Mercurial > repos > bgruening > create_tool_recommendation_model

annotate utils.py @ 0:22ebbac136c7 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 7fac577189d01cedd01118a77fc2baaefe7d5cad"
author bgruening
date Wed, 28 Aug 2019 07:19:13 -0400
parents
children 50753817983a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
1 import os
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
2 import numpy as np
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
3 import json
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
4 import h5py
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
5
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
6 from keras.models import model_from_json, Sequential
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
7 from keras.layers import Dense, GRU, Dropout
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
8 from keras.layers.embeddings import Embedding
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
9 from keras.layers.core import SpatialDropout1D
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
10 from keras.optimizers import RMSprop
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
11 from keras import backend as K
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
12
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
13
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
14 def read_file(file_path):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
15 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
16 Read a file
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
17 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
18 with open(file_path, "r") as json_file:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
19 file_content = json.loads(json_file.read())
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
20 return file_content
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
21
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
22
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
23 def write_file(file_path, content):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
24 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
25 Write a file
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
26 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
27 remove_file(file_path)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
28 with open(file_path, "w") as json_file:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
29 json_file.write(json.dumps(content))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
30
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
31
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
32 def save_processed_workflows(file_path, unique_paths):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
33 workflow_paths_unique = ""
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
34 for path in unique_paths:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
35 workflow_paths_unique += path + "\n"
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
36 with open(file_path, "w") as workflows_file:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
37 workflows_file.write(workflow_paths_unique)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
38
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
39
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
40 def load_saved_model(model_config, model_weights):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
41 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
42 Load the saved trained model using the saved network and its weights
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
43 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
44 # load the network
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
45 loaded_model = model_from_json(model_config)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
46 # load the saved weights into the model
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
47 loaded_model.set_weights(model_weights)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
48 return loaded_model
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
49
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
50
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
51 def format_tool_id(tool_link):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
52 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
53 Extract tool id from tool link
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
54 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
55 tool_id_split = tool_link.split("/")
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
56 tool_id = tool_id_split[-2] if len(tool_id_split) > 1 else tool_link
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
57 return tool_id
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
58
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
59
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
60 def get_HDF5(hf, d_key):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
61 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
62 Read h5 file to get train and test data
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
63 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
64 return hf.get(d_key).value
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
65
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
66
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
67 def save_HDF5(hf_file, d_key, data, d_type=""):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
68 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
69 Save datasets as h5 file
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
70 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
71 if (d_type == 'json'):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
72 data = json.dumps(data)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
73 hf_file.create_dataset(d_key, data=data)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
74
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
75
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
76 def set_trained_model(dump_file, model_values):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
77 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
78 Create an h5 file with the trained weights and associated dicts
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
79 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
80 hf_file = h5py.File(dump_file, 'w')
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
81 for key in model_values:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
82 value = model_values[key]
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
83 if key == 'model_weights':
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
84 for idx, item in enumerate(value):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
85 w_key = "weight_" + str(idx)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
86 if w_key in hf_file:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
87 hf_file.modify(w_key, item)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
88 else:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
89 hf_file.create_dataset(w_key, data=item)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
90 else:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
91 if key in hf_file:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
92 hf_file.modify(key, json.dumps(value))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
93 else:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
94 hf_file.create_dataset(key, data=json.dumps(value))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
95 hf_file.close()
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
96
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
97
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
98 def remove_file(file_path):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
99 if os.path.exists(file_path):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
100 os.remove(file_path)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
101
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
102
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
103 def extract_configuration(config_object):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
104 config_loss = dict()
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
105 for index, item in enumerate(config_object):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
106 config_loss[index] = list()
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
107 d_config = dict()
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
108 d_config['loss'] = item['result']['loss']
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
109 d_config['params_config'] = item['misc']['vals']
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
110 config_loss[index].append(d_config)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
111 return config_loss
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
112
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
113
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
114 def get_best_parameters(mdl_dict):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
115 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
116 Get param values (defaults as well)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
117 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
118 lr = float(mdl_dict.get("learning_rate", "0.001"))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
119 embedding_size = int(mdl_dict.get("embedding_size", "512"))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
120 dropout = float(mdl_dict.get("dropout", "0.2"))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
121 recurrent_dropout = float(mdl_dict.get("recurrent_dropout", "0.2"))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
122 spatial_dropout = float(mdl_dict.get("spatial_dropout", "0.2"))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
123 units = int(mdl_dict.get("units", "512"))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
124 batch_size = int(mdl_dict.get("batch_size", "512"))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
125 activation_recurrent = mdl_dict.get("activation_recurrent", "elu")
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
126 activation_output = mdl_dict.get("activation_output", "sigmoid")
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
127
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
128 return {
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
129 "lr": lr,
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
130 "embedding_size": embedding_size,
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
131 "dropout": dropout,
22ebbac136c7 "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": recurrent_dropout,
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
133 "spatial_dropout": spatial_dropout,
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
134 "units": units,
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
135 "batch_size": batch_size,
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
136 "activation_recurrent": activation_recurrent,
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
137 "activation_output": activation_output,
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
138 }
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
139
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
140
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
141 def weighted_loss(class_weights):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
142 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
143 Create a weighted loss function. Penalise the misclassification
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
144 of classes more with the higher usage
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
145 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
146 weight_values = list(class_weights.values())
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
147
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
148 def weighted_binary_crossentropy(y_true, y_pred):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
149 # add another dimension to compute dot product
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
150 expanded_weights = K.expand_dims(weight_values, axis=-1)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
151 return K.dot(K.binary_crossentropy(y_true, y_pred), expanded_weights)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
152 return weighted_binary_crossentropy
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
153
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
154
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
155 def set_recurrent_network(mdl_dict, reverse_dictionary, class_weights):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
156 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
157 Create a RNN network and set its parameters
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
158 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
159 dimensions = len(reverse_dictionary) + 1
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
160 model_params = get_best_parameters(mdl_dict)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
161
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
162 # define the architecture of the neural network
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
163 model = Sequential()
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
164 model.add(Embedding(dimensions, model_params["embedding_size"], mask_zero=True))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
165 model.add(SpatialDropout1D(model_params["spatial_dropout"]))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
166 model.add(GRU(model_params["units"], dropout=model_params["spatial_dropout"], recurrent_dropout=model_params["recurrent_dropout"], activation=model_params["activation_recurrent"], return_sequences=True))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
167 model.add(Dropout(model_params["dropout"]))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
168 model.add(GRU(model_params["units"], dropout=model_params["spatial_dropout"], recurrent_dropout=model_params["recurrent_dropout"], activation=model_params["activation_recurrent"], return_sequences=False))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
169 model.add(Dropout(model_params["dropout"]))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
170 model.add(Dense(dimensions, activation=model_params["activation_output"]))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
171 optimizer = RMSprop(lr=model_params["lr"])
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
172 model.compile(loss=weighted_loss(class_weights), optimizer=optimizer)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
173 return model, model_params
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
174
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
175
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
176 def compute_precision(model, x, y, reverse_data_dictionary, next_compatible_tools, usage_scores, actual_classes_pos, topk):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
177 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
178 Compute absolute and compatible precision
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
179 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
180 absolute_precision = 0.0
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
181 test_sample = np.reshape(x, (1, len(x)))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
182
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
183 # predict next tools for a test path
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
184 prediction = model.predict(test_sample, verbose=0)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
185
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
186 nw_dimension = prediction.shape[1]
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
187
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
188 # remove the 0th position as there is no tool at this index
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
189 prediction = np.reshape(prediction, (nw_dimension,))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
190
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
191 prediction_pos = np.argsort(prediction, axis=-1)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
192 topk_prediction_pos = prediction_pos[-topk:]
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
193
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
194 # remove the wrong tool position from the predicted list of tool positions
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
195 topk_prediction_pos = [x for x in topk_prediction_pos if x > 0]
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
196
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
197 # read tool names using reverse dictionary
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
198 actual_next_tool_names = [reverse_data_dictionary[int(tool_pos)] for tool_pos in actual_classes_pos]
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
199 top_predicted_next_tool_names = [reverse_data_dictionary[int(tool_pos)] for tool_pos in topk_prediction_pos]
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
200
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
201 # compute the class weights of predicted tools
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
202 mean_usg_score = 0
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
203 usg_wt_scores = list()
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
204 for t_id in topk_prediction_pos:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
205 t_name = reverse_data_dictionary[int(t_id)]
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
206 if t_id in usage_scores and t_name in actual_next_tool_names:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
207 usg_wt_scores.append(np.log(usage_scores[t_id] + 1.0))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
208 if len(usg_wt_scores) > 0:
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
209 mean_usg_score = np.sum(usg_wt_scores) / float(topk)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
210 false_positives = [tool_name for tool_name in top_predicted_next_tool_names if tool_name not in actual_next_tool_names]
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
211 absolute_precision = 1 - (len(false_positives) / float(topk))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
212 return mean_usg_score, absolute_precision
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
213
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
214
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
215 def verify_model(model, x, y, reverse_data_dictionary, next_compatible_tools, usage_scores, topk_list=[1, 2, 3]):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
216 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
217 Verify the model on test data
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
218 """
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
219 print("Evaluating performance on test data...")
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
220 print("Test data size: %d" % len(y))
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
221 size = y.shape[0]
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
222 precision = np.zeros([len(y), len(topk_list)])
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
223 usage_weights = np.zeros([len(y), len(topk_list)])
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
224 # loop over all the test samples and find prediction precision
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
225 for i in range(size):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
226 actual_classes_pos = np.where(y[i] > 0)[0]
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
227 for index, abs_topk in enumerate(topk_list):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
228 abs_mean_usg_score, absolute_precision = compute_precision(model, x[i, :], y, reverse_data_dictionary, next_compatible_tools, usage_scores, actual_classes_pos, abs_topk)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
229 precision[i][index] = absolute_precision
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
230 usage_weights[i][index] = abs_mean_usg_score
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
231 mean_precision = np.mean(precision, axis=0)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
232 mean_usage = np.mean(usage_weights, axis=0)
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
233 return mean_precision, mean_usage
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
234
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
235
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
236 def save_model(results, data_dictionary, compatible_next_tools, trained_model_path, class_weights):
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
237 # save files
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
238 trained_model = results["model"]
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
239 best_model_parameters = results["best_parameters"]
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
240 model_config = trained_model.to_json()
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
241 model_weights = trained_model.get_weights()
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
242
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
243 model_values = {
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
244 'data_dictionary': data_dictionary,
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
245 'model_config': model_config,
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
246 'best_parameters': best_model_parameters,
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
247 'model_weights': model_weights,
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
248 "compatible_tools": compatible_next_tools,
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
249 "class_weights": class_weights
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
250 }
22ebbac136c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
251 set_trained_model(trained_model_path, model_values)