ddi-fw 0.0.185__tar.gz → 0.0.186__tar.gz

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Files changed (109) hide show
  1. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/PKG-INFO +1 -1
  2. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/pyproject.toml +1 -1
  3. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/ml/ml_helper.py +1 -1
  4. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/ml/tensorflow_wrapper.py +3 -2
  5. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/pipeline/ner_pipeline.py +3 -3
  6. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/pipeline/pipeline.py +1 -1
  7. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw.egg-info/PKG-INFO +1 -1
  8. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/README.md +0 -0
  9. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/setup.cfg +0 -0
  10. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/__init__.py +0 -0
  11. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/core.py +0 -0
  12. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/dataset_splitter.py +0 -0
  13. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/db_utils.py +0 -0
  14. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/base.py +0 -0
  15. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/data/event.db +0 -0
  16. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/debug.log +0 -0
  17. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes/test_indexes.txt +0 -0
  18. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_0.txt +0 -0
  19. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_1.txt +0 -0
  20. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_2.txt +0 -0
  21. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_3.txt +0 -0
  22. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_4.txt +0 -0
  23. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes/train_indexes.txt +0 -0
  24. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_0.txt +0 -0
  25. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_1.txt +0 -0
  26. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_2.txt +0 -0
  27. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_3.txt +0 -0
  28. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_4.txt +0 -0
  29. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes_old/test_indexes.txt +0 -0
  30. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_0.txt +0 -0
  31. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_1.txt +0 -0
  32. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_2.txt +0 -0
  33. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_3.txt +0 -0
  34. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_4.txt +0 -0
  35. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_indexes.txt +0 -0
  36. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_0.txt +0 -0
  37. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_1.txt +0 -0
  38. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_2.txt +0 -0
  39. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_3.txt +0 -0
  40. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_4.txt +0 -0
  41. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl/readme.md +0 -0
  42. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl_text/base.py +0 -0
  43. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl_text/data/event.db +0 -0
  44. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl_text/indexes/test_indexes.txt +0 -0
  45. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_0.txt +0 -0
  46. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_1.txt +0 -0
  47. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_2.txt +0 -0
  48. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_3.txt +0 -0
  49. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_4.txt +0 -0
  50. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_indexes.txt +0 -0
  51. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_0.txt +0 -0
  52. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_1.txt +0 -0
  53. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_2.txt +0 -0
  54. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_3.txt +0 -0
  55. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_4.txt +0 -0
  56. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/mdf_sa_ddi/__init__.py +0 -0
  57. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/mdf_sa_ddi/base.py +0 -0
  58. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/mdf_sa_ddi/df_extraction_cleanxiaoyu50.csv +0 -0
  59. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/mdf_sa_ddi/drug_information_del_noDDIxiaoyu50.csv +0 -0
  60. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/test_indexes.txt +0 -0
  61. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_0.txt +0 -0
  62. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_1.txt +0 -0
  63. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_2.txt +0 -0
  64. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_3.txt +0 -0
  65. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_4.txt +0 -0
  66. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_indexes.txt +0 -0
  67. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_0.txt +0 -0
  68. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_1.txt +0 -0
  69. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_2.txt +0 -0
  70. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_3.txt +0 -0
  71. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_4.txt +0 -0
  72. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/mdf_sa_ddi/mdf-sa-ddi.zip +0 -0
  73. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/datasets/setup_._py +0 -0
  74. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/drugbank/__init__.py +0 -0
  75. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/drugbank/drugbank.xsd +0 -0
  76. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/drugbank/drugbank_parser.py +0 -0
  77. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/drugbank/drugbank_processor.py +0 -0
  78. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/drugbank/drugbank_processor_org.py +0 -0
  79. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/drugbank/event_extractor.py +0 -0
  80. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/langchain/__init__.py +0 -0
  81. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/langchain/embeddings.py +0 -0
  82. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/langchain/sentence_splitter.py +0 -0
  83. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/langchain/storage.py +0 -0
  84. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/ml/__init__.py +0 -0
  85. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/ml/evaluation_helper.py +0 -0
  86. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/ml/model_wrapper.py +0 -0
  87. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/ml/pytorch_wrapper.py +0 -0
  88. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/ner/__init__.py +0 -0
  89. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/ner/mmlrestclient.py +0 -0
  90. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/ner/ner.py +0 -0
  91. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/pipeline/__init__.py +0 -0
  92. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/pipeline/multi_modal_combination_strategy.py +0 -0
  93. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/pipeline/multi_pipeline.py +0 -0
  94. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/utils/__init__.py +0 -0
  95. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/utils/categorical_data_encoding_checker.py +0 -0
  96. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/utils/enums.py +0 -0
  97. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/utils/json_helper.py +0 -0
  98. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/utils/kaggle.py +0 -0
  99. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/utils/package_helper.py +0 -0
  100. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/utils/py7zr_helper.py +0 -0
  101. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/utils/utils.py +0 -0
  102. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/utils/zip_helper.py +0 -0
  103. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/vectorization/__init__.py +0 -0
  104. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/vectorization/feature_vector_generation.py +0 -0
  105. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw/vectorization/idf_helper.py +0 -0
  106. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw.egg-info/SOURCES.txt +0 -0
  107. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw.egg-info/dependency_links.txt +0 -0
  108. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw.egg-info/requires.txt +0 -0
  109. {ddi_fw-0.0.185 → ddi_fw-0.0.186}/src/ddi_fw.egg-info/top_level.txt +0 -0
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: ddi_fw
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- Version: 0.0.185
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+ Version: 0.0.186
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  Summary: Do not use :)
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  Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
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  Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
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  [project]
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  name = "ddi_fw"
9
- version = "0.0.185"
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+ version = "0.0.186"
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  description = "Do not use :)"
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  readme = "README.md"
12
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  authors = [
@@ -32,7 +32,7 @@ import ddi_fw.utils as utils
32
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33
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  class MultiModalRunner:
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  # todo model related parameters to config
35
- def __init__(self, library, multi_modal, use_mlflow=True):
35
+ def __init__(self, library, multi_modal, use_mlflow=False):
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  self.library = library
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  self.multi_modal = multi_modal
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  self.use_mlflow = use_mlflow
@@ -120,7 +120,7 @@ class TFModelWrapper(ModelWrapper):
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  print(self.train_data.shape)
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  models = {}
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  models_val_acc = {}
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- if self.train_idx_arr is not None and self.val_idx_arr is not None:
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+ if self.train_idx_arr and self.val_idx_arr:
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  for i, (train_idx, val_idx) in enumerate(zip(self.train_idx_arr, self.val_idx_arr)):
125
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  print(f"Validation {i}")
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@@ -155,7 +155,8 @@ class TFModelWrapper(ModelWrapper):
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  self.train_data, self.train_label, None, None)
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  models[self.descriptor] = model
157
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  models_val_acc[self.descriptor] = checkpoint.best
158
-
158
+ if models_val_acc == {}:
159
+ return model, None
159
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  best_model_key = max(models_val_acc, key=lambda k: models_val_acc[k])
160
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  # best_model_key = max(models_val_acc, key=models_val_acc.get)
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  best_model = models[best_model_key]
@@ -106,7 +106,7 @@ class NerParameterSearch:
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  **kwargs)
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108
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  # train_idx_arr, val_idx_arr bir kez hesaplanması yeterli aslında
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- X_train, X_test, y_train, y_test, X_train.index, X_test.index, train_idx_arr, val_idx_arr = dataset.load()
109
+ dataset.load()
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  group_items = dataset.produce_inputs()
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  for item in group_items:
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  # item[0] = f'threshold_{threshold}_{item[0]}'
@@ -115,8 +115,8 @@ class NerParameterSearch:
115
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  self.items.extend(group_items)
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  self.y_test_label = self.items[0][4]
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- self.train_idx_arr = train_idx_arr
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- self.val_idx_arr = val_idx_arr
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+ self.train_idx_arr = dataset.train_idx_arr
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+ self.val_idx_arr = dataset.val_idx_arr
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121
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  def run(self, model_func, batch_size=128, epochs=100):
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  mlflow.set_tracking_uri(self.tracking_uri)
@@ -244,7 +244,7 @@ class Pipeline(BaseModel):
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244
 
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  y_test_label = self.items[0][4]
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  multi_modal_runner = MultiModalRunner(
247
- library=self.library, multi_modal=self.multi_modal)
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+ library=self.library, multi_modal=self.multi_modal, use_mlflow=self.use_mlflow)
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  # multi_modal_runner = MultiModalRunner(
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  # library=self.library, model_func=model_func, batch_size=batch_size, epochs=epochs)
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  # multi_modal = TFMultiModal(
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: ddi_fw
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- Version: 0.0.185
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+ Version: 0.0.186
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  Summary: Do not use :)
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  Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
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  Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
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