ddi-fw 0.0.47__tar.gz → 0.0.49__tar.gz

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Files changed (91) hide show
  1. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/PKG-INFO +1 -1
  2. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/pyproject.toml +1 -1
  3. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/core.py +6 -6
  4. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/embedding_generator_new.py +18 -6
  5. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw.egg-info/PKG-INFO +1 -1
  6. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/README.md +0 -0
  7. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/setup.cfg +0 -0
  8. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/__init__.py +0 -0
  9. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/db_utils.py +0 -0
  10. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/base.py +0 -0
  11. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/data/event.db +0 -0
  12. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes/test_indexes.txt +0 -0
  13. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_0.txt +0 -0
  14. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_1.txt +0 -0
  15. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_2.txt +0 -0
  16. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_3.txt +0 -0
  17. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_4.txt +0 -0
  18. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes/train_indexes.txt +0 -0
  19. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_0.txt +0 -0
  20. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_1.txt +0 -0
  21. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_2.txt +0 -0
  22. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_3.txt +0 -0
  23. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_4.txt +0 -0
  24. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes_old/test_indexes.txt +0 -0
  25. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_0.txt +0 -0
  26. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_1.txt +0 -0
  27. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_2.txt +0 -0
  28. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_3.txt +0 -0
  29. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_4.txt +0 -0
  30. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_indexes.txt +0 -0
  31. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_0.txt +0 -0
  32. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_1.txt +0 -0
  33. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_2.txt +0 -0
  34. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_3.txt +0 -0
  35. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_4.txt +0 -0
  36. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/ddi_mdl/readme.md +0 -0
  37. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/embedding_generator.py +0 -0
  38. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/feature_vector_generation.py +0 -0
  39. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/idf_helper.py +0 -0
  40. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/mdf_sa_ddi/__init__.py +0 -0
  41. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/mdf_sa_ddi/base.py +0 -0
  42. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/mdf_sa_ddi/df_extraction_cleanxiaoyu50.csv +0 -0
  43. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/mdf_sa_ddi/drug_information_del_noDDIxiaoyu50.csv +0 -0
  44. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/test_indexes.txt +0 -0
  45. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_0.txt +0 -0
  46. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_1.txt +0 -0
  47. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_2.txt +0 -0
  48. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_3.txt +0 -0
  49. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_4.txt +0 -0
  50. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_indexes.txt +0 -0
  51. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_0.txt +0 -0
  52. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_1.txt +0 -0
  53. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_2.txt +0 -0
  54. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_3.txt +0 -0
  55. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_4.txt +0 -0
  56. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/mdf_sa_ddi/mdf-sa-ddi.zip +0 -0
  57. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/datasets/setup_._py +0 -0
  58. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/drugbank/__init__.py +0 -0
  59. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/drugbank/drugbank.xsd +0 -0
  60. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/drugbank/drugbank_parser.py +0 -0
  61. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/drugbank/drugbank_processor.py +0 -0
  62. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/drugbank/drugbank_processor_org.py +0 -0
  63. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/drugbank/event_extractor.py +0 -0
  64. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/experiments/__init__.py +0 -0
  65. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/experiments/custom_torch_model.py +0 -0
  66. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/experiments/evaluation_helper.py +0 -0
  67. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/experiments/tensorflow_helper.py +0 -0
  68. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/experiments/test.py +0 -0
  69. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/ner/__init__.py +0 -0
  70. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/ner/mmlrestclient.py +0 -0
  71. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/ner/ner.py +0 -0
  72. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/test/basic_test.py +0 -0
  73. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/test/combination_test.py +0 -0
  74. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/test/compress_json_test.py +0 -0
  75. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/test/date_test.py +0 -0
  76. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/test/idf_score.py +0 -0
  77. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/test/jaccard_similarity.py +0 -0
  78. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/test/mlfow_test.py +0 -0
  79. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/test/sklearn-tfidf.py +0 -0
  80. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/test/test.py +0 -0
  81. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/test/torch_cuda_test.py +0 -0
  82. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/test/type_guarding_test.py +0 -0
  83. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/utils/__init__.py +0 -0
  84. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/utils/enums.py +0 -0
  85. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/utils/py7zr_helper.py +0 -0
  86. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/utils/utils.py +0 -0
  87. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw/utils/zip_helper.py +0 -0
  88. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw.egg-info/SOURCES.txt +0 -0
  89. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw.egg-info/dependency_links.txt +0 -0
  90. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw.egg-info/requires.txt +0 -0
  91. {ddi_fw-0.0.47 → ddi_fw-0.0.49}/src/ddi_fw.egg-info/top_level.txt +0 -0
@@ -1,6 +1,6 @@
1
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  Metadata-Version: 2.1
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  Name: ddi_fw
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- Version: 0.0.47
3
+ Version: 0.0.49
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  Summary: Do not use :)
5
5
  Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
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  Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
5
5
 
6
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  [project]
7
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  name = "ddi_fw"
8
- version = "0.0.47"
8
+ version = "0.0.49"
9
9
  description = "Do not use :)"
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  readme = "README.md"
11
11
  authors = [
@@ -379,13 +379,13 @@ class BaseDataset(ABC):
379
379
  # return np.hstack(
380
380
  # (value[row['id1']], value[row['id2']]), dtype=np.float16)
381
381
 
382
- def x_fnc(row, embedding_column, embeddings_after_pooling):
383
- if row['id1'] in self.embedding_dict[embedding_column]:
384
- v1 = embeddings_after_pooling[embedding_column][row['id1']]
382
+ def x_fnc(row, embeddings_after_pooling):
383
+ if row['id1'] in embeddings_after_pooling:
384
+ v1 = embeddings_after_pooling[row['id1']]
385
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  else:
386
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  v1 = np.zeros(self.embedding_size)
387
- if row['id2'] in self.embedding_dict[embedding_column]:
388
- v2 = embeddings_after_pooling[embedding_column][row['id2']]
387
+ if row['id2'] in embeddings_after_pooling:
388
+ v2 = embeddings_after_pooling[row['id2']]
389
389
  else:
390
390
  v2 = np.zeros(self.embedding_size)
391
391
  return np.float16(np.hstack(
@@ -404,7 +404,7 @@ class BaseDataset(ABC):
404
404
  v) for k, v in self.embedding_dict[embedding_column].items()}
405
405
  # column_embeddings_dict = embedding_values[embedding_column]
406
406
  self.ddis_df[embedding_column+'_embedding'] = self.ddis_df.apply(
407
- x_fnc, args=(embedding_column, embeddings_after_pooling), axis=1)
407
+ x_fnc, args=(embeddings_after_pooling,), axis=1)
408
408
 
409
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  self.dataframe = self.ddis_df.copy()
410
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  self.dataframe['class'] = list(classes)
@@ -17,7 +17,7 @@ from sentence_transformers import SentenceTransformer, util
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17
 
18
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  from typing import Any, Dict, List, Optional
19
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  from langchain_core.embeddings import Embeddings
20
- from pydantic import BaseModel, ConfigDict, Field, SecretStr
20
+ from pydantic import BaseModel, ConfigDict, Field, SecretStr, computed_field
21
21
  from langchain.embeddings import SentenceTransformerEmbeddings
22
22
 
23
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  from langchain.text_splitter import RecursiveCharacterTextSplitter
@@ -56,7 +56,7 @@ class SumPoolingStrategy(PoolingStrategy):
56
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  return np.sum(embeddings, axis=0)
57
57
 
58
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59
- class SentenceTransformerDecorator(BaseModel, Embeddings):
59
+ class SentenceTransformerDecorator(Embeddings):
60
60
  def __init__(self, model_name="all-MiniLM-L6-v2", **kwargs: Any):
61
61
  self.embeddings = SentenceTransformerEmbeddings(model_name=model_name)
62
62
 
@@ -67,7 +67,7 @@ class SentenceTransformerDecorator(BaseModel, Embeddings):
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  return self.embeddings.embed_query(text)
68
68
 
69
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70
- class PretrainedEmbeddings(BaseModel, Embeddings):
70
+ class PretrainedEmbeddings( Embeddings):
71
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  def __init__(self, model_name):
72
72
  self.mmodel_name = model_name
73
73
  self.model = AutoModel.from_pretrained(model_name)
@@ -88,11 +88,23 @@ class PretrainedEmbeddings(BaseModel, Embeddings):
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89
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90
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  class SBertEmbeddings(BaseModel, Embeddings):
91
- def __init__(self, model_name):
92
- self.model = SentenceTransformer(model_name)
91
+ # class Config:
92
+ # arbitrary_types_allowed = True
93
+
94
+ model_config = ConfigDict(
95
+ arbitrary_types_allowed = True,
96
+ protected_namespaces=()
97
+ )
98
+
99
+ model_name:str
100
+
101
+ @computed_field
102
+ @property
103
+ def model(self) -> SentenceTransformer:
104
+ return SentenceTransformer(self.model_name)
93
105
 
94
106
  def embed_documents(self, texts: List[str]) -> List[List[float]]:
95
- return self.model.encode(texts)
107
+ return self.model.encode(texts).tolist()
96
108
 
97
109
  def embed_query(self, text: str) -> List[float]:
98
110
  return self.embed_documents([text])[0]
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: ddi_fw
3
- Version: 0.0.47
3
+ Version: 0.0.49
4
4
  Summary: Do not use :)
5
5
  Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
6
6
  Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
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