset=10.0, max_doc_update_iter=100, max_iter=10, mean_change_tol=0.001, n_components=10, n_topics=None, perp_tol=0.1, random_state=None, topic_word_prior=None, total_samples=1000000.0, verbose=0." /> | |
1694 </when> | |
1695 <when value="MiniBatchDictionaryLearning"> | |
1696 <expand macro="estimator_params_text" help="Default(=blank): alpha=1, batch_size=3, dict_init=None, fit_algorithm='lars', n_components=None, n_iter=1000, random_state=None, shuffle=True, split_sign=False, transform_algorithm='omp', transform_alpha=None, transform_n_nonzero_coefs=None, verbose=False." /> | |
1697 </when> | |
1698 <when value="MiniBatchSparsePCA"> | |
1699 <expand macro="estimator_params_text" help="Default(=blank): alpha=1, batch_size=3, callback=None, method='lars', n_components=None, n_iter=100, random_state=None, ridge_alpha=0.01, shuffle=True, verbose=False." /> | |
1700 </when> | |
1701 <when value="NMF"> | |
1702 <expand macro="estimator_params_text" help="Default(=blank): alpha=0.0, beta_loss='frobenius', init=None, l1_ratio=0.0, max_iter=200, n_components=None, random_state=None, shuffle=False, solver='cd', tol=0.0001, verbose=0." /> | |
1703 </when> | |
1704 <when value="PCA"> | |
1705 <expand macro="estimator_params_text" help="Default(=blank): copy=True, iterated_power='auto', n_components=None, random_state=None, svd_solver='auto', tol=0.0, whiten=False." /> | |
1706 </when> | |
1707 <when value="SparsePCA"> | |
1708 <expand macro="estimator_params_text" help="Default(=blank): U_init=None, V_init=None, alpha=1, max_iter=1000, method='lars', n_components=None, random_state=None, ridge_alpha=0.01, tol=1e-08, verbose=False." /> | |
1709 </when> | |
1710 <when value="TruncatedSVD"> | |
1711 <expand macro="estimator_params_text" help="Default(=blank): algorithm='randomized', n_components=2, n_iter=5, random_state=None, tol=0.0." /> | |
1712 </when> | |
1713 </conditional> | |
1714 </xml> | |
1715 | |
1716 <xml name="FeatureAgglomeration"> | |
1717 <conditional name="FeatureAgglomeration_selector"> | |
1718 <param name="select_algorithm" type="select" label="Choose the algorithm:"> | |
1719 <option value="FeatureAgglomeration" selected="true">FeatureAgglomeration</option> | |
1720 </param> | |
1721 <when value="FeatureAgglomeration"> | |
1722 <expand macro="estimator_params_text" help="Default(=blank): affinity='euclidean', compute_full_tree='auto', connectivity=None, linkage='ward', memory=None, n_clusters=2, pooling_func=np.mean." /> | |
1723 </when> | |
1724 </conditional> | |
1725 </xml> | |
1726 | |
1727 <xml name="skrebate"> | |
1728 <conditional name="skrebate_selector"> | |
1729 <param name="select_algorithm" type="select" label="Choose the algorithm:"> | |
1730 <option value="ReliefF">ReliefF</option> | |
1731 <option value="SURF">SURF</option> | |
1732 <option value="SURFstar">SURFstar</option> | |
1733 <option value="MultiSURF">MultiSURF</option> | |
1734 <option value="MultiSURFstar">MultiSURFstar</option> | |
1735 <!--option value="TuRF">TuRF</option> --> | |
1736 </param> | |
1737 <when value="ReliefF"> | |
1738 <expand macro="estimator_params_text" help="Default(=blank): discrete_threshold=10, n_features_to_select=10, n_neighbors=100, verbose=False." /> | |
1739 </when> | |
1740 <when value="SURF"> | |
1741 <expand macro="estimator_params_text" help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False." /> | |
1742 </when> | |
1743 <when value="SURFstar"> | |
1744 <expand macro="estimator_params_text" help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False." /> | |
1745 </when> | |
1746 <when value="MultiSURF"> | |
1747 <expand macro="estimator_params_text" help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False." /> | |
1748 </when> | |
1749 <when value="MultiSURFstar"> | |
1750 <expand macro="estimator_params_text" help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False." /> | |
1751 </when> | |
1752 <!--when value="TuRF"> | |
1753 <expand macro="estimator_params_text" help="Default(=blank): core_algorithm='ReliefF', discrete_threshold=10, n_features_to_select=10, n_neighbors=100, pct=0.5, verbose=False."/> | |
1754 </when> --> | |
1755 </conditional> | |
1756 </xml> | |
1757 | |
1758 <xml name="imbalanced_learn_sampling"> | |
1759 <conditional name="imblearn_selector"> | |
1760 <param name="select_algorithm" type="select" label="Choose the algorithm:"> | |
1761 <option value="under_sampling.ClusterCentroids" selected="true">under_sampling.ClusterCentroids</option> | |
1762 <option value="under_sampling.CondensedNearestNeighbour">under_sampling.CondensedNearestNeighbour</option> | |
1763 <option value="under_sampling.EditedNearestNeighbours">under_sampling.EditedNearestNeighbours</option> | |
1764 <option value="under_sampling.RepeatedEditedNearestNeighbours">under_sampling.RepeatedEditedNearestNeighbours</option> | |
1765 <option value="under_sampling.AllKNN">under_sampling.AllKNN</option> | |
1766 <option value="under_sampling.InstanceHardnessThreshold">under_sampling.InstanceHardnessThreshold</option> | |
1767 <option value="under_sampling.NearMiss">under_sampling.NearMiss</option> | |
1768 <option value="under_sampling.NeighbourhoodCleaningRule">under_sampling.NeighbourhoodCleaningRule</option> | |
1769 <option value="under_sampling.OneSidedSelection">under_sampling.OneSidedSelection</option> | |
1770 <option value="under_sampling.RandomUnderSampler">under_sampling.RandomUnderSampler</option> | |
1771 <option value="under_sampling.TomekLinks">under_sampling.TomekLinks</option> | |
1772 <option value="over_sampling.ADASYN">over_sampling.ADASYN</option> | |
1773 <option value="over_sampling.RandomOverSampler">over_sampling.RandomOverSampler</option> | |
1774 <option value="over_sampling.SMOTE">over_sampling.SMOTE</option> | |
1775 <option value="over_sampling.SVMSMOTE">over_sampling.SVMSMOTE</option> | |
1776 <option value="over_sampling.BorderlineSMOTE">over_sampling.BorderlineSMOTE</option> | |
1777 <option value="over_sampling.SMOTENC">over_sampling.SMOTENC</option> | |
1778 <option value="combine.SMOTEENN">combine.SMOTEENN</option> | |
1779 <option value="combine.SMOTETomek">combine.SMOTETomek</option> | |
1780 <option value="Z_RandomOverSampler">Z_RandomOverSampler - for regression</option> | |
1781 </param> | |
1782 <when value="under_sampling.ClusterCentroids"> | |
1783 <expand macro="estimator_params_text" help="Default(=blank): sampling_strategy='auto', random_state=None, estimator=None, voting='auto'." /> | |
1784 </when> | |
1785 <when value="under_sampling.CondensedNearestNeighbour"> | |
1786 <expand macro="estimator_params_text" help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=None, n_seeds_S=1." /> | |
1787 </when> | |
1788 <when value="under_sampling.EditedNearestNeighbours"> | |
1789 <expand macro="estimator_params_text" help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, max_iter=100, kind_sel='all'." /> | |
1790 </when> | |
1791 <when value="under_sampling.RepeatedEditedNearestNeighbours"> | |
1792 <expand macro="estimator_params_text" help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, max_iter=100, kind_sel='all'." /> | |
1793 </when> | |
1794 <when value="under_sampling.AllKNN"> | |
1795 <expand macro="estimator_params_text" help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, kind_sel='all', allow_minority=False." /> | |
1796 </when> | |
1797 <when value="under_sampling.InstanceHardnessThreshold"> | |
1798 <expand macro="estimator_params_text" help="Default(=blank): estimator=None, sampling_strategy='auto', random_state=None, cv=5." /> | |
1799 </when> | |
1800 <when value="under_sampling.NearMiss"> | |
1801 <expand macro="estimator_params_text" help="Default(=blank): sampling_strategy='auto', random_state=None, version=1, n_neighbors=3, n_neighbors_ver3=3." /> | |
1802 </when> | |
1803 <when value="under_sampling.NeighbourhoodCleaningRule"> | |
1804 <expand macro="estimator_params_text" help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, kind_sel='all', threshold_cleaning=0.5." /> | |
1805 </when> | |
1806 <when value="under_sampling.OneSidedSelection"> | |
1807 <expand macro="estimator_params_text" help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=None, n_seeds_S=1." /> | |
1808 </when> | |
1809 <when value="under_sampling.RandomUnderSampler"> | |
1810 <expand macro="estimator_params_text" help="Default(=blank): sampling_strategy='auto', random_state=None, replacement=False." /> | |
1811 </when> | |
1812 <when value="under_sampling.TomekLinks"> | |
1813 <expand macro="estimator_params_text" help="Default(=blank): sampling_strategy='auto', random_state=None." /> | |
1814 </when> | |
1815 <when value="over_sampling.ADASYN"> | |
1816 <expand macro="estimator_params_text" help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=5." /> | |
1817 </when> | |
1818 <when value="over_sampling.RandomOverSampler"> | |
1819 <expand macro="estimator_params_text" help="Default(=blank): sampling_strategy='auto', random_state=None." /> | |
1820 </when> | |
1821 <when value="over_sampling.SMOTE"> | |
1822 <expand macro="estimator_params_text" help="Default(=blank): sampling_strategy='auto', random_state=None, k_neighbors=5." /> | |
1823 </when> | |
1824 <when value="over_sampling.SVMSMOTE"> | |
1825 <expand macro="estimator_params_text" help="Default(=blank): sampling_strategy='auto', k_neighbors=5, m_neighbors=10, out_step=0.5, random_state=None, svm_estimator=None." /> | |
1826 </when> | |
1827 <when value="over_sampling.BorderlineSMOTE"> | |
1828 <expand macro="estimator_params_text" help="Default(=blank): sampling_strategy='auto', k_neighbors=5, kind='borderline-1', m_neighbors=10, random_state=None." /> | |
1829 </when> | |
1830 <when value="over_sampling.SMOTENC"> | |
1831 <expand macro="estimator_params_text" help="Default: categorical_features=[], sampling_strategy='auto', random_state=None, k_neighbors=5." /> | |
1832 </when> | |
1833 <when value="combine.SMOTEENN"> | |
1834 <expand macro="estimator_params_text" help="Default(=blank): sampling_strategy='auto', random_state=None, smote=None, enn=None." /> | |
1835 </when> | |
1836 <when value="combine.SMOTETomek"> | |
1837 <expand macro="estimator_params_text" help="Default(=blank): sampling_strategy='auto', random_state=None, smote=None, tomek=None." /> | |
1838 </when> | |
1839 <when value="Z_RandomOverSampler"> | |
1840 <expand macro="estimator_params_text" help="Default(=blank): sampling_strategy='auto', random_state=None, negative_thres=0, positive_thres=-1." /> | |
1841 </when> | |
1842 </conditional> | |
1843 </xml> | |
1844 | |
1845 <xml name="stacking_ensemble_inputs"> | |
1846 <section name="options" title="Advanced Options" expanded="false"> | |
1847 <yield /> | |
1848 <param argument="use_features_in_secondary" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" /> | |
1849 <param argument="store_train_meta_features" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" /> | |
836 </section> | 1850 </section> |
837 </when> | 1851 </xml> |
838 <when value="MinMaxScaler"> | 1852 |
839 <section name="options" title="Advanced Options" expanded="False"> | 1853 <xml name="stacking_base_estimator"> |
840 <param argument="feature_range" type="text" value="(0, 1)" optional="true" help="Desired range of transformed data. None or tuple (min, max). None equals to (0, 1)"/> | 1854 <conditional name="estimator_selector"> |
841 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" | 1855 <param name="selected_module" type="select" label="Choose the module that contains target estimator:"> |
842 label="Use a copy of data for precomputing normalization" help=" "/> | 1856 <expand macro="estimator_module_options"> |
843 </section> | 1857 <option value="custom_estimator">Load a custom estimator</option> |
844 </when> | 1858 </expand> |
845 <when value="PolynomialFeatures"> | 1859 </param> |
846 <section name="options" title="Advanced Options" expanded="False"> | 1860 <expand macro="estimator_suboptions"> |
847 <param argument="degree" type="integer" optional="true" value="2" label="The degree of the polynomial features " help=""/> | 1861 <when value="custom_estimator"> |
848 <param argument="interaction_only" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Produce interaction features only" help="(Features that are products of at most degree distinct input features) "/> | 1862 <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline" /> |
849 <param argument="include_bias" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Include a bias column" help="Feature in which all polynomial powers are zero "/> | 1863 </when> |
850 </section> | |
851 </when> | |
852 <when value="RobustScaler"> | |
853 <section name="options" title="Advanced Options" expanded="False"> | |
854 <!--=True, =True, copy=True--> | |
855 <param argument="with_centering" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" | |
856 label="Center the data before scaling" help=" "/> | |
857 <param argument="with_scaling" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" | |
858 label="Scale the data to interquartile range" help=" "/> | |
859 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" | |
860 label="Use a copy of data for inplace scaling" help=" "/> | |
861 </section> | |
862 </when> | |
863 <when value="QuantileTransformer"> | |
864 <section name="options" title="Advanced Options" expanded="False"> | |
865 <param name="n_quantiles" type="integer" value="1000" min="0" label="Number of quantiles to be computed" /> | |
866 <param name="output_distribution" type="select" label="Marginal distribution for the transformed data"> | |
867 <option value="uniform" selected="true">uniform</option> | |
868 <option value="normal">normal</option> | |
869 </param> | |
870 <param name="ignore_implicit_zeros" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Whether to discard sparse entries" help="Only applies to sparse matrices. If False, sparse entries are treated as zeros"/> | |
871 <param name="subsample" type="integer" value="100000" label="Maximum number of samples used to estimate the quantiles for computational efficiency" help="Note that the subsampling procedure may differ for value-identical sparse and dense matrices."/> | |
872 <expand macro="random_state" help_text="This is used by subsampling and smoothing noise"/> | |
873 </section> | |
874 </when> | |
875 <when value="PowerTransformer"> | |
876 <section name="options" title="Advanced Options" expanded="False"> | |
877 <param name="method" type="select" label="The power transform method"> | |
878 <option value="yeo-johnson" selected="true">yeo-johnson (works with positive and negative values)</option> | |
879 <option value="box-cox">box-cox (might perform better, but only works with strictly positive values)</option> | |
880 </param> | |
881 <param name="standardize" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Whether to apply zero-mean, unit-variance normalization to the transformed output."/> | |
882 </section> | |
883 </when> | |
884 <when value="KBinsDiscretizer"> | |
885 <section name="options" title="Advanced Options" expanded="False"> | |
886 <param name="n_bins" type="integer" value="5" min="2" label="The number of bins to produce"/> | |
887 <param name="encode" type="select" label="Method used to encode the transformed result"> | |
888 <option value="onehot" selected="true">onehot (encode the transformed result with one-hot encoding and return a sparse matrix)</option> | |
889 <option value="onehot-dense">onehot-dense (encode the transformed result with one-hot encoding and return a dense array)</option> | |
890 <option value="ordinal">ordinal (return the bin identifier encoded as an integer value)</option> | |
891 </param> | |
892 <param name="strategy" type="select" label="Strategy used to define the widths of the bins"> | |
893 <option value="uniform">uniform (all bins in each feature have identical widths)</option> | |
894 <option value="quantile" selected="true">quantile (all bins in each feature have the same number of points)</option> | |
895 <option value="kmeans">kmeans (values in each bin have the same nearest center of a 1D k-means cluster)</option> | |
896 </param> | |
897 </section> | |
898 </when> | |
899 </expand> | |
900 </xml> | |
901 | |
902 <xml name="cv_splitter"> | |
903 <option value="default" selected="true">default splitter</option> | |
904 <option value="KFold">KFold</option> | |
905 <option value="StratifiedKFold">StratifiedKFold</option> | |
906 <option value="LeaveOneOut">LeaveOneOut</option> | |
907 <option value="LeavePOut">LeavePOut</option> | |
908 <option value="RepeatedKFold">RepeatedKFold</option> | |
909 <option value="RepeatedStratifiedKFold">RepeatedStratifiedKFold</option> | |
910 <option value="ShuffleSplit">ShuffleSplit</option> | |
911 <option value="StratifiedShuffleSplit">StratifiedShuffleSplit</option> | |
912 <option value="TimeSeriesSplit">TimeSeriesSplit</option> | |
913 <option value="PredefinedSplit">PredefinedSplit</option> | |
914 <option value="OrderedKFold">OrderedKFold</option> | |
915 <option value="RepeatedOrderedKFold">RepeatedOrderedKFold</option> | |
916 <yield/> | |
917 </xml> | |
918 | |
919 <xml name="cv_splitter_options"> | |
920 <when value="default"> | |
921 <expand macro="cv_n_splits"/> | |
922 </when> | |
923 <when value="KFold"> | |
924 <expand macro="cv_n_splits"/> | |
925 <expand macro="cv_shuffle"/> | |
926 <expand macro="random_state"/> | |
927 </when> | |
928 <when value="StratifiedKFold"> | |
929 <expand macro="cv_n_splits"/> | |
930 <expand macro="cv_shuffle"/> | |
931 <expand macro="random_state"/> | |
932 </when> | |
933 <when value="LeaveOneOut"> | |
934 </when> | |
935 <when value="LeavePOut"> | |
936 <param argument="p" type="integer" value="" label="p" help="Integer. Size of the test sets."/> | |
937 </when> | |
938 <when value="RepeatedKFold"> | |
939 <expand macro="cv_n_splits" value="5"/> | |
940 <param argument="n_repeats" type="integer" value="10" label="n_repeats" help="Number of times cross-validator needs to be repeated." /> | |
941 <expand macro="random_state" /> | |
942 </when> | |
943 <when value="RepeatedStratifiedKFold"> | |
944 <expand macro="cv_n_splits" value="5"/> | |
945 <param argument="n_repeats" type="integer" value="10" label="n_repeats" help="Number of times cross-validator needs to be repeated." /> | |
946 <expand macro="random_state" /> | |
947 </when> | |
948 <when value="ShuffleSplit"> | |
949 <expand macro="cv_n_splits" value="10" help="Number of re-shuffling and splitting iterations."/> | |
950 <expand macro="cv_test_size" value="0.1" /> | |
951 <expand macro="random_state"/> | |
952 </when> | |
953 <when value="StratifiedShuffleSplit"> | |
954 <expand macro="cv_n_splits" value="10" help="Number of re-shuffling and splitting iterations."/> | |
955 <expand macro="cv_test_size" value="0.1" /> | |
956 <expand macro="random_state"/> | |
957 </when> | |
958 <when value="TimeSeriesSplit"> | |
959 <expand macro="cv_n_splits"/> | |
960 <param argument="max_train_size" type="integer" value="" optional="true" label="Maximum size of the training set" help="Maximum size for a single training set." /> | |
961 </when> | |
962 <when value="PredefinedSplit"> | |
963 <param argument="test_fold" type="text" value="" area="true" label="test_fold" help="List, e.g., [0, 1, -1, 1], represents two test sets, [X[0]] and [X[1], X[3]], X[2] is excluded from any test set due to '-1'."/> | |
964 </when> | |
965 <when value="OrderedKFold"> | |
966 <expand macro="cv_n_splits"/> | |
967 <expand macro="cv_shuffle"/> | |
968 <expand macro="random_state"/> | |
969 </when> | |
970 <when value="RepeatedOrderedKFold"> | |
971 <expand macro="cv_n_splits"/> | |
972 <param argument="n_repeats" type="integer" value="5"/> | |
973 <expand macro="random_state"/> | |
974 </when> | |
975 <yield/> | |
976 </xml> | |
977 | |
978 <xml name="cv"> | |
979 <conditional name="cv_selector"> | |
980 <param name="selected_cv" type="select" label="Select the cv splitter:"> | |
981 <expand macro="cv_splitter"> | |
982 <option value="GroupKFold">GroupKFold</option> | |
983 <option value="GroupShuffleSplit">GroupShuffleSplit</option> | |
984 <option value="LeaveOneGroupOut">LeaveOneGroupOut</option> | |
985 <option value="LeavePGroupsOut">LeavePGroupsOut</option> | |
986 </expand> | |
987 </param> | |
988 <expand macro="cv_splitter_options"> | |
989 <when value="GroupKFold"> | |
990 <expand macro="cv_n_splits"/> | |
991 <expand macro="cv_groups" /> | |
992 </when> | |
993 <when value="GroupShuffleSplit"> | |
994 <expand macro="cv_n_splits" value="5"/> | |
995 <expand macro="cv_test_size"/> | |
996 <expand macro="random_state"/> | |
997 <expand macro="cv_groups"/> | |
998 </when> | |
999 <when value="LeaveOneGroupOut"> | |
1000 <expand macro="cv_groups"/> | |
1001 </when> | |
1002 <when value="LeavePGroupsOut"> | |
1003 <param argument="n_groups" type="integer" value="" label="n_groups" help="Number of groups (p) to leave out in the test split." /> | |
1004 <expand macro="cv_groups"/> | |
1005 </when> | |
1006 </expand> | |
1007 </conditional> | |
1008 </xml> | |
1009 | |
1010 <xml name="cv_reduced" token_label="Select the cv splitter"> | |
1011 <conditional name="cv_selector"> | |
1012 <param name="selected_cv" type="select" label="@LABEL@"> | |
1013 <expand macro="cv_splitter"/> | |
1014 </param> | |
1015 <expand macro="cv_splitter_options"/> | |
1016 </conditional> | |
1017 </xml> | |
1018 | |
1019 <xml name="cv_n_splits" token_value="3" token_help="Number of folds. Must be at least 2."> | |
1020 <param argument="n_splits" type="integer" value="@VALUE@" min="1" label="n_splits" help="@HELP@"/> | |
1021 </xml> | |
1022 | |
1023 <xml name="cv_shuffle"> | |
1024 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Whether to shuffle data before splitting" /> | |
1025 </xml> | |
1026 | |
1027 <xml name="cv_test_size" token_value="0.2"> | |
1028 <param argument="test_size" type="float" value="@VALUE@" min="0.0" label="Portion or number of the test set" help="0.0-1.0, proportion of the dataset to include in the test split; >1, integer only, the absolute number of test samples "/> | |
1029 </xml> | |
1030 | |
1031 <xml name="cv_groups" > | |
1032 <section name="groups_selector" title="Groups column selector" expanded="true"> | |
1033 <param name="infile_g" type="data" format="tabular" label="Choose dataset containing groups info:"/> | |
1034 <param name="header_g" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" /> | |
1035 <conditional name="column_selector_options_g"> | |
1036 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option_g" col_name="col_g" multiple="False" infile="infile_g"/> | |
1037 </conditional> | |
1038 </section> | |
1039 </xml> | |
1040 | |
1041 <xml name="train_test_split_params"> | |
1042 <conditional name="split_algos"> | |
1043 <param name="shuffle" type="select" label="Select the splitting method"> | |
1044 <option value="None">No shuffle</option> | |
1045 <option value="simple" selected="true">ShuffleSplit</option> | |
1046 <option value="stratified">StratifiedShuffleSplit -- target values serve as class labels</option> | |
1047 <option value="group">GroupShuffleSplit or split by group names</option> | |
1048 </param> | |
1049 <when value="None"> | |
1050 <expand macro="train_test_split_test_size"/> | |
1051 </when> | |
1052 <when value="simple"> | |
1053 <expand macro="train_test_split_test_size"/> | |
1054 <expand macro="random_state"/> | |
1055 </when> | |
1056 <when value="stratified"> | |
1057 <expand macro="train_test_split_test_size"/> | |
1058 <expand macro="random_state"/> | |
1059 </when> | |
1060 <when value="group"> | |
1061 <expand macro="train_test_split_test_size" optional="true"/> | |
1062 <expand macro="random_state"/> | |
1063 <param argument="group_names" type="text" value="" optional="true" label="Type in group names instead" | |
1064 help="For example: chr6, chr7. This parameter is optional. If used, it will override the holdout size and random seed."/> | |
1065 <yield/> | |
1066 </when> | |
1067 </conditional> | |
1068 <!--param argument="train_size" type="float" optional="True" value="" label="Train size:"/>--> | |
1069 </xml> | |
1070 | |
1071 <xml name="train_test_split_test_size" token_optional="false"> | |
1072 <param name="test_size" type="float" value="0.2" optional="@OPTIONAL@" label="Holdout size" help="Leass than 1, for preportion; greater than 1 (integer), for number of samples."/> | |
1073 </xml> | |
1074 | |
1075 <xml name="feature_selection_algorithms"> | |
1076 <option value="SelectKBest" selected="true">SelectKBest - Select features according to the k highest scores</option> | |
1077 <option value="GenericUnivariateSelect">GenericUnivariateSelect - Univariate feature selector with configurable strategy</option> | |
1078 <option value="SelectPercentile">SelectPercentile - Select features according to a percentile of the highest scores</option> | |
1079 <option value="SelectFpr">SelectFpr - Filter: Select the p-values below alpha based on a FPR test</option> | |
1080 <option value="SelectFdr">SelectFdr - Filter: Select the p-values for an estimated false discovery rate</option> | |
1081 <option value="SelectFwe">SelectFwe - Filter: Select the p-values corresponding to Family-wise error rate</option> | |
1082 <option value="VarianceThreshold">VarianceThreshold - Feature selector that removes all low-variance features</option> | |
1083 <option value="SelectFromModel">SelectFromModel - Meta-transformer for selecting features based on importance weights</option> | |
1084 <option value="RFE">RFE - Feature ranking with recursive feature elimination</option> | |
1085 <option value="RFECV">RFECV - Feature ranking with recursive feature elimination and cross-validated selection of the best number of features</option> | |
1086 <yield/> | |
1087 </xml> | |
1088 | |
1089 <xml name="feature_selection_algorithm_details"> | |
1090 <when value="GenericUnivariateSelect"> | |
1091 <expand macro="feature_selection_score_function" /> | |
1092 <section name="options" title="Advanced Options" expanded="False"> | |
1093 <param argument="mode" type="select" label="Feature selection mode"> | |
1094 <option value="percentile">percentile</option> | |
1095 <option value="k_best">k_best</option> | |
1096 <option value="fpr">fpr</option> | |
1097 <option value="fdr">fdr</option> | |
1098 <option value="fwe">fwe</option> | |
1099 </param> | |
1100 <param argument="param" type="float" value="" optional="true" label="Parameter of the corresponding mode" help="float or int depending on the feature selection mode" /> | |
1101 </section> | |
1102 </when> | |
1103 <when value="SelectPercentile"> | |
1104 <expand macro="feature_selection_score_function" /> | |
1105 <section name="options" title="Advanced Options" expanded="False"> | |
1106 <param argument="percentile" type="integer" value="10" optional="True" label="Percent of features to keep" /> | |
1107 </section> | |
1108 </when> | |
1109 <when value="SelectKBest"> | |
1110 <expand macro="feature_selection_score_function" /> | |
1111 <section name="options" title="Advanced Options" expanded="False"> | |
1112 <param argument="k" type="integer" value="10" optional="True" label="Number of top features to select" help="No 'all' option is supported." /> | |
1113 </section> | |
1114 </when> | |
1115 <when value="SelectFpr"> | |
1116 <expand macro="feature_selection_score_function" /> | |
1117 <section name="options" title="Advanced Options" expanded="False"> | |
1118 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest p-value for features to be kept."/> | |
1119 </section> | |
1120 </when> | |
1121 <when value="SelectFdr"> | |
1122 <expand macro="feature_selection_score_function" /> | |
1123 <section name="options" title="Advanced Options" expanded="False"> | |
1124 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest uncorrected p-value for features to keep."/> | |
1125 </section> | |
1126 </when> | |
1127 <when value="SelectFwe"> | |
1128 <expand macro="feature_selection_score_function" /> | |
1129 <section name="options" title="Advanced Options" expanded="False"> | |
1130 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest uncorrected p-value for features to keep."/> | |
1131 </section> | |
1132 </when> | |
1133 <when value="VarianceThreshold"> | |
1134 <section name="options" title="Options" expanded="False"> | |
1135 <param argument="threshold" type="float" value="0.0" optional="True" label="Threshold" help="Features with a training-set variance lower than this threshold will be removed."/> | |
1136 </section> | |
1137 </when> | |
1138 </xml> | |
1139 | |
1140 <xml name="feature_selection_SelectFromModel"> | |
1141 <when value="SelectFromModel"> | |
1142 <conditional name="model_inputter"> | |
1143 <param name="input_mode" type="select" label="Construct a new estimator from a selection list?" > | |
1144 <option value="new" selected="true">Yes</option> | |
1145 <option value="prefitted">No. Load a prefitted estimator</option> | |
1146 </param> | |
1147 <when value="new"> | |
1148 <expand macro="estimator_selector_fs"/> | |
1149 </when> | |
1150 <when value="prefitted"> | |
1151 <param name="fitted_estimator" type="data" format='zip' label="Load a prefitted estimator" /> | |
1152 </when> | |
1153 </conditional> | |
1154 <expand macro="feature_selection_SelectFromModel_options"/> | |
1155 </when> | |
1156 </xml> | |
1157 | |
1158 <xml name="feature_selection_SelectFromModel_no_prefitted"> | |
1159 <when value="SelectFromModel"> | |
1160 <conditional name="model_inputter"> | |
1161 <param name="input_mode" type="select" label="Construct a new estimator from a selection list?" > | |
1162 <option value="new" selected="true">Yes</option> | |
1163 </param> | |
1164 <when value="new"> | |
1165 <expand macro="estimator_selector_all"/> | |
1166 </when> | |
1167 </conditional> | |
1168 <expand macro="feature_selection_SelectFromModel_options"/> | |
1169 </when> | |
1170 </xml> | |
1171 | |
1172 <xml name="feature_selection_SelectFromModel_options"> | |
1173 <section name="options" title="Advanced Options" expanded="False"> | |
1174 <param argument="threshold" type="text" value="" optional="true" label="threshold" help="The threshold value to use for feature selection. e.g. 'mean', 'median', '1.25*mean'." /> | |
1175 <param argument="norm_order" type="integer" value="1" label="norm_order" help="Order of the norm used to filter the vectors of coefficients below threshold in the case where the coef_ attribute of the estimator is of dimension 2. " /> | |
1176 <param argument="max_features" type="integer" value="" optional="true" label="The maximum number of features selected scoring above threshold" help="To disable threshold and only select based on max_features, set threshold=-np.inf."/> | |
1177 </section> | |
1178 </xml> | |
1179 | |
1180 <xml name="feature_selection_RFE"> | |
1181 <when value="RFE"> | |
1182 <yield/> | |
1183 <section name="options" title="Advanced Options" expanded="False"> | |
1184 <param argument="n_features_to_select" type="integer" value="" optional="true" label="n_features_to_select" help="The number of features to select. If None, half of the features are selected." /> | |
1185 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " /> | |
1186 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." /> | |
1187 </section> | |
1188 </when> | |
1189 </xml> | |
1190 | |
1191 <xml name="feature_selection_RFECV_fs"> | |
1192 <when value="RFECV"> | |
1193 <yield/> | |
1194 <section name="options" title="Advanced Options" expanded="False"> | |
1195 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " /> | |
1196 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected"/> | |
1197 <expand macro="cv"/> | |
1198 <expand macro="scoring_selection"/> | |
1199 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." /> | |
1200 </section> | |
1201 </when> | |
1202 </xml> | |
1203 | |
1204 <xml name="feature_selection_RFECV_pipeline"> | |
1205 <when value="RFECV"> | |
1206 <yield/> | |
1207 <section name="options" title="Advanced Options" expanded="False"> | |
1208 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " /> | |
1209 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected"/> | |
1210 <expand macro="cv_reduced"/> | |
1211 <!-- TODO: group splitter support--> | |
1212 <expand macro="scoring_selection"/> | |
1213 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." /> | |
1214 </section> | |
1215 </when> | |
1216 </xml> | |
1217 | |
1218 <xml name="feature_selection_DyRFECV_fs"> | |
1219 <when value="DyRFECV"> | |
1220 <yield/> | |
1221 <section name="options" title="Advanced Options" expanded="False"> | |
1222 <param argument="step" type="text" size="30" value="1" label="step" optional="true" help="Default = 1. Support float, int and list." > | |
1223 <sanitizer> | |
1224 <valid initial="default"> | |
1225 <add value="["/> | |
1226 <add value="]"/> | |
1227 </valid> | |
1228 </sanitizer> | |
1229 </param> | |
1230 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected"/> | |
1231 <expand macro="cv"/> | |
1232 <expand macro="scoring_selection"/> | |
1233 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." /> | |
1234 </section> | |
1235 </when> | |
1236 </xml> | |
1237 | |
1238 <xml name="feature_selection_pipeline"> | |
1239 <!--compare to `feature_selection_fs`, no fitted estimator for SelectFromModel and no custom estimator for RFE and RFECV--> | |
1240 <conditional name="fs_algorithm_selector"> | |
1241 <param name="selected_algorithm" type="select" label="Select a feature selection algorithm"> | |
1242 <expand macro="feature_selection_algorithms"/> | |
1243 </param> | |
1244 <expand macro="feature_selection_algorithm_details"/> | |
1245 <expand macro="feature_selection_SelectFromModel_no_prefitted"/> | |
1246 <expand macro="feature_selection_RFE"> | |
1247 <expand macro="estimator_selector_all"/> | |
1248 </expand> | |
1249 <expand macro="feature_selection_RFECV_pipeline"> | |
1250 <expand macro="estimator_selector_all"/> | |
1251 </expand> | |
1252 <!-- TODO: add DyRFECV to pipeline--> | |
1253 </conditional> | |
1254 </xml> | |
1255 | |
1256 <xml name="feature_selection_fs"> | |
1257 <conditional name="fs_algorithm_selector"> | |
1258 <param name="selected_algorithm" type="select" label="Select a feature selection algorithm"> | |
1259 <expand macro="feature_selection_algorithms"> | |
1260 <option value="DyRFECV">DyRFECV - Extended RFECV with changeable steps</option> | |
1261 </expand> | |
1262 </param> | |
1263 <expand macro="feature_selection_algorithm_details"/> | |
1264 <expand macro="feature_selection_SelectFromModel"/> | |
1265 <expand macro="feature_selection_RFE"> | |
1266 <expand macro="estimator_selector_fs"/> | |
1267 </expand> | |
1268 <expand macro="feature_selection_RFECV_fs"> | |
1269 <expand macro="estimator_selector_fs"/> | |
1270 </expand> | |
1271 <expand macro="feature_selection_DyRFECV_fs"> | |
1272 <expand macro="estimator_selector_fs"/> | |
1273 </expand> | |
1274 </conditional> | |
1275 </xml> | |
1276 | |
1277 <xml name="feature_selection_score_function"> | |
1278 <param argument="score_func" type="select" label="Select a score function"> | |
1279 <option value="chi2">chi2 - Compute chi-squared stats between each non-negative feature and class</option> | |
1280 <option value="f_classif">f_classif - Compute the ANOVA F-value for the provided sample</option> | |
1281 <option value="f_regression">f_regression - Univariate linear regression tests</option> | |
1282 <option value="mutual_info_classif">mutual_info_classif - Estimate mutual information for a discrete target variable</option> | |
1283 <option value="mutual_info_regression">mutual_info_regression - Estimate mutual information for a continuous target variable</option> | |
1284 </param> | |
1285 </xml> | |
1286 | |
1287 <xml name="model_validation_common_options"> | |
1288 <expand macro="cv"/> | |
1289 <expand macro="verbose"/> | |
1290 <yield/> | |
1291 </xml> | |
1292 | |
1293 <xml name="scoring_selection"> | |
1294 <conditional name="scoring"> | |
1295 <param name="primary_scoring" type="select" multiple="false" label="Select the primary metric (scoring):" help="Metric to refit the best estimator."> | |
1296 <option value="default" selected="true">default with estimator</option> | |
1297 <option value="accuracy">Classification -- 'accuracy'</option> | |
1298 <option value="balanced_accuracy">Classification -- 'balanced_accuracy'</option> | |
1299 <option value="average_precision">Classification -- 'average_precision'</option> | |
1300 <option value="f1">Classification -- 'f1'</option> | |
1301 <option value="f1_micro">Classification -- 'f1_micro'</option> | |
1302 <option value="f1_macro">Classification -- 'f1_macro'</option> | |
1303 <option value="f1_weighted">Classification -- 'f1_weighted'</option> | |
1304 <option value="f1_samples">Classification -- 'f1_samples'</option> | |
1305 <option value="neg_log_loss">Classification -- 'neg_log_loss'</option> | |
1306 <option value="precision">Classification -- 'precision'</option> | |
1307 <option value="precision_micro">Classification -- 'precision_micro'</option> | |
1308 <option value="precision_macro">Classification -- 'precision_macro'</option> | |
1309 <option value="precision_wighted">Classification -- 'precision_wighted'</option> | |
1310 <option value="precision_samples">Classification -- 'precision_samples'</option> | |
1311 <option value="recall">Classification -- 'recall'</option> | |
1312 <option value="recall_micro">Classification -- 'recall_micro'</option> | |
1313 <option value="recall_macro">Classification -- 'recall_macro'</option> | |
1314 <option value="recall_wighted">Classification -- 'recall_wighted'</option> | |
1315 <option value="recall_samples">Classification -- 'recall_samples'</option> | |
1316 <option value="roc_auc">Classification -- 'roc_auc'</option> | |
1317 <option value="explained_variance">Regression -- 'explained_variance'</option> | |
1318 <option value="neg_mean_absolute_error">Regression -- 'neg_mean_absolute_error'</option> | |
1319 <option value="neg_mean_squared_error">Regression -- 'neg_mean_squared_error'</option> | |
1320 <option value="neg_mean_squared_log_error">Regression -- 'neg_mean_squared_log_error'</option> | |
1321 <option value="neg_median_absolute_error">Regression -- 'neg_median_absolute_error'</option> | |
1322 <option value="r2">Regression -- 'r2'</option> | |
1323 <option value="max_error">Regression -- 'max_error'</option> | |
1324 <option value="binarize_auc_scorer">anomaly detection -- binarize_auc_scorer</option> | |
1325 <option value="binarize_average_precision_scorer">anomaly detection -- binarize_average_precision_scorer</option> | |
1326 </param> | |
1327 <when value="default"/> | |
1328 <when value="accuracy"><expand macro="secondary_scoring_selection_classification"/></when> | |
1329 <when value="balanced_accuracy"><expand macro="secondary_scoring_selection_classification"/></when> | |
1330 <when value="average_precision"><expand macro="secondary_scoring_selection_classification"/></when> | |
1331 <when value="f1"><expand macro="secondary_scoring_selection_classification"/></when> | |
1332 <when value="f1_micro"><expand macro="secondary_scoring_selection_classification"/></when> | |
1333 <when value="f1_macro"><expand macro="secondary_scoring_selection_classification"/></when> | |
1334 <when value="f1_weighted"><expand macro="secondary_scoring_selection_classification"/></when> | |
1335 <when value="f1_samples"><expand macro="secondary_scoring_selection_classification"/></when> | |
1336 <when value="neg_log_loss"><expand macro="secondary_scoring_selection_classification"/></when> | |
1337 <when value="precision"><expand macro="secondary_scoring_selection_classification"/></when> | |
1338 <when value="precision_micro"><expand macro="secondary_scoring_selection_classification"/></when> | |
1339 <when value="precision_macro"><expand macro="secondary_scoring_selection_classification"/></when> | |
1340 <when value="precision_wighted"><expand macro="secondary_scoring_selection_classification"/></when> | |
1341 <when value="precision_samples"><expand macro="secondary_scoring_selection_classification"/></when> | |
1342 <when value="recall"><expand macro="secondary_scoring_selection_classification"/></when> | |
1343 <when value="recall_micro"><expand macro="secondary_scoring_selection_classification"/></when> | |
1344 <when value="recall_macro"><expand macro="secondary_scoring_selection_classification"/></when> | |
1345 <when value="recall_wighted"><expand macro="secondary_scoring_selection_classification"/></when> | |
1346 <when value="recall_samples"><expand macro="secondary_scoring_selection_classification"/></when> | |
1347 <when value="roc_auc"><expand macro="secondary_scoring_selection_classification"/></when> | |
1348 <when value="explained_variance"><expand macro="secondary_scoring_selection_regression"/></when> | |
1349 <when value="neg_mean_absolute_error"><expand macro="secondary_scoring_selection_regression"/></when> | |
1350 <when value="neg_mean_squared_error"><expand macro="secondary_scoring_selection_regression"/></when> | |
1351 <when value="neg_mean_squared_log_error"><expand macro="secondary_scoring_selection_regression"/></when> | |
1352 <when value="neg_median_absolute_error"><expand macro="secondary_scoring_selection_regression"/></when> | |
1353 <when value="r2"><expand macro="secondary_scoring_selection_regression"/></when> | |
1354 <when value="max_error"><expand macro="secondary_scoring_selection_regression"/></when> | |
1355 <when value="binarize_auc_scorer"><expand macro="secondary_scoring_selection_anormaly"/></when> | |
1356 <when value="binarize_average_precision_scorer"><expand macro="secondary_scoring_selection_anormaly"/></when> | |
1357 </conditional> | |
1358 </xml> | |
1359 | |
1360 <xml name="secondary_scoring_selection_classification"> | |
1361 <param name="secondary_scoring" type="select" multiple="true" label="Additional scoring used in multi-metric mode:" help="If the same metric with the primary is chosen, the metric will be ignored."> | |
1362 <option value="accuracy">Classification -- 'accuracy'</option> | |
1363 <option value="balanced_accuracy">Classification -- 'balanced_accuracy'</option> | |
1364 <option value="average_precision">Classification -- 'average_precision'</option> | |
1365 <option value="f1">Classification -- 'f1'</option> | |
1366 <option value="f1_micro">Classification -- 'f1_micro'</option> | |
1367 <option value="f1_macro">Classification -- 'f1_macro'</option> | |
1368 <option value="f1_weighted">Classification -- 'f1_weighted'</option> | |
1369 <option value="f1_samples">Classification -- 'f1_samples'</option> | |
1370 <option value="neg_log_loss">Classification -- 'neg_log_loss'</option> | |
1371 <option value="precision">Classification -- 'precision'</option> | |
1372 <option value="precision_micro">Classification -- 'precision_micro'</option> | |
1373 <option value="precision_macro">Classification -- 'precision_macro'</option> | |
1374 <option value="precision_wighted">Classification -- 'precision_wighted'</option> | |
1375 <option value="precision_samples">Classification -- 'precision_samples'</option> | |
1376 <option value="recall">Classification -- 'recall'</option> | |
1377 <option value="recall_micro">Classification -- 'recall_micro'</option> | |
1378 <option value="recall_macro">Classification -- 'recall_macro'</option> | |
1379 <option value="recall_wighted">Classification -- 'recall_wighted'</option> | |
1380 <option value="recall_samples">Classification -- 'recall_samples'</option> | |
1381 <option value="roc_auc">Classification -- 'roc_auc'</option> | |
1382 </param> | |
1383 </xml> | |
1384 | |
1385 <xml name="secondary_scoring_selection_regression"> | |
1386 <param name="secondary_scoring" type="select" multiple="true" label="Additional scoring used in multi-metric mode:" help="If the same metric with the primary is chosen, the metric will be ignored."> | |
1387 <option value="explained_variance">Regression -- 'explained_variance'</option> | |
1388 <option value="neg_mean_absolute_error">Regression -- 'neg_mean_absolute_error'</option> | |
1389 <option value="neg_mean_squared_error">Regression -- 'neg_mean_squared_error'</option> | |
1390 <option value="neg_mean_squared_log_error">Regression -- 'neg_mean_squared_log_error'</option> | |
1391 <option value="neg_median_absolute_error">Regression -- 'neg_median_absolute_error'</option> | |
1392 <option value="r2">Regression -- 'r2'</option> | |
1393 <option value="max_error">Regression -- 'max_error'</option> | |
1394 </param> | |
1395 </xml> | |
1396 | |
1397 <xml name="secondary_scoring_selection_anormaly"> | |
1398 <param name="secondary_scoring" type="select" multiple="true" label="Additional scoring used in multi-metric mode:" help="If the same metric with the primary is chosen, the metric will be ignored."> | |
1399 <option value="binarize_auc_scorer">anomaly detection -- binarize_auc_scorer</option> | |
1400 <option value="binarize_average_precision_scorer">anomaly detection -- binarize_average_precision_scorer</option> | |
1401 </param> | |
1402 </xml> | |
1403 | |
1404 <xml name="pre_dispatch" token_type="hidden" token_default_value="all" token_help="Number of predispatched jobs for parallel execution"> | |
1405 <param argument="pre_dispatch" type="@TYPE@" value="@DEFAULT_VALUE@" optional="true" label="pre_dispatch" help="@HELP@"/> | |
1406 </xml> | |
1407 | |
1408 <xml name="estimator_and_hyperparameter"> | |
1409 <param name="infile_estimator" type="data" format="zip" label="Choose the dataset containing pipeline/estimator object"/> | |
1410 <section name="hyperparams_swapping" title="Hyperparameter Swapping" expanded="false"> | |
1411 <param name="infile_params" type="data" format="tabular" optional="true" label="Choose the dataset containing hyperparameters for the pipeline/estimator above" help="This dataset could be the output of `get_params` in the `Estimator Attributes` tool."/> | |
1412 <repeat name="param_set" min="1" max="30" title="New hyperparameter setting"> | |
1413 <param name="sp_name" type="select" optional="true" label="Choose a parameter name (with current value)"> | |
1414 <options from_dataset="infile_params" startswith="@"> | |
1415 <column name="name" index="2"/> | |
1416 <column name="value" index="1"/> | |
1417 <filter type="unique_value" name="unique_param" column="1"/> | |
1418 </options> | |
1419 </param> | |
1420 <param name="sp_value" type="text" value="" optional="true" label="New value" help="Supports int, float, boolean, single quoted string, and selected object constructor. Similar to the `Parameter settings for search` section in `searchcv` tool except that only single value is expected here."> | |
1421 <sanitizer> | |
1422 <valid initial="default"> | |
1423 <add value="'"/> | |
1424 <add value="""/> | |
1425 </valid> | |
1426 </sanitizer> | |
1427 </param> | |
1428 </repeat> | |
1429 </section> | |
1430 </xml> | |
1431 | |
1432 <xml name="search_cv_options"> | |
1433 <expand macro="scoring_selection"/> | |
1434 <expand macro="model_validation_common_options"/> | |
1435 <!--expand macro="pre_dispatch" default_value="2*n_jobs" help="Controls the number of jobs that get dispatched during parallel execution"/--> | |
1436 <param argument="iid" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="iid" help="If True, data is identically distributed across the folds"/> | |
1437 <!--param argument="refit" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="refit" help="Refit an estimator using the best found parameters on the whole dataset. Be aware that `refit=True` invokes extra computation, but it's REQUIRED for outputting the best estimator!"/> --> | |
1438 <param argument="error_score" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Raise fit error:" help="If false, the metric score is assigned to NaN if an error occurs in estimator fitting and FitFailedWarning is raised."/> | |
1439 <param argument="return_train_score" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="return_train_score" help=""/> | |
1440 </xml> | |
1441 | |
1442 <xml name="estimator_module_options"> | |
1443 <option value="svm" selected="true">sklearn.svm</option> | |
1444 <option value="linear_model">sklearn.linear_model</option> | |
1445 <option value="ensemble">sklearn.ensemble</option> | |
1446 <option value="naive_bayes">sklearn.naive_bayes</option> | |
1447 <option value="tree">sklearn.tree</option> | |
1448 <option value="neighbors">sklearn.neighbors</option> | |
1449 <option value="xgboost">xgboost</option> | |
1450 <yield/> | |
1451 </xml> | |
1452 | |
1453 <xml name="estimator_suboptions"> | |
1454 <when value="svm"> | |
1455 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
1456 <option value="LinearSVC" selected="true">LinearSVC</option> | |
1457 <option value="LinearSVR">LinearSVR</option> | |
1458 <option value="NuSVC">NuSVC</option> | |
1459 <option value="NuSVR">NuSVR</option> | |
1460 <option value="OneClassSVM">OneClassSVM</option> | |
1461 <option value="SVC">SVC</option> | |
1462 <option value="SVR">SVR</option> | |
1463 </param> | |
1464 <expand macro="estimator_params_text"/> | |
1465 </when> | |
1466 <when value="linear_model"> | |
1467 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
1468 <option value="ARDRegression" selected="true">ARDRegression</option> | |
1469 <option value="BayesianRidge">BayesianRidge</option> | |
1470 <option value="ElasticNet">ElasticNet</option> | |
1471 <option value="ElasticNetCV">ElasticNetCV</option> | |
1472 <option value="HuberRegressor">HuberRegressor</option> | |
1473 <option value="Lars">Lars</option> | |
1474 <option value="LarsCV">LarsCV</option> | |
1475 <option value="Lasso">Lasso</option> | |
1476 <option value="LassoCV">LassoCV</option> | |
1477 <option value="LassoLars">LassoLars</option> | |
1478 <option value="LassoLarsCV">LassoLarsCV</option> | |
1479 <option value="LassoLarsIC">LassoLarsIC</option> | |
1480 <option value="LinearRegression">LinearRegression</option> | |
1481 <option value="LogisticRegression">LogisticRegression</option> | |
1482 <option value="LogisticRegressionCV">LogisticRegressionCV</option> | |
1483 <option value="MultiTaskLasso">MultiTaskLasso</option> | |
1484 <option value="MultiTaskElasticNet">MultiTaskElasticNet</option> | |
1485 <option value="MultiTaskLassoCV">MultiTaskLassoCV</option> | |
1486 <option value="MultiTaskElasticNetCV">MultiTaskElasticNetCV</option> | |
1487 <option value="OrthogonalMatchingPursuit">OrthogonalMatchingPursuit</option> | |
1488 <option value="OrthogonalMatchingPursuitCV">OrthogonalMatchingPursuitCV</option> | |
1489 <option value="PassiveAggressiveClassifier">PassiveAggressiveClassifier</option> | |
1490 <option value="PassiveAggressiveRegressor">PassiveAggressiveRegressor</option> | |
1491 <option value="Perceptron">Perceptron</option> | |
1492 <option value="RANSACRegressor">RANSACRegressor</option> | |
1493 <option value="Ridge">Ridge</option> | |
1494 <option value="RidgeClassifier">RidgeClassifier</option> | |
1495 <option value="RidgeClassifierCV">RidgeClassifierCV</option> | |
1496 <option value="RidgeCV">RidgeCV</option> | |
1497 <option value="SGDClassifier">SGDClassifier</option> | |
1498 <option value="SGDRegressor">SGDRegressor</option> | |
1499 <option value="TheilSenRegressor">TheilSenRegressor</option> | |
1500 </param> | |
1501 <expand macro="estimator_params_text"/> | |
1502 </when> | |
1503 <when value="ensemble"> | |
1504 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
1505 <option value="AdaBoostClassifier" selected="true">AdaBoostClassifier</option> | |
1506 <option value="AdaBoostRegressor">AdaBoostRegressor</option> | |
1507 <option value="BaggingClassifier">BaggingClassifier</option> | |
1508 <option value="BaggingRegressor">BaggingRegressor</option> | |
1509 <option value="ExtraTreesClassifier">ExtraTreesClassifier</option> | |
1510 <option value="ExtraTreesRegressor">ExtraTreesRegressor</option> | |
1511 <option value="GradientBoostingClassifier">GradientBoostingClassifier</option> | |
1512 <option value="GradientBoostingRegressor">GradientBoostingRegressor</option> | |
1513 <option value="IsolationForest">IsolationForest</option> | |
1514 <option value="HistGradientBoostingClassifier">HistGradientBoostingClassifier</option> | |
1515 <option value="HistGradientBoostingRegressor">HistGradientBoostingRegressor</option> | |
1516 <option value="RandomForestClassifier">RandomForestClassifier</option> | |
1517 <option value="RandomForestRegressor">RandomForestRegressor</option> | |
1518 <option value="RandomTreesEmbedding">RandomTreesEmbedding</option> | |
1519 <!--option value="VotingClassifier">VotingClassifier</option--> | |
1520 </param> | |
1521 <expand macro="estimator_params_text"/> | |
1522 </when> | |
1523 <when value="naive_bayes"> | |
1524 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
1525 <option value="BernoulliNB" selected="true">BernoulliNB</option> | |
1526 <option value="GaussianNB">GaussianNB</option> | |
1527 <option value="MultinomialNB">MultinomialNB</option> | |
1528 </param> | |
1529 <expand macro="estimator_params_text"/> | |
1530 </when> | |
1531 <when value="tree"> | |
1532 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
1533 <option value="DecisionTreeClassifier" selected="true">DecisionTreeClassifier</option> | |
1534 <option value="DecisionTreeRegressor">DecisionTreeRegressor</option> | |
1535 <option value="ExtraTreeClassifier">ExtraTreeClassifier</option> | |
1536 <option value="ExtraTreeRegressor">ExtraTreeRegressor</option> | |
1537 </param> | |
1538 <expand macro="estimator_params_text"/> | |
1539 </when> | |
1540 <when value="neighbors"> | |
1541 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
1542 <option value="KNeighborsClassifier" selected="true">KNeighborsClassifier</option> | |
1543 <option value="KNeighborsRegressor">KNeighborsRegressor</option> | |
1544 <!--option value="BallTree">BallTree</option--> | |
1545 <!--option value="KDTree">KDTree</option--> | |
1546 <option value="KernelDensity">KernelDensity</option> | |
1547 <option value="LocalOutlierFactor">LocalOutlierFactor</option> | |
1548 <option value="RadiusNeighborsClassifier">RadiusNeighborsClassifier</option> | |
1549 <option value="RadiusNeighborsRegressor">RadiusNeighborsRegressor</option> | |
1550 <option value="NearestCentroid">NearestCentroid</option> | |
1551 <option value="NearestNeighbors">NearestNeighbors</option> | |
1552 </param> | |
1553 <expand macro="estimator_params_text"/> | |
1554 </when> | |
1555 <when value="xgboost"> | |
1556 <param name="selected_estimator" type="select" label="Choose estimator class:"> | |
1557 <option value="XGBRegressor" selected="true">XGBRegressor</option> | |
1558 <option value="XGBClassifier">XGBClassifier</option> | |
1559 </param> | |
1560 <expand macro="estimator_params_text"/> | |
1561 </when> | |
1562 <yield/> | |
1563 </xml> | |
1564 | |
1565 <xml name="estimator_selector_all"> | |
1566 <conditional name="estimator_selector"> | |
1567 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" > | |
1568 <expand macro="estimator_module_options"/> | |
1569 </param> | |
1570 <expand macro="estimator_suboptions"/> | |
1571 </conditional> | |
1572 </xml> | |
1573 | |
1574 <xml name="estimator_selector_fs"> | |
1575 <conditional name="estimator_selector"> | |
1576 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" > | |
1577 <expand macro="estimator_module_options"> | |
1578 <option value="custom_estimator">Load a custom estimator</option> | |
1579 </expand> | |
1580 </param> | |
1581 <expand macro="estimator_suboptions"> | |
1582 <when value="custom_estimator"> | |
1583 <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline:"/> | |
1584 </when> | |
1585 </expand> | |
1586 </conditional> | |
1587 </xml> | |
1588 | |
1589 <xml name="estimator_params_text" token_label="Type in parameter settings if different from default:" token_default_value='' | |
1590 token_help="Dictionary-capable, e.g., C=1, kernel='linear'. No double quotes. Leave this box blank for default estimator."> | |
1591 <param name="text_params" type="text" value="@DEFAULT_VALUE@" optional="true" label="@LABEL@" help="@HELP@"> | |
1592 <sanitizer> | |
1593 <valid initial="default"> | |
1594 <add value="'"/> | |
1595 </valid> | |
1596 </sanitizer> | |
1597 </param> | |
1598 </xml> | |
1599 | |
1600 <xml name="kernel_approximation_all"> | |
1601 <conditional name="kernel_approximation_selector"> | |
1602 <param name="select_algorithm" type="select" label="Choose a kernel approximation algorithm:"> | |
1603 <option value="Nystroem" selected="true">Nystroem</option> | |
1604 <option value="RBFSampler">RBFSampler</option> | |
1605 <option value="AdditiveChi2Sampler">AdditiveChi2Sampler</option> | |
1606 <option value="SkewedChi2Sampler">SkewedChi2Sampler</option> | |
1607 </param> | |
1608 <when value="Nystroem"> | |
1609 <expand macro="estimator_params_text" | |
1610 help="Default(=blank): coef0=None, degree=None, gamma=None, kernel='rbf', kernel_params=None, n_components=100, random_state=None. No double quotes"/> | |
1611 </when> | |
1612 <when value="RBFSampler"> | |
1613 <expand macro="estimator_params_text" | |
1614 help="Default(=blank): gamma=1.0, n_components=100, random_state=None."/> | |
1615 </when> | |
1616 <when value="AdditiveChi2Sampler"> | |
1617 <expand macro="estimator_params_text" | |
1618 help="Default(=blank): sample_interval=None, sample_steps=2."/> | |
1619 </when> | |
1620 <when value="SkewedChi2Sampler"> | |
1621 <expand macro="estimator_params_text" | |
1622 help="Default(=blank): n_components=100, random_state=None, skewedness=1.0."/> | |
1623 </when> | |
1624 </conditional> | |
1625 </xml> | |
1626 | |
1627 <xml name="matrix_decomposition_all"> | |
1628 <conditional name="matrix_decomposition_selector"> | |
1629 <param name="select_algorithm" type="select" label="Choose a matrix decomposition algorithm:"> | |
1630 <option value="DictionaryLearning" selected="true">DictionaryLearning</option> | |
1631 <option value="FactorAnalysis">FactorAnalysis</option> | |
1632 <option value="FastICA">FastICA</option> | |
1633 <option value="IncrementalPCA">IncrementalPCA</option> | |
1634 <option value="KernelPCA">KernelPCA</option> | |
1635 <option value="LatentDirichletAllocation">LatentDirichletAllocation</option> | |
1636 <option value="MiniBatchDictionaryLearning">MiniBatchDictionaryLearning</option> | |
1637 <option value="MiniBatchSparsePCA">MiniBatchSparsePCA</option> | |
1638 <option value="NMF">NMF</option> | |
1639 <option value="PCA">PCA</option> | |
1640 <option value="SparsePCA">SparsePCA</option> | |
1641 <!--option value="SparseCoder">SparseCoder</option--> | |
1642 <option value="TruncatedSVD">TruncatedSVD</option> | |
1643 </param> | |
1644 <when value="DictionaryLearning"> | |
1645 <expand macro="estimator_params_text" | |
1646 help="Default(=blank): alpha=1, code_init=None, dict_init=None, fit_algorithm='lars', max_iter=1000, n_components=None, random_state=None, split_sign=False, tol=1e-08, transform_algorithm='omp', transform_alpha=None, transform_n_nonzero_coefs=None, verbose=False."/> | |
1647 </when> | |
1648 <when value="FactorAnalysis"> | |
1649 <expand macro="estimator_params_text" | |
1650 help="Default(=blank): copy=True, iterated_power=3, max_iter=1000, n_components=None, noise_variance_init=None, random_state=0, svd_method='randomized', tol=0.01."/> | |
1651 </when> | |
1652 <when value="FastICA"> | |
1653 <expand macro="estimator_params_text" | |
1654 help="Default(=blank): algorithm='parallel', fun='logcosh', fun_args=None, max_iter=200, n_components=None, random_state=None, tol=0.0001, w_init=None, whiten=True. No double quotes."/> | |
1655 </when> | |
1656 <when value="IncrementalPCA"> | |
1657 <expand macro="estimator_params_text" | |
1658 help="Default(=blank): batch_size=None, copy=True, n_components=None, whiten=False."/> | |
1659 </when> | |
1660 <when value="KernelPCA"> | |
1661 <expand macro="estimator_params_text" | |
1662 help="Default(=blank): alpha=1.0, coef0=1, copy_X=True, degree=3, eigen_solver='auto', fit_inverse_transform=False, gamma=None, kernel='linear', kernel_params=None, max_iter=None, n_components=None, random_state=None, remove_zero_eig=False, tol=0. No double quotes."/> | |
1663 </when> | |
1664 <when value="LatentDirichletAllocation"> | |
1665 <expand macro="estimator_params_text" | |
1666 help="Default(=blank): batch_size=128, doc_topic_prior=None, evaluate_every=-1, learning_decay=0.7, learning_method=None, learning_offset=10.0, max_doc_update_iter=100, max_iter=10, mean_change_tol=0.001, n_components=10, n_topics=None, perp_tol=0.1, random_state=None, topic_word_prior=None, total_samples=1000000.0, verbose=0."/> | |
1667 </when> | |
1668 <when value="MiniBatchDictionaryLearning"> | |
1669 <expand macro="estimator_params_text" | |
1670 help="Default(=blank): alpha=1, batch_size=3, dict_init=None, fit_algorithm='lars', n_components=None, n_iter=1000, random_state=None, shuffle=True, split_sign=False, transform_algorithm='omp', transform_alpha=None, transform_n_nonzero_coefs=None, verbose=False."/> | |
1671 </when> | |
1672 <when value="MiniBatchSparsePCA"> | |
1673 <expand macro="estimator_params_text" | |
1674 help="Default(=blank): alpha=1, batch_size=3, callback=None, method='lars', n_components=None, n_iter=100, random_state=None, ridge_alpha=0.01, shuffle=True, verbose=False."/> | |
1675 </when> | |
1676 <when value="NMF"> | |
1677 <expand macro="estimator_params_text" | |
1678 help="Default(=blank): alpha=0.0, beta_loss='frobenius', init=None, l1_ratio=0.0, max_iter=200, n_components=None, random_state=None, shuffle=False, solver='cd', tol=0.0001, verbose=0."/> | |
1679 </when> | |
1680 <when value="PCA"> | |
1681 <expand macro="estimator_params_text" | |
1682 help="Default(=blank): copy=True, iterated_power='auto', n_components=None, random_state=None, svd_solver='auto', tol=0.0, whiten=False."/> | |
1683 </when> | |
1684 <when value="SparsePCA"> | |
1685 <expand macro="estimator_params_text" | |
1686 help="Default(=blank): U_init=None, V_init=None, alpha=1, max_iter=1000, method='lars', n_components=None, random_state=None, ridge_alpha=0.01, tol=1e-08, verbose=False."/> | |
1687 </when> | |
1688 <when value="TruncatedSVD"> | |
1689 <expand macro="estimator_params_text" | |
1690 help="Default(=blank): algorithm='randomized', n_components=2, n_iter=5, random_state=None, tol=0.0."/> | |
1691 </when> | |
1692 </conditional> | |
1693 </xml> | |
1694 | |
1695 <xml name="FeatureAgglomeration"> | |
1696 <conditional name="FeatureAgglomeration_selector"> | |
1697 <param name="select_algorithm" type="select" label="Choose the algorithm:"> | |
1698 <option value="FeatureAgglomeration" selected="true">FeatureAgglomeration</option> | |
1699 </param> | |
1700 <when value="FeatureAgglomeration"> | |
1701 <expand macro="estimator_params_text" | |
1702 help="Default(=blank): affinity='euclidean', compute_full_tree='auto', connectivity=None, linkage='ward', memory=None, n_clusters=2, pooling_func=np.mean."/> | |
1703 </when> | |
1704 </conditional> | |
1705 </xml> | |
1706 | |
1707 <xml name="skrebate"> | |
1708 <conditional name="skrebate_selector"> | |
1709 <param name="select_algorithm" type="select" label="Choose the algorithm:"> | |
1710 <option value="ReliefF">ReliefF</option> | |
1711 <option value="SURF">SURF</option> | |
1712 <option value="SURFstar">SURFstar</option> | |
1713 <option value="MultiSURF">MultiSURF</option> | |
1714 <option value="MultiSURFstar">MultiSURFstar</option> | |
1715 <!--option value="TuRF">TuRF</option> --> | |
1716 </param> | |
1717 <when value="ReliefF"> | |
1718 <expand macro="estimator_params_text" | |
1719 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, n_neighbors=100, verbose=False."/> | |
1720 </when> | |
1721 <when value="SURF"> | |
1722 <expand macro="estimator_params_text" | |
1723 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False."/> | |
1724 </when> | |
1725 <when value="SURFstar"> | |
1726 <expand macro="estimator_params_text" | |
1727 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False."/> | |
1728 </when> | |
1729 <when value="MultiSURF"> | |
1730 <expand macro="estimator_params_text" | |
1731 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False."/> | |
1732 </when> | |
1733 <when value="MultiSURFstar"> | |
1734 <expand macro="estimator_params_text" | |
1735 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False."/> | |
1736 </when> | |
1737 <!--when value="TuRF"> | |
1738 <expand macro="estimator_params_text" | |
1739 help="Default(=blank): core_algorithm='ReliefF', discrete_threshold=10, n_features_to_select=10, n_neighbors=100, pct=0.5, verbose=False."/> | |
1740 </when> --> | |
1741 </conditional> | |
1742 </xml> | |
1743 | |
1744 <xml name="imbalanced_learn_sampling"> | |
1745 <conditional name="imblearn_selector"> | |
1746 <param name="select_algorithm" type="select" label="Choose the algorithm:"> | |
1747 <option value="under_sampling.ClusterCentroids" selected="true">under_sampling.ClusterCentroids</option> | |
1748 <option value="under_sampling.CondensedNearestNeighbour">under_sampling.CondensedNearestNeighbour</option> | |
1749 <option value="under_sampling.EditedNearestNeighbours">under_sampling.EditedNearestNeighbours</option> | |
1750 <option value="under_sampling.RepeatedEditedNearestNeighbours">under_sampling.RepeatedEditedNearestNeighbours</option> | |
1751 <option value="under_sampling.AllKNN">under_sampling.AllKNN</option> | |
1752 <option value="under_sampling.InstanceHardnessThreshold">under_sampling.InstanceHardnessThreshold</option> | |
1753 <option value="under_sampling.NearMiss">under_sampling.NearMiss</option> | |
1754 <option value="under_sampling.NeighbourhoodCleaningRule">under_sampling.NeighbourhoodCleaningRule</option> | |
1755 <option value="under_sampling.OneSidedSelection">under_sampling.OneSidedSelection</option> | |
1756 <option value="under_sampling.RandomUnderSampler">under_sampling.RandomUnderSampler</option> | |
1757 <option value="under_sampling.TomekLinks">under_sampling.TomekLinks</option> | |
1758 <option value="over_sampling.ADASYN">over_sampling.ADASYN</option> | |
1759 <option value="over_sampling.RandomOverSampler">over_sampling.RandomOverSampler</option> | |
1760 <option value="over_sampling.SMOTE">over_sampling.SMOTE</option> | |
1761 <option value="over_sampling.SVMSMOTE">over_sampling.SVMSMOTE</option> | |
1762 <option value="over_sampling.BorderlineSMOTE">over_sampling.BorderlineSMOTE</option> | |
1763 <option value="over_sampling.SMOTENC">over_sampling.SMOTENC</option> | |
1764 <option value="combine.SMOTEENN">combine.SMOTEENN</option> | |
1765 <option value="combine.SMOTETomek">combine.SMOTETomek</option> | |
1766 <option value="Z_RandomOverSampler">Z_RandomOverSampler - for regression</option> | |
1767 </param> | |
1768 <when value="under_sampling.ClusterCentroids"> | |
1769 <expand macro="estimator_params_text" | |
1770 help="Default(=blank): sampling_strategy='auto', random_state=None, estimator=None, voting='auto'."/> | |
1771 </when> | |
1772 <when value="under_sampling.CondensedNearestNeighbour"> | |
1773 <expand macro="estimator_params_text" | |
1774 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=None, n_seeds_S=1."/> | |
1775 </when> | |
1776 <when value="under_sampling.EditedNearestNeighbours"> | |
1777 <expand macro="estimator_params_text" | |
1778 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, max_iter=100, kind_sel='all'."/> | |
1779 </when> | |
1780 <when value="under_sampling.RepeatedEditedNearestNeighbours"> | |
1781 <expand macro="estimator_params_text" | |
1782 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, max_iter=100, kind_sel='all'."/> | |
1783 </when> | |
1784 <when value="under_sampling.AllKNN"> | |
1785 <expand macro="estimator_params_text" | |
1786 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, kind_sel='all', allow_minority=False."/> | |
1787 </when> | |
1788 <when value="under_sampling.InstanceHardnessThreshold"> | |
1789 <expand macro="estimator_params_text" | |
1790 help="Default(=blank): estimator=None, sampling_strategy='auto', random_state=None, cv=5."/> | |
1791 </when> | |
1792 <when value="under_sampling.NearMiss"> | |
1793 <expand macro="estimator_params_text" | |
1794 help="Default(=blank): sampling_strategy='auto', random_state=None, version=1, n_neighbors=3, n_neighbors_ver3=3."/> | |
1795 </when> | |
1796 <when value="under_sampling.NeighbourhoodCleaningRule"> | |
1797 <expand macro="estimator_params_text" | |
1798 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, kind_sel='all', threshold_cleaning=0.5."/> | |
1799 </when> | |
1800 <when value="under_sampling.OneSidedSelection"> | |
1801 <expand macro="estimator_params_text" | |
1802 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=None, n_seeds_S=1."/> | |
1803 </when> | |
1804 <when value="under_sampling.RandomUnderSampler"> | |
1805 <expand macro="estimator_params_text" | |
1806 help="Default(=blank): sampling_strategy='auto', random_state=None, replacement=False."/> | |
1807 </when> | |
1808 <when value="under_sampling.TomekLinks"> | |
1809 <expand macro="estimator_params_text" | |
1810 help="Default(=blank): sampling_strategy='auto', random_state=None."/> | |
1811 </when> | |
1812 <when value="over_sampling.ADASYN"> | |
1813 <expand macro="estimator_params_text" | |
1814 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=5."/> | |
1815 </when> | |
1816 <when value="over_sampling.RandomOverSampler"> | |
1817 <expand macro="estimator_params_text" | |
1818 help="Default(=blank): sampling_strategy='auto', random_state=None."/> | |
1819 </when> | |
1820 <when value="over_sampling.SMOTE"> | |
1821 <expand macro="estimator_params_text" | |
1822 help="Default(=blank): sampling_strategy='auto', random_state=None, k_neighbors=5."/> | |
1823 </when> | |
1824 <when value="over_sampling.SVMSMOTE"> | |
1825 <expand macro="estimator_params_text" | |
1826 help="Default(=blank): sampling_strategy='auto', k_neighbors=5, m_neighbors=10, out_step=0.5, random_state=None, svm_estimator=None."/> | |
1827 </when> | |
1828 <when value="over_sampling.BorderlineSMOTE"> | |
1829 <expand macro="estimator_params_text" | |
1830 help="Default(=blank): sampling_strategy='auto', k_neighbors=5, kind='borderline-1', m_neighbors=10, random_state=None."/> | |
1831 </when> | |
1832 <when value="over_sampling.SMOTENC"> | |
1833 <expand macro="estimator_params_text" | |
1834 help="Default: categorical_features=[], sampling_strategy='auto', random_state=None, k_neighbors=5."/> | |
1835 </when> | |
1836 <when value="combine.SMOTEENN"> | |
1837 <expand macro="estimator_params_text" | |
1838 help="Default(=blank): sampling_strategy='auto', random_state=None, smote=None, enn=None."/> | |
1839 </when> | |
1840 <when value="combine.SMOTETomek"> | |
1841 <expand macro="estimator_params_text" | |
1842 help="Default(=blank): sampling_strategy='auto', random_state=None, smote=None, tomek=None."/> | |
1843 </when> | |
1844 <when value="Z_RandomOverSampler"> | |
1845 <expand macro="estimator_params_text" | |
1846 help="Default(=blank): sampling_strategy='auto', random_state=None, negative_thres=0, positive_thres=-1."/> | |
1847 </when> | |
1848 </conditional> | |
1849 </xml> | |
1850 | |
1851 <xml name="stacking_ensemble_inputs"> | |
1852 <section name="options" title="Advanced Options" expanded="false"> | |
1853 <yield/> | |
1854 <param argument="use_features_in_secondary" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false"/> | |
1855 <param argument="store_train_meta_features" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false"/> | |
1856 </section> | |
1857 </xml> | |
1858 | |
1859 <xml name="stacking_base_estimator"> | |
1860 <conditional name="estimator_selector"> | |
1861 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" > | |
1862 <expand macro="estimator_module_options"> | |
1863 <option value="custom_estimator">Load a custom estimator</option> | |
1864 </expand> | 1864 </expand> |
1865 </param> | 1865 </conditional> |
1866 <expand macro="estimator_suboptions"> | 1866 </xml> |
1867 <when value="custom_estimator"> | 1867 |
1868 <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline"/> | 1868 <xml name="stacking_voting_weights"> |
1869 </when> | 1869 <section name="options" title="Advanced Options" expanded="false"> |
1870 </expand> | 1870 <param argument="weights" type="text" value="[]" optional="true" help="Sequence of weights (float or int). Uses uniform weights if None (`[]`)."> |
1871 </conditional> | 1871 <sanitizer> |
1872 </xml> | 1872 <valid initial="default"> |
1873 | 1873 <add value="[" /> |
1874 <xml name="stacking_voting_weights"> | 1874 <add value="]" /> |
1875 <section name="options" title="Advanced Options" expanded="false"> | 1875 </valid> |
1876 <param argument="weights" type="text" value="[]" optional="true" help="Sequence of weights (float or int). Uses uniform weights if None (`[]`)."> | 1876 </sanitizer> |
1877 <sanitizer> | 1877 </param> |
1878 <valid initial="default"> | 1878 <yield /> |
1879 <add value="["/> | 1879 </section> |
1880 <add value="]"/> | 1880 </xml> |
1881 </valid> | 1881 |
1882 </sanitizer> | 1882 <xml name="preprocessors_sequence_encoders"> |
1883 </param> | 1883 <conditional name="encoder_selection"> |
1884 <yield/> | 1884 <param name="encoder_type" type="select" label="Choose the sequence encoder class"> |
1885 </section> | 1885 <option value="GenomeOneHotEncoder">GenomeOneHotEncoder</option> |
1886 </xml> | 1886 <option value="ProteinOneHotEncoder">ProteinOneHotEncoder</option> |
1887 | 1887 </param> |
1888 <xml name="preprocessors_sequence_encoders"> | 1888 <when value="GenomeOneHotEncoder"> |
1889 <conditional name="encoder_selection"> | 1889 <expand macro="preprocessors_sequence_encoder_arguments" /> |
1890 <param name="encoder_type" type="select" label="Choose the sequence encoder class"> | 1890 </when> |
1891 <option value="GenomeOneHotEncoder">GenomeOneHotEncoder</option> | 1891 <when value="ProteinOneHotEncoder"> |
1892 <option value="ProteinOneHotEncoder">ProteinOneHotEncoder</option> | 1892 <expand macro="preprocessors_sequence_encoder_arguments" /> |
1893 </param> | 1893 </when> |
1894 <when value="GenomeOneHotEncoder"> | 1894 </conditional> |
1895 <expand macro="preprocessors_sequence_encoder_arguments"/> | 1895 </xml> |
1896 </when> | 1896 |
1897 <when value="ProteinOneHotEncoder"> | 1897 <xml name="preprocessors_sequence_encoder_arguments"> |
1898 <expand macro="preprocessors_sequence_encoder_arguments"/> | 1898 <param argument="seq_length" type="integer" value="" min="0" optional="true" help="Integer. Sequence length" /> |
1899 </when> | 1899 <param argument="padding" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" help="Whether to pad or truncate sequence to meet the sequence length." /> |
1900 </conditional> | 1900 </xml> |
1901 </xml> | 1901 |
1902 | 1902 <!-- Outputs --> |
1903 <xml name="preprocessors_sequence_encoder_arguments"> | 1903 |
1904 <param argument="seq_length" type="integer" value="" min="0" optional="true" help="Integer. Sequence length"/> | 1904 <xml name="output"> |
1905 <param argument="padding" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" help="Whether to pad or truncate sequence to meet the sequence length."/> | 1905 <outputs> |
1906 </xml> | 1906 <data format="tabular" name="outfile_predict"> |
1907 | 1907 <filter>selected_tasks['selected_task'] == 'load'</filter> |
1908 <!-- Outputs --> | 1908 </data> |
1909 | 1909 <data format="zip" name="outfile_fit" label="${tool.name}.${selected_tasks.selected_algorithms.selected_algorithm}"> |
1910 <xml name="output"> | 1910 <filter>selected_tasks['selected_task'] == 'train'</filter> |
1911 <outputs> | 1911 </data> |
1912 <data format="tabular" name="outfile_predict"> | 1912 </outputs> |
1913 <filter>selected_tasks['selected_task'] == 'load'</filter> | 1913 </xml> |
1914 </data> | 1914 |
1915 <data format="zip" name="outfile_fit" label="${tool.name}.${selected_tasks.selected_algorithms.selected_algorithm}"> | 1915 <!--Citations--> |
1916 <filter>selected_tasks['selected_task'] == 'train'</filter> | 1916 <xml name="eden_citation"> |
1917 </data> | 1917 <citations> |
1918 </outputs> | 1918 <citation type="doi">10.5281/zenodo.15094</citation> |
1919 </xml> | 1919 </citations> |
1920 | 1920 </xml> |
1921 <!--Citations--> | 1921 |
1922 <xml name="eden_citation"> | 1922 <xml name="sklearn_citation"> |
1923 <citations> | 1923 <citations> |
1924 <citation type="doi">10.5281/zenodo.15094</citation> | 1924 <citation type="bibtex"> |
1925 </citations> | 1925 @article{scikit-learn, title={Scikit-learn: Machine Learning in {P}ython}, author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V. |
1926 </xml> | |
1927 | |
1928 <xml name="sklearn_citation"> | |
1929 <citations> | |
1930 <citation type="bibtex"> | |
1931 @article{scikit-learn, | |
1932 title={Scikit-learn: Machine Learning in {P}ython}, | |
1933 author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V. | |
1934 and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P. | 1926 and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P. |
1935 and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and | 1927 and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and |
1936 Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.}, | 1928 Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.}, journal={Journal of Machine Learning Research}, volume={12}, pages={2825--2830}, year={2011} |
1937 journal={Journal of Machine Learning Research}, | |
1938 volume={12}, | |
1939 pages={2825--2830}, | |
1940 year={2011} | |
1941 } | 1929 } |
1942 </citation> | 1930 </citation> |
1943 <yield/> | 1931 <yield /> |
1944 </citations> | 1932 </citations> |
1945 </xml> | 1933 </xml> |
1946 | 1934 |
1947 <xml name="scipy_citation"> | 1935 <xml name="scipy_citation"> |
1948 <citations> | 1936 <citations> |
1949 <citation type="bibtex"> | 1937 <citation type="bibtex"> |
1950 @Misc{, | 1938 @Misc{, |
1951 author = {Eric Jones and Travis Oliphant and Pearu Peterson and others}, | 1939 author = {Eric Jones and Travis Oliphant and Pearu Peterson and others}, |
1952 title = {{SciPy}: Open source scientific tools for {Python}}, | 1940 title = {{SciPy}: Open source scientific tools for {Python}}, |
1953 year = {2001--}, | 1941 year = {2001--}, |
1954 url = "http://www.scipy.org/", | 1942 url = "http://www.scipy.org/", |
1955 note = {[Online; accessed 2016-04-09]} | 1943 note = {[Online; accessed 2016-04-09]} |
1956 } | 1944 } |
1957 </citation> | 1945 </citation> |
1958 </citations> | 1946 </citations> |
1959 </xml> | 1947 </xml> |
1960 | 1948 |
1961 <xml name="skrebate_citation"> | 1949 <xml name="skrebate_citation"> |
1962 <citation type="bibtex"> | 1950 <citation type="bibtex"> |
1963 @article{DBLP:journals/corr/abs-1711-08477, | 1951 @article{DBLP:journals/corr/abs-1711-08477, |
1964 author = {Ryan J. Urbanowicz and | 1952 author = {Ryan J. Urbanowicz and |
1965 Randal S. Olson and | 1953 Randal S. Olson and |
1966 Peter Schmitt and | 1954 Peter Schmitt and |
1967 Melissa Meeker and | 1955 Melissa Meeker and |
1975 eprint = {1711.08477}, | 1963 eprint = {1711.08477}, |
1976 timestamp = {Mon, 13 Aug 2018 16:46:04 +0200}, | 1964 timestamp = {Mon, 13 Aug 2018 16:46:04 +0200}, |
1977 biburl = {https://dblp.org/rec/bib/journals/corr/abs-1711-08477}, | 1965 biburl = {https://dblp.org/rec/bib/journals/corr/abs-1711-08477}, |
1978 bibsource = {dblp computer science bibliography, https://dblp.org} | 1966 bibsource = {dblp computer science bibliography, https://dblp.org} |
1979 } | 1967 } |
1980 </citation> | 1968 </citation> |
1981 </xml> | 1969 </xml> |
1982 | 1970 |
1983 <xml name="xgboost_citation"> | 1971 <xml name="xgboost_citation"> |
1984 <citation type="bibtex"> | 1972 <citation type="bibtex"> |
1985 @inproceedings{Chen:2016:XST:2939672.2939785, | 1973 @inproceedings{Chen:2016:XST:2939672.2939785, |
1986 author = {Chen, Tianqi and Guestrin, Carlos}, | 1974 author = {Chen, Tianqi and Guestrin, Carlos}, |
1987 title = {{XGBoost}: A Scalable Tree Boosting System}, | 1975 title = {{XGBoost}: A Scalable Tree Boosting System}, |
1988 booktitle = {Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining}, | 1976 booktitle = {Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining}, |
1989 series = {KDD '16}, | 1977 series = {KDD '16}, |
1997 acmid = {2939785}, | 1985 acmid = {2939785}, |
1998 publisher = {ACM}, | 1986 publisher = {ACM}, |
1999 address = {New York, NY, USA}, | 1987 address = {New York, NY, USA}, |
2000 keywords = {large-scale machine learning}, | 1988 keywords = {large-scale machine learning}, |
2001 } | 1989 } |
2002 </citation> | 1990 </citation> |
2003 </xml> | 1991 </xml> |
2004 | 1992 |
2005 <xml name="imblearn_citation"> | 1993 <xml name="imblearn_citation"> |
2006 <citation type="bibtex"> | 1994 <citation type="bibtex"> |
2007 @article{JMLR:v18:16-365, | 1995 @article{JMLR:v18:16-365, |
2008 author = {Guillaume Lema{{\^i}}tre and Fernando Nogueira and Christos K. Aridas}, | 1996 author = {Guillaume Lema{{\^i}}tre and Fernando Nogueira and Christos K. Aridas}, |
2009 title = {Imbalanced-learn: A Python Toolbox to Tackle the Curse of Imbalanced Datasets in Machine Learning}, | 1997 title = {Imbalanced-learn: A Python Toolbox to Tackle the Curse of Imbalanced Datasets in Machine Learning}, |
2010 journal = {Journal of Machine Learning Research}, | 1998 journal = {Journal of Machine Learning Research}, |
2011 year = {2017}, | 1999 year = {2017}, |
2012 volume = {18}, | 2000 volume = {18}, |
2013 number = {17}, | 2001 number = {17}, |
2014 pages = {1-5}, | 2002 pages = {1-5}, |
2015 url = {http://jmlr.org/papers/v18/16-365.html} | 2003 url = {http://jmlr.org/papers/v18/16-365.html} |
2016 } | 2004 } |
2017 </citation> | 2005 </citation> |
2018 </xml> | 2006 </xml> |
2019 | 2007 |
2020 <xml name="selene_citation"> | 2008 <xml name="selene_citation"> |
2021 <citation type="bibtex"> | 2009 <citation type="bibtex"> |
2022 @article{chen2019selene, | 2010 @article{chen2019selene, title={Selene: a PyTorch-based deep learning library for sequence data}, author={Chen, Kathleen M and Cofer, Evan M and Zhou, Jian and Troyanskaya, Olga G}, journal={Nature methods}, volume={16}, number={4}, pages={315}, year={2019}, publisher={Nature Publishing Group} |
2023 title={Selene: a PyTorch-based deep learning library for sequence data}, | |
2024 author={Chen, Kathleen M and Cofer, Evan M and Zhou, Jian and Troyanskaya, Olga G}, | |
2025 journal={Nature methods}, | |
2026 volume={16}, | |
2027 number={4}, | |
2028 pages={315}, | |
2029 year={2019}, | |
2030 publisher={Nature Publishing Group} | |
2031 } | 2011 } |
2032 </citation> | 2012 </citation> |
2033 </xml> | 2013 </xml> |
2034 | 2014 |
2035 </macros> | 2015 </macros> |