Mercurial > repos > bgruening > create_tool_recommendation_model

annotate main.py @ 1:12764915e1c5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit edeb85d311990eabd65f3c4576fbeabc6d9165c9"
author bgruening
date Wed, 25 Sep 2019 06:42:40 -0400
parents 9bf25dbe00ad
children 76251d1ccdcc
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
1 """
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
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"
bgruening
parents:
diff changeset
3 using machine learning (recurrent neural network)
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
4 """
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
5
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
6 import numpy as np
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
7 import argparse
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
8 import time
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
9
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
10 # machine learning library
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
11 import keras.callbacks as callbacks
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
12
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
13 import extract_workflow_connections
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
14 import prepare_data
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
15 import optimise_hyperparameters
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
16 import utils
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
17
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
18
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
19 class PredictTool:
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
20
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
21 @classmethod
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
22 def __init__(self):
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
23 """ Init method. """
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
24
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
25 @classmethod
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
26 def find_train_best_network(self, network_config, reverse_dictionary, train_data, train_labels, test_data, test_labels, n_epochs, class_weights, usage_pred, compatible_next_tools):
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
27 """
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
28 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"
bgruening
parents:
diff changeset
29 """
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
30 print("Start hyperparameter optimisation...")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
31 hyper_opt = optimise_hyperparameters.HyperparameterOptimisation()
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
32 best_params = hyper_opt.train_model(network_config, reverse_dictionary, train_data, train_labels, test_data, test_labels, class_weights)
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
33
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
34 # retrieve the model and train on complete dataset without validation set
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
35 model, best_params = utils.set_recurrent_network(best_params, reverse_dictionary, class_weights)
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
36
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
37 # define callbacks
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
38 predict_callback_test = PredictCallback(test_data, test_labels, reverse_dictionary, n_epochs, compatible_next_tools, usage_pred)
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
39 # tensor_board = callbacks.TensorBoard(log_dir=log_directory, histogram_freq=0, write_graph=True, write_images=True)
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
40 callbacks_list = [predict_callback_test]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
41
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
42 print("Start training on the best model...")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
43 model_fit = model.fit(
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
44 train_data,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
45 train_labels,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
46 batch_size=int(best_params["batch_size"]),
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
47 epochs=n_epochs,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
48 verbose=2,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
49 callbacks=callbacks_list,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
50 shuffle="batch",
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
51 validation_data=(test_data, test_labels)
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
52 )
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
53
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
54 train_performance = {
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
55 "train_loss": np.array(model_fit.history["loss"]),
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
56 "model": model,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
57 "best_parameters": best_params
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
58 }
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
59
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
60 # if there is test data, add more information
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
61 if len(test_data) > 0:
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
62 train_performance["validation_loss"] = np.array(model_fit.history["val_loss"])
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
63 train_performance["precision"] = predict_callback_test.precision
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
64 train_performance["usage_weights"] = predict_callback_test.usage_weights
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
65 return train_performance
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
66
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
67
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
68 class PredictCallback(callbacks.Callback):
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
69 def __init__(self, test_data, test_labels, reverse_data_dictionary, n_epochs, next_compatible_tools, usg_scores):
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
70 self.test_data = test_data
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
71 self.test_labels = test_labels
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
72 self.reverse_data_dictionary = reverse_data_dictionary
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
73 self.precision = list()
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
74 self.usage_weights = list()
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
75 self.n_epochs = n_epochs
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
76 self.next_compatible_tools = next_compatible_tools
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
77 self.pred_usage_scores = usg_scores
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
78
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
79 def on_epoch_end(self, epoch, logs={}):
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
80 """
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
81 Compute absolute and compatible precision for test data
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
82 """
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
83 if len(self.test_data) > 0:
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
84 precision, usage_weights = utils.verify_model(self.model, self.test_data, self.test_labels, self.reverse_data_dictionary, self.next_compatible_tools, self.pred_usage_scores)
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
85 self.precision.append(precision)
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
86 self.usage_weights.append(usage_weights)
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
87 print("Epoch %d precision: %s" % (epoch + 1, precision))
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
88 print("Epoch %d usage weights: %s" % (epoch + 1, usage_weights))
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
89
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
90
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
91 if __name__ == "__main__":
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
92 start_time = time.time()
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
93 arg_parser = argparse.ArgumentParser()
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
94 arg_parser.add_argument("-wf", "--workflow_file", required=True, help="workflows tabular file")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
95 arg_parser.add_argument("-tu", "--tool_usage_file", required=True, help="tool usage file")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
96 arg_parser.add_argument("-om", "--output_model", required=True, help="trained model file")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
97 # data parameters
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
98 arg_parser.add_argument("-cd", "--cutoff_date", required=True, help="earliest date for taking tool usage")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
99 arg_parser.add_argument("-pl", "--maximum_path_length", required=True, help="maximum length of tool path")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
100 arg_parser.add_argument("-ep", "--n_epochs", required=True, help="number of iterations to run to create model")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
101 arg_parser.add_argument("-oe", "--optimize_n_epochs", required=True, help="number of iterations to run to find best model parameters")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
102 arg_parser.add_argument("-me", "--max_evals", required=True, help="maximum number of configuration evaluations")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
103 arg_parser.add_argument("-ts", "--test_share", required=True, help="share of data to be used for testing")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
104 arg_parser.add_argument("-vs", "--validation_share", required=True, help="share of data to be used for validation")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
105 # neural network parameters
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
106 arg_parser.add_argument("-bs", "--batch_size", required=True, help="size of the tranining batch i.e. the number of samples per batch")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
107 arg_parser.add_argument("-ut", "--units", required=True, help="number of hidden recurrent units")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
108 arg_parser.add_argument("-es", "--embedding_size", required=True, help="size of the fixed vector learned for each tool")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
109 arg_parser.add_argument("-dt", "--dropout", required=True, help="percentage of neurons to be dropped")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
110 arg_parser.add_argument("-sd", "--spatial_dropout", required=True, help="1d dropout used for embedding layer")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
111 arg_parser.add_argument("-rd", "--recurrent_dropout", required=True, help="dropout for the recurrent layers")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
112 arg_parser.add_argument("-lr", "--learning_rate", required=True, help="learning rate")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
113 arg_parser.add_argument("-ar", "--activation_recurrent", required=True, help="activation function for recurrent layers")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
114 arg_parser.add_argument("-ao", "--activation_output", required=True, help="activation function for output layers")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
115 # get argument values
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
116 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"
bgruening
parents:
diff changeset
117 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"
bgruening
parents:
diff changeset
118 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
parents:
diff changeset
119 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
parents:
diff changeset
120 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"
bgruening
parents:
diff changeset
121 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
parents:
diff changeset
122 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
parents:
diff changeset
123 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
parents:
diff changeset
124 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
parents:
diff changeset
125 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"
bgruening
parents:
diff changeset
126 validation_share = float(args["validation_share"])
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
127 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
parents:
diff changeset
128 units = args["units"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
129 embedding_size = args["embedding_size"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
130 dropout = args["dropout"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
131 spatial_dropout = args["spatial_dropout"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
132 recurrent_dropout = args["recurrent_dropout"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
133 learning_rate = args["learning_rate"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
134 activation_recurrent = args["activation_recurrent"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
135 activation_output = args["activation_output"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
136
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
137 config = {
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
138 'cutoff_date': cutoff_date,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
139 'maximum_path_length': maximum_path_length,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
140 'n_epochs': n_epochs,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
141 'optimize_n_epochs': optimize_n_epochs,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
142 'max_evals': max_evals,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
143 'test_share': test_share,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
144 'validation_share': validation_share,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
145 'batch_size': batch_size,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
146 'units': units,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
147 'embedding_size': embedding_size,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
148 'dropout': dropout,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
149 'spatial_dropout': spatial_dropout,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
150 'recurrent_dropout': recurrent_dropout,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
151 'learning_rate': learning_rate,
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
152 'activation_recurrent': activation_recurrent,
1
12764915e1c5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit edeb85d311990eabd65f3c4576fbeabc6d9165c9"
bgruening
parents: 0
diff changeset
153 'activation_output': activation_output
0
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
154 }
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
155
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
156 # Extract and process workflows
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
157 connections = extract_workflow_connections.ExtractWorkflowConnections()
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
158 workflow_paths, compatible_next_tools = connections.read_tabular_file(workflows_path)
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
159 # 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
parents:
diff changeset
160 print("Dividing data...")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
161 data = prepare_data.PrepareData(maximum_path_length, test_share)
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
162 train_data, train_labels, test_data, test_labels, data_dictionary, reverse_dictionary, class_weights, usage_pred = data.get_data_labels_matrices(workflow_paths, tool_usage_path, cutoff_date, compatible_next_tools)
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
163 # find the best model and start training
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
164 predict_tool = PredictTool()
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
165 # 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
parents:
diff changeset
166 print("Training with weighted classes and samples ...")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
167 results_weighted = predict_tool.find_train_best_network(config, reverse_dictionary, train_data, train_labels, test_data, test_labels, n_epochs, class_weights, usage_pred, compatible_next_tools)
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
168 print()
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
169 print("Best parameters \n")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
170 print(results_weighted["best_parameters"])
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
171 print()
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
172 utils.save_model(results_weighted, data_dictionary, compatible_next_tools, trained_model_path, class_weights)
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
173 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:
diff changeset
174 print()
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
175 print("Program finished in %s seconds" % str(end_time - start_time))