ddi-fw 0.0.183__tar.gz → 0.0.185__tar.gz

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Files changed (109) hide show
  1. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/PKG-INFO +1 -1
  2. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/pyproject.toml +1 -1
  3. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/core.py +21 -16
  4. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/ml/ml_helper.py +2 -2
  5. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/pipeline/pipeline.py +8 -7
  6. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw.egg-info/PKG-INFO +1 -1
  7. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/README.md +0 -0
  8. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/setup.cfg +0 -0
  9. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/__init__.py +0 -0
  10. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/dataset_splitter.py +0 -0
  11. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/db_utils.py +0 -0
  12. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/base.py +0 -0
  13. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/data/event.db +0 -0
  14. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/debug.log +0 -0
  15. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes/test_indexes.txt +0 -0
  16. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_0.txt +0 -0
  17. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_1.txt +0 -0
  18. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_2.txt +0 -0
  19. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_3.txt +0 -0
  20. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_4.txt +0 -0
  21. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes/train_indexes.txt +0 -0
  22. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_0.txt +0 -0
  23. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_1.txt +0 -0
  24. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_2.txt +0 -0
  25. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_3.txt +0 -0
  26. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_4.txt +0 -0
  27. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes_old/test_indexes.txt +0 -0
  28. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_0.txt +0 -0
  29. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_1.txt +0 -0
  30. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_2.txt +0 -0
  31. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_3.txt +0 -0
  32. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_4.txt +0 -0
  33. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_indexes.txt +0 -0
  34. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_0.txt +0 -0
  35. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_1.txt +0 -0
  36. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_2.txt +0 -0
  37. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_3.txt +0 -0
  38. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_4.txt +0 -0
  39. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl/readme.md +0 -0
  40. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl_text/base.py +0 -0
  41. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl_text/data/event.db +0 -0
  42. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl_text/indexes/test_indexes.txt +0 -0
  43. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_0.txt +0 -0
  44. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_1.txt +0 -0
  45. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_2.txt +0 -0
  46. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_3.txt +0 -0
  47. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_4.txt +0 -0
  48. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_indexes.txt +0 -0
  49. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_0.txt +0 -0
  50. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_1.txt +0 -0
  51. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_2.txt +0 -0
  52. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_3.txt +0 -0
  53. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_4.txt +0 -0
  54. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/mdf_sa_ddi/__init__.py +0 -0
  55. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/mdf_sa_ddi/base.py +0 -0
  56. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/mdf_sa_ddi/df_extraction_cleanxiaoyu50.csv +0 -0
  57. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/mdf_sa_ddi/drug_information_del_noDDIxiaoyu50.csv +0 -0
  58. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/test_indexes.txt +0 -0
  59. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_0.txt +0 -0
  60. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_1.txt +0 -0
  61. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_2.txt +0 -0
  62. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_3.txt +0 -0
  63. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_4.txt +0 -0
  64. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_indexes.txt +0 -0
  65. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_0.txt +0 -0
  66. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_1.txt +0 -0
  67. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_2.txt +0 -0
  68. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_3.txt +0 -0
  69. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_4.txt +0 -0
  70. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/mdf_sa_ddi/mdf-sa-ddi.zip +0 -0
  71. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/datasets/setup_._py +0 -0
  72. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/drugbank/__init__.py +0 -0
  73. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/drugbank/drugbank.xsd +0 -0
  74. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/drugbank/drugbank_parser.py +0 -0
  75. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/drugbank/drugbank_processor.py +0 -0
  76. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/drugbank/drugbank_processor_org.py +0 -0
  77. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/drugbank/event_extractor.py +0 -0
  78. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/langchain/__init__.py +0 -0
  79. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/langchain/embeddings.py +0 -0
  80. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/langchain/sentence_splitter.py +0 -0
  81. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/langchain/storage.py +0 -0
  82. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/ml/__init__.py +0 -0
  83. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/ml/evaluation_helper.py +0 -0
  84. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/ml/model_wrapper.py +0 -0
  85. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/ml/pytorch_wrapper.py +0 -0
  86. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/ml/tensorflow_wrapper.py +0 -0
  87. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/ner/__init__.py +0 -0
  88. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/ner/mmlrestclient.py +0 -0
  89. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/ner/ner.py +0 -0
  90. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/pipeline/__init__.py +0 -0
  91. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/pipeline/multi_modal_combination_strategy.py +0 -0
  92. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/pipeline/multi_pipeline.py +0 -0
  93. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/pipeline/ner_pipeline.py +0 -0
  94. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/utils/__init__.py +0 -0
  95. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/utils/categorical_data_encoding_checker.py +0 -0
  96. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/utils/enums.py +0 -0
  97. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/utils/json_helper.py +0 -0
  98. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/utils/kaggle.py +0 -0
  99. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/utils/package_helper.py +0 -0
  100. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/utils/py7zr_helper.py +0 -0
  101. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/utils/utils.py +0 -0
  102. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/utils/zip_helper.py +0 -0
  103. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/vectorization/__init__.py +0 -0
  104. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/vectorization/feature_vector_generation.py +0 -0
  105. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw/vectorization/idf_helper.py +0 -0
  106. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw.egg-info/SOURCES.txt +0 -0
  107. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw.egg-info/dependency_links.txt +0 -0
  108. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw.egg-info/requires.txt +0 -0
  109. {ddi_fw-0.0.183 → ddi_fw-0.0.185}/src/ddi_fw.egg-info/top_level.txt +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: ddi_fw
3
- Version: 0.0.183
3
+ Version: 0.0.185
4
4
  Summary: Do not use :)
5
5
  Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
6
6
  Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
6
6
 
7
7
  [project]
8
8
  name = "ddi_fw"
9
- version = "0.0.183"
9
+ version = "0.0.185"
10
10
  description = "Do not use :)"
11
11
  readme = "README.md"
12
12
  authors = [
@@ -77,17 +77,23 @@ class BaseDataset(BaseModel):
77
77
  items = []
78
78
  if self.X_train is None or self.X_test is None:
79
79
  raise Exception("There is no data to produce inputs")
80
- y_train_label, y_test_label = np.array(self.y_train), np.array(self.y_test)
81
-
82
- for index,column in enumerate(self.columns):
83
- train_data, test_data = self.X_train[:,index], self.X_test[:,index]
84
- items.append([f'{column}', np.nan_to_num(train_data),
85
- y_train_label, np.nan_to_num(test_data), y_test_label])
86
-
87
- # items.append([f'{column}_embedding', train_data,
88
- # y_train_label, test_data, y_test_label])
80
+ y_train_label, y_test_label = np.array(
81
+ self.y_train), np.array(self.y_test)
82
+
83
+ if self.columns is None or len(self.columns) == 0:
84
+ items.append([f'defaukt', np.nan_to_num(self.X_train),
85
+ y_train_label, np.nan_to_num(self.X_test), y_test_label])
86
+ else:
87
+ for index, column in enumerate(self.columns):
88
+ train_data, test_data = self.X_train[:,
89
+ index], self.X_test[:, index]
90
+ items.append([f'{column}', np.nan_to_num(train_data),
91
+ y_train_label, np.nan_to_num(test_data), y_test_label])
92
+
93
+ # items.append([f'{column}_embedding', train_data,
94
+ # y_train_label, test_data, y_test_label])
89
95
  return items
90
-
96
+
91
97
  def produce_inputs_ex(self):
92
98
  items = []
93
99
  if self.X_train is None or self.X_test is None:
@@ -145,16 +151,16 @@ class BaseDataset(BaseModel):
145
151
  train = self.dataframe[self.dataframe.index.isin(train_idx_all)]
146
152
  test = self.dataframe[self.dataframe.index.isin(test_idx_all)]
147
153
 
148
- self.X_train = train.drop(self.class_column, axis=1)
154
+ self.X_train = train.drop(self.class_column, axis=1)
149
155
  self.y_train = train[self.class_column]
150
156
  self.X_test = test.drop(self.class_column, axis=1)
151
157
  self.y_test = test[self.class_column]
152
-
158
+
153
159
  self.train_indexes = self.X_train.index
154
160
  self.test_indexes = self.X_test.index
155
161
  self.train_idx_arr = train_idx_arr
156
162
  self.val_idx_arr = val_idx_arr
157
-
163
+
158
164
  # Dataframe to numpy array conversion
159
165
  self.X_train = np.array(self.X_train)
160
166
  self.y_train = np.array(self.y_train)
@@ -201,13 +207,12 @@ class BaseDataset(BaseModel):
201
207
  if self.X_train is not None or self.X_test is not None:
202
208
  raise Exception(
203
209
  "X_train and X_test are already present. Splitting is not allowed.")
204
-
210
+
205
211
  self.prep()
206
212
  if self.dataframe is None:
207
213
  raise Exception("There is no dataframe to split.")
208
214
 
209
215
  save_path = self.index_path
210
-
211
216
 
212
217
  X = self.dataframe.drop(self.class_column, axis=1)
213
218
  y = self.dataframe[self.class_column]
@@ -222,7 +227,7 @@ class BaseDataset(BaseModel):
222
227
  self.test_indexes = X_test.index
223
228
  self.train_idx_arr = train_idx_arr
224
229
  self.val_idx_arr = val_idx_arr
225
-
230
+
226
231
  # Dataframe to numpy array conversion
227
232
  self.X_train = np.array(self.X_train)
228
233
  self.y_train = np.array(self.y_train.tolist())
@@ -99,8 +99,8 @@ class MultiModalRunner:
99
99
  def predict(self, combinations: list = [], generate_combinations=False):
100
100
  self.prefix = utils.utc_time_as_string()
101
101
  self.date = utils.utc_time_as_string_simple_format()
102
- sum = np.zeros(
103
- (self.y_test_label.shape[0], self.y_test_label.shape[1]))
102
+ # sum = np.zeros(
103
+ # (self.y_test_label.shape[0], self.y_test_label.shape[1]))
104
104
  single_results = dict()
105
105
 
106
106
  if generate_combinations:
@@ -199,7 +199,8 @@ class Pipeline(BaseModel):
199
199
  else:
200
200
  dataset = self.dataset_type(**kwargs)
201
201
 
202
- X_train, X_test, y_train, y_test, X_train.index, X_test.index, train_idx_arr, val_idx_arr = dataset.load()
202
+ # X_train, X_test, y_train, y_test, train_indexes, test_indexes, train_idx_arr, val_idx_arr = dataset.load()
203
+ dataset.load()
203
204
 
204
205
  dataframe = dataset.dataframe
205
206
 
@@ -207,12 +208,12 @@ class Pipeline(BaseModel):
207
208
  raise ValueError("The dataset is not loaded")
208
209
 
209
210
  # dataframe.dropna()
210
- X_train = dataset.X_train
211
- X_test = dataset.X_test
212
- y_train = dataset.y_train
213
- y_test = dataset.y_test
214
- self._train_idx_arr = dataset.train_idx_arr
215
- self._val_idx_arr = dataset.val_idx_arr
211
+ # X_train = dataset.X_train
212
+ # X_test = dataset.X_test
213
+ # y_train = dataset.y_train
214
+ # y_test = dataset.y_test
215
+ # self._train_idx_arr = dataset.train_idx_arr
216
+ # self._val_idx_arr = dataset.val_idx_arr
216
217
  # Logic to set up the experiment
217
218
  # column name, train data, train label, test data, test label
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219
  self._items = dataset.produce_inputs()
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: ddi_fw
3
- Version: 0.0.183
3
+ Version: 0.0.185
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4
  Summary: Do not use :)
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5
  Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
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6
  Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
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