Mercurial > repos > bgruening > create_tool_recommendation_model

annotate main.py @ 5:4f7e6612906b draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
author bgruening
date Fri, 06 May 2022 09:05:18 +0000
parents afec8c595124
children e94dc7945639
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9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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1 """
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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2 Predict next tools in the Galaxy workflows
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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3 using machine learning (recurrent neural network)
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4 """
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9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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6 import argparse
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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7 import time
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8
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9 import extract_workflow_connections
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10 import keras.callbacks as callbacks
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11 import numpy as np
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12 import optimise_hyperparameters
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13 import prepare_data
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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14 import utils
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17 class PredictTool:
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18 def __init__(self, num_cpus):
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19 """ Init method. """
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20
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21 def find_train_best_network(
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22 self,
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23 network_config,
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24 reverse_dictionary,
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25 train_data,
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26 train_labels,
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27 test_data,
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28 test_labels,
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29 n_epochs,
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30 class_weights,
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31 usage_pred,
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32 standard_connections,
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33 tool_freq,
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34 tool_tr_samples,
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35 ):
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36 """
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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37 Define recurrent neural network and train sequential data
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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38 """
3
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39 # get tools with lowest representation
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40 lowest_tool_ids = utils.get_lowest_tools(tool_freq)
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41
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42 print("Start hyperparameter optimisation...")
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43 hyper_opt = optimise_hyperparameters.HyperparameterOptimisation()
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44 best_params, best_model = hyper_opt.train_model(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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45 network_config,
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46 reverse_dictionary,
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47 train_data,
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48 train_labels,
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49 test_data,
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50 test_labels,
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51 tool_tr_samples,
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52 class_weights,
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53 )
0
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54
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55 # define callbacks
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56 early_stopping = callbacks.EarlyStopping(
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57 monitor="loss",
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58 mode="min",
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59 verbose=1,
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60 min_delta=1e-1,
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61 restore_best_weights=True,
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62 )
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63 predict_callback_test = PredictCallback(
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64 test_data,
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65 test_labels,
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66 reverse_dictionary,
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67 n_epochs,
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68 usage_pred,
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69 standard_connections,
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70 lowest_tool_ids,
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71 )
2
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72
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73 callbacks_list = [predict_callback_test, early_stopping]
3
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74 batch_size = int(best_params["batch_size"])
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75
0
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76 print("Start training on the best model...")
2
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77 train_performance = dict()
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78 trained_model = best_model.fit_generator(
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79 utils.balanced_sample_generator(
2
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80 train_data,
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81 train_labels,
3
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82 batch_size,
4
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83 tool_tr_samples,
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84 reverse_dictionary,
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85 ),
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86 steps_per_epoch=len(train_data) // batch_size,
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87 epochs=n_epochs,
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88 callbacks=callbacks_list,
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89 validation_data=(test_data, test_labels),
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90 verbose=2,
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91 shuffle=True,
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92 )
5
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93 train_performance["validation_loss"] = np.array(
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94 trained_model.history["val_loss"]
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95 )
3
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96 train_performance["precision"] = predict_callback_test.precision
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97 train_performance["usage_weights"] = predict_callback_test.usage_weights
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98 train_performance[
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99 "published_precision"
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100 ] = predict_callback_test.published_precision
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101 train_performance[
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102 "lowest_pub_precision"
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103 ] = predict_callback_test.lowest_pub_precision
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104 train_performance[
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105 "lowest_norm_precision"
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106 ] = predict_callback_test.lowest_norm_precision
2
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107 train_performance["train_loss"] = np.array(trained_model.history["loss"])
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108 train_performance["model"] = best_model
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109 train_performance["best_parameters"] = best_params
0
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110 return train_performance
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111
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112
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113 class PredictCallback(callbacks.Callback):
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114 def __init__(
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115 self,
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116 test_data,
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117 test_labels,
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118 reverse_data_dictionary,
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119 n_epochs,
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120 usg_scores,
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121 standard_connections,
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122 lowest_tool_ids,
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123 ):
0
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124 self.test_data = test_data
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125 self.test_labels = test_labels
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126 self.reverse_data_dictionary = reverse_data_dictionary
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127 self.precision = list()
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128 self.usage_weights = list()
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129 self.published_precision = list()
0
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130 self.n_epochs = n_epochs
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131 self.pred_usage_scores = usg_scores
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132 self.standard_connections = standard_connections
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133 self.lowest_tool_ids = lowest_tool_ids
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134 self.lowest_pub_precision = list()
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135 self.lowest_norm_precision = list()
0
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136
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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137 def on_epoch_end(self, epoch, logs={}):
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138 """
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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139 Compute absolute and compatible precision for test data
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140 """
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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141 if len(self.test_data) > 0:
5
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142 (
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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143 usage_weights,
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144 precision,
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145 precision_pub,
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146 low_pub_prec,
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147 low_norm_prec,
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148 low_num,
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149 ) = utils.verify_model(
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150 self.model,
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151 self.test_data,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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152 self.test_labels,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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153 self.reverse_data_dictionary,
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154 self.pred_usage_scores,
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155 self.standard_connections,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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156 self.lowest_tool_ids,
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157 )
0
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158 self.precision.append(precision)
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159 self.usage_weights.append(usage_weights)
3
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160 self.published_precision.append(precision_pub)
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161 self.lowest_pub_precision.append(low_pub_prec)
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162 self.lowest_norm_precision.append(low_norm_prec)
0
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163 print("Epoch %d usage weights: %s" % (epoch + 1, usage_weights))
3
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164 print("Epoch %d normal precision: %s" % (epoch + 1, precision))
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165 print("Epoch %d published precision: %s" % (epoch + 1, precision_pub))
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166 print("Epoch %d lowest published precision: %s" % (epoch + 1, low_pub_prec))
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167 print("Epoch %d lowest normal precision: %s" % (epoch + 1, low_norm_prec))
5
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168 print(
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169 "Epoch %d number of test samples with lowest tool ids: %s"
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170 % (epoch + 1, low_num)
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171 )
0
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172
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173
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174 if __name__ == "__main__":
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175 start_time = time.time()
2
76251d1ccdcc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 6fa2a0294d615c9f267b766337dca0b2d3637219"
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176
0
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177 arg_parser = argparse.ArgumentParser()
5
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178 arg_parser.add_argument(
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179 "-wf", "--workflow_file", required=True, help="workflows tabular file"
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180 )
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181 arg_parser.add_argument(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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182 "-tu", "--tool_usage_file", required=True, help="tool usage file"
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183 )
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184 arg_parser.add_argument(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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185 "-om", "--output_model", required=True, help="trained model file"
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186 )
0
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187 # data parameters
5
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188 arg_parser.add_argument(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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189 "-cd",
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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190 "--cutoff_date",
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191 required=True,
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192 help="earliest date for taking tool usage",
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193 )
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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194 arg_parser.add_argument(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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195 "-pl",
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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196 "--maximum_path_length",
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197 required=True,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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198 help="maximum length of tool path",
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199 )
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200 arg_parser.add_argument(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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201 "-ep",
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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202 "--n_epochs",
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203 required=True,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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204 help="number of iterations to run to create model",
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205 )
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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206 arg_parser.add_argument(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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207 "-oe",
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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208 "--optimize_n_epochs",
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209 required=True,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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210 help="number of iterations to run to find best model parameters",
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211 )
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212 arg_parser.add_argument(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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213 "-me",
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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214 "--max_evals",
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215 required=True,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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216 help="maximum number of configuration evaluations",
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217 )
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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218 arg_parser.add_argument(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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219 "-ts",
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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220 "--test_share",
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221 required=True,
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222 help="share of data to be used for testing",
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223 )
0
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224 # neural network parameters
5
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225 arg_parser.add_argument(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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226 "-bs",
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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227 "--batch_size",
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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228 required=True,
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229 help="size of the tranining batch i.e. the number of samples per batch",
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230 )
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231 arg_parser.add_argument(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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232 "-ut", "--units", required=True, help="number of hidden recurrent units"
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233 )
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234 arg_parser.add_argument(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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235 "-es",
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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236 "--embedding_size",
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237 required=True,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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238 help="size of the fixed vector learned for each tool",
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239 )
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240 arg_parser.add_argument(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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241 "-dt", "--dropout", required=True, help="percentage of neurons to be dropped"
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242 )
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243 arg_parser.add_argument(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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244 "-sd",
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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245 "--spatial_dropout",
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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246 required=True,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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247 help="1d dropout used for embedding layer",
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248 )
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249 arg_parser.add_argument(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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250 "-rd",
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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251 "--recurrent_dropout",
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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252 required=True,
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253 help="dropout for the recurrent layers",
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254 )
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
255 arg_parser.add_argument(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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256 "-lr", "--learning_rate", required=True, help="learning rate"
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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257 )
2
76251d1ccdcc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 6fa2a0294d615c9f267b766337dca0b2d3637219"
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258
0
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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259 # get argument values
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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260 args = vars(arg_parser.parse_args())
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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261 tool_usage_path = args["tool_usage_file"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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262 workflows_path = args["workflow_file"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
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263 cutoff_date = args["cutoff_date"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
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diff changeset
264 maximum_path_length = int(args["maximum_path_length"])
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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265 trained_model_path = args["output_model"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
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266 n_epochs = int(args["n_epochs"])
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
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267 optimize_n_epochs = int(args["optimize_n_epochs"])
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
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268 max_evals = int(args["max_evals"])
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
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269 test_share = float(args["test_share"])
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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270 batch_size = args["batch_size"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
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diff changeset
271 units = args["units"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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diff changeset
272 embedding_size = args["embedding_size"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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273 dropout = args["dropout"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
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diff changeset
274 spatial_dropout = args["spatial_dropout"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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275 recurrent_dropout = args["recurrent_dropout"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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276 learning_rate = args["learning_rate"]
2
76251d1ccdcc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 6fa2a0294d615c9f267b766337dca0b2d3637219"
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277 num_cpus = 16
0
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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278
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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279 config = {
5
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diff changeset
280 "cutoff_date": cutoff_date,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
281 "maximum_path_length": maximum_path_length,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
282 "n_epochs": n_epochs,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
283 "optimize_n_epochs": optimize_n_epochs,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
284 "max_evals": max_evals,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
285 "test_share": test_share,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
286 "batch_size": batch_size,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
287 "units": units,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
288 "embedding_size": embedding_size,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
289 "dropout": dropout,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
290 "spatial_dropout": spatial_dropout,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
291 "recurrent_dropout": recurrent_dropout,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
292 "learning_rate": learning_rate,
0
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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diff changeset
293 }
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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diff changeset
294
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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295 # Extract and process workflows
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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296 connections = extract_workflow_connections.ExtractWorkflowConnections()
5
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
297 (
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
298 workflow_paths,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
299 compatible_next_tools,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
300 standard_connections,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
301 ) = connections.read_tabular_file(workflows_path)
0
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
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diff changeset
302 # Process the paths from workflows
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
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diff changeset
303 print("Dividing data...")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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diff changeset
304 data = prepare_data.PrepareData(maximum_path_length, test_share)
5
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
305 (
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
306 train_data,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
307 train_labels,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
308 test_data,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
309 test_labels,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
310 data_dictionary,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
311 reverse_dictionary,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
312 class_weights,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
313 usage_pred,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
314 train_tool_freq,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
315 tool_tr_samples,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
316 ) = data.get_data_labels_matrices(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
317 workflow_paths,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
318 tool_usage_path,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
319 cutoff_date,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
320 compatible_next_tools,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
321 standard_connections,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
322 )
0
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
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diff changeset
323 # find the best model and start training
2
76251d1ccdcc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 6fa2a0294d615c9f267b766337dca0b2d3637219"
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diff changeset
324 predict_tool = PredictTool(num_cpus)
0
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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diff changeset
325 # start training with weighted classes
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
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diff changeset
326 print("Training with weighted classes and samples ...")
5
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
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diff changeset
327 results_weighted = predict_tool.find_train_best_network(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
328 config,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
329 reverse_dictionary,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
330 train_data,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
331 train_labels,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
332 test_data,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
333 test_labels,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
334 n_epochs,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
335 class_weights,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
336 usage_pred,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
337 standard_connections,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
parents: 4
diff changeset
338 train_tool_freq,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
339 tool_tr_samples,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
340 )
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
341 utils.save_model(
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
342 results_weighted,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
343 data_dictionary,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
344 compatible_next_tools,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
345 trained_model_path,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
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diff changeset
346 class_weights,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
parents: 4
diff changeset
347 standard_connections,
4f7e6612906b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
bgruening
parents: 4
diff changeset
348 )
0
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
349 end_time = time.time()
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
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350 print("Program finished in %s seconds" % str(end_time - start_time))