ddi-fw 0.0.179__tar.gz → 0.0.180__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (109) hide show
  1. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/PKG-INFO +1 -1
  2. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/pyproject.toml +1 -1
  3. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/ml/tensorflow_wrapper.py +10 -4
  4. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/utils/__init__.py +2 -1
  5. ddi_fw-0.0.180/src/ddi_fw/utils/categorical_data_encoding_checker.py +32 -0
  6. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw.egg-info/PKG-INFO +1 -1
  7. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw.egg-info/SOURCES.txt +1 -0
  8. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/README.md +0 -0
  9. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/setup.cfg +0 -0
  10. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/__init__.py +0 -0
  11. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/core.py +0 -0
  12. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/dataset_splitter.py +0 -0
  13. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/db_utils.py +0 -0
  14. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/base.py +0 -0
  15. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/data/event.db +0 -0
  16. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/debug.log +0 -0
  17. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes/test_indexes.txt +0 -0
  18. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_0.txt +0 -0
  19. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_1.txt +0 -0
  20. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_2.txt +0 -0
  21. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_3.txt +0 -0
  22. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_4.txt +0 -0
  23. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes/train_indexes.txt +0 -0
  24. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_0.txt +0 -0
  25. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_1.txt +0 -0
  26. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_2.txt +0 -0
  27. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_3.txt +0 -0
  28. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_4.txt +0 -0
  29. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes_old/test_indexes.txt +0 -0
  30. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_0.txt +0 -0
  31. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_1.txt +0 -0
  32. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_2.txt +0 -0
  33. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_3.txt +0 -0
  34. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_4.txt +0 -0
  35. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_indexes.txt +0 -0
  36. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_0.txt +0 -0
  37. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_1.txt +0 -0
  38. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_2.txt +0 -0
  39. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_3.txt +0 -0
  40. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_4.txt +0 -0
  41. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl/readme.md +0 -0
  42. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl_text/base.py +0 -0
  43. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl_text/data/event.db +0 -0
  44. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl_text/indexes/test_indexes.txt +0 -0
  45. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_0.txt +0 -0
  46. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_1.txt +0 -0
  47. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_2.txt +0 -0
  48. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_3.txt +0 -0
  49. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_4.txt +0 -0
  50. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_indexes.txt +0 -0
  51. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_0.txt +0 -0
  52. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_1.txt +0 -0
  53. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_2.txt +0 -0
  54. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_3.txt +0 -0
  55. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_4.txt +0 -0
  56. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/mdf_sa_ddi/__init__.py +0 -0
  57. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/mdf_sa_ddi/base.py +0 -0
  58. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/mdf_sa_ddi/df_extraction_cleanxiaoyu50.csv +0 -0
  59. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/mdf_sa_ddi/drug_information_del_noDDIxiaoyu50.csv +0 -0
  60. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/test_indexes.txt +0 -0
  61. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_0.txt +0 -0
  62. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_1.txt +0 -0
  63. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_2.txt +0 -0
  64. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_3.txt +0 -0
  65. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_4.txt +0 -0
  66. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_indexes.txt +0 -0
  67. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_0.txt +0 -0
  68. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_1.txt +0 -0
  69. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_2.txt +0 -0
  70. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_3.txt +0 -0
  71. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_4.txt +0 -0
  72. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/mdf_sa_ddi/mdf-sa-ddi.zip +0 -0
  73. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/datasets/setup_._py +0 -0
  74. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/drugbank/__init__.py +0 -0
  75. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/drugbank/drugbank.xsd +0 -0
  76. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/drugbank/drugbank_parser.py +0 -0
  77. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/drugbank/drugbank_processor.py +0 -0
  78. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/drugbank/drugbank_processor_org.py +0 -0
  79. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/drugbank/event_extractor.py +0 -0
  80. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/langchain/__init__.py +0 -0
  81. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/langchain/embeddings.py +0 -0
  82. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/langchain/sentence_splitter.py +0 -0
  83. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/langchain/storage.py +0 -0
  84. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/ml/__init__.py +0 -0
  85. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/ml/evaluation_helper.py +0 -0
  86. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/ml/ml_helper.py +0 -0
  87. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/ml/model_wrapper.py +0 -0
  88. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/ml/pytorch_wrapper.py +0 -0
  89. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/ner/__init__.py +0 -0
  90. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/ner/mmlrestclient.py +0 -0
  91. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/ner/ner.py +0 -0
  92. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/pipeline/__init__.py +0 -0
  93. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/pipeline/multi_modal_combination_strategy.py +0 -0
  94. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/pipeline/multi_pipeline.py +0 -0
  95. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/pipeline/ner_pipeline.py +0 -0
  96. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/pipeline/pipeline.py +0 -0
  97. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/utils/enums.py +0 -0
  98. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/utils/json_helper.py +0 -0
  99. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/utils/kaggle.py +0 -0
  100. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/utils/package_helper.py +0 -0
  101. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/utils/py7zr_helper.py +0 -0
  102. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/utils/utils.py +0 -0
  103. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/utils/zip_helper.py +0 -0
  104. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/vectorization/__init__.py +0 -0
  105. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/vectorization/feature_vector_generation.py +0 -0
  106. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw/vectorization/idf_helper.py +0 -0
  107. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw.egg-info/dependency_links.txt +0 -0
  108. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/src/ddi_fw.egg-info/requires.txt +0 -0
  109. {ddi_fw-0.0.179 → ddi_fw-0.0.180}/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: 0.0.179
3
+ Version: 0.0.180
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 = "0.0.179"
9
+ version = "0.0.180"
10
10
  description = "Do not use :)"
11
11
  readme = "README.md"
12
12
  authors = [
@@ -136,8 +136,11 @@ class TFModelWrapper(ModelWrapper):
136
136
  print(best_model_key)
137
137
  self.best_model: Model = best_model
138
138
  pred = self.predict()
139
- pred = tf.keras.utils.to_categorical(np.argmax(pred,axis=1), num_classes=self.num_classes)
140
- actual = tf.keras.utils.to_categorical(self.test_label, num_classes=self.num_classes)
139
+ actual = self.test_label
140
+ if not utils.is_binary_encoded(pred):
141
+ pred = tf.keras.utils.to_categorical(np.argmax(pred,axis=1), num_classes=self.num_classes)
142
+ if not utils.is_binary_encoded(actual):
143
+ actual = tf.keras.utils.to_categorical(actual, num_classes=self.num_classes)
141
144
 
142
145
  logs, metrics = evaluate(
143
146
  actual=actual, pred=pred, info=self.descriptor, print_detail=print_detail)
@@ -155,8 +158,11 @@ class TFModelWrapper(ModelWrapper):
155
158
  print(best_model_key)
156
159
  self.best_model = best_model
157
160
  pred = self.predict()
158
- pred = tf.keras.utils.to_categorical(np.argmax(pred,axis=1), num_classes=self.num_classes)
159
- actual = tf.keras.utils.to_categorical(self.test_label, num_classes=self.num_classes)
161
+ actual = self.test_label
162
+ if not utils.is_binary_encoded(pred):
163
+ pred = tf.keras.utils.to_categorical(np.argmax(pred,axis=1), num_classes=self.num_classes)
164
+ if not utils.is_binary_encoded(actual):
165
+ actual = tf.keras.utils.to_categorical(actual, num_classes=self.num_classes)
160
166
 
161
167
  logs, metrics = evaluate(
162
168
  actual=actual, pred=pred, info=self.descriptor)
@@ -3,4 +3,5 @@ from .zip_helper import ZipHelper
3
3
  from .py7zr_helper import Py7ZipHelper
4
4
  from .enums import UMLSCodeTypes, DrugBankTextDataTypes
5
5
  from .package_helper import get_import
6
- from .kaggle import create_kaggle_dataset
6
+ from .kaggle import create_kaggle_dataset
7
+ from .categorical_data_encoding_checker import is_one_hot_encoded, is_binary_encoded, is_binary_vector
@@ -0,0 +1,32 @@
1
+ import numpy as np
2
+
3
+
4
+ def is_one_hot_encoded(arr):
5
+ # Check if the array is one-hot encoded
6
+ # Ensure the input is a numpy ndarray and is 2D
7
+ if not isinstance(arr, np.ndarray):
8
+ raise ValueError("Input must be a NumPy ndarray.")
9
+ if not np.all(np.isin(arr, [0, 1])):
10
+ return False
11
+ # Check if each row (or column) has exactly one "1"
12
+ return np.all(np.sum(arr, axis=1) == 1) # For row-wise checking
13
+
14
+
15
+ def is_binary_encoded(arr):
16
+ # Ensure the input is a numpy ndarray and is 2D
17
+ if not isinstance(arr, np.ndarray):
18
+ raise ValueError("Input must be a NumPy ndarray.")
19
+ if arr.ndim != 2:
20
+ raise ValueError("Input must be a 2D array.")
21
+
22
+ # Check if all elements are either 0 or 1
23
+ return np.all(np.isin(arr, [0, 1]))
24
+
25
+
26
+ def is_binary_vector(arr):
27
+ # Ensure the input is a numpy ndarray and is 1D
28
+ if not isinstance(arr, np.ndarray):
29
+ raise ValueError("Input must be a NumPy ndarray.")
30
+ if arr.ndim != 1:
31
+ raise ValueError("Input must be a 1D array.")
32
+ return arr.ndim == 1 and np.all(np.isin(arr, [0, 1]))
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: ddi_fw
3
- Version: 0.0.179
3
+ Version: 0.0.180
4
4
  Summary: Do not use :)
5
5
  Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
6
6
  Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
@@ -94,6 +94,7 @@ src/ddi_fw/pipeline/multi_pipeline.py
94
94
  src/ddi_fw/pipeline/ner_pipeline.py
95
95
  src/ddi_fw/pipeline/pipeline.py
96
96
  src/ddi_fw/utils/__init__.py
97
+ src/ddi_fw/utils/categorical_data_encoding_checker.py
97
98
  src/ddi_fw/utils/enums.py
98
99
  src/ddi_fw/utils/json_helper.py
99
100
  src/ddi_fw/utils/kaggle.py
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