ddi-fw 0.0.35__py3-none-any.whl → 0.0.37__py3-none-any.whl

ddi_fw/datasets/core.py

@@ -21,8 +21,9 @@ def stack(df_column):
 
 
 class BaseDataset(ABC):
-    def __init__(self,embedding_dict, ner_df, chemical_property_columns, embedding_columns, ner_columns,
+    def __init__(self,embedding_size,embedding_dict, ner_df, chemical_property_columns, embedding_columns, ner_columns,
                  **kwargs):
+        self.embedding_size = embedding_size
         self.embedding_dict = embedding_dict
         self.ner_df = ner_df
         self.__similarity_related_columns__ = []
@@ -366,6 +367,10 @@ class BaseDataset(ABC):
         def x_fnc(row, embedding_column):
             v1 = self.embedding_dict[embedding_column][row['id1']]
             v2 = self.embedding_dict[embedding_column][row['id2']]
+            if v1 == None:
+                v1 = np.zeros(self.embedding_size)
+            if v2 == None:
+                v2 = np.zeros(self.embedding_size)
             return np.float16(np.hstack(
                 (v1, v2)))
 
@@ -380,7 +385,7 @@ class BaseDataset(ABC):
             print(f"concat {embedding_column} embeddings")
             # column_embeddings_dict = embedding_values[embedding_column]
             self.ddis_df[embedding_column+'_embedding'] = self.ddis_df.apply(
-                x_fnc, args=(embedding_column), axis=1)
+                x_fnc, args=(embedding_column,), axis=1)
 
         self.dataframe = self.ddis_df.copy()
         self.dataframe['class'] = list(classes)

ddi_fw/datasets/ddi_mdl/base.py

@@ -8,7 +8,7 @@ HERE = pathlib.Path(__file__).resolve().parent
 
 
 class DDIMDLDataset(BaseDataset):
-    def __init__(self, embedding_dict, ner_df, chemical_property_columns=['enzyme',
+    def __init__(self, embedding_size, embedding_dict, ner_df, chemical_property_columns=['enzyme',
                                                    'target',
                                                    'pathway',
                                                    'smile'],
@@ -16,7 +16,7 @@ class DDIMDLDataset(BaseDataset):
                  ner_columns=[],
                  **kwargs):
 
-        super().__init__(embedding_dict,ner_df, chemical_property_columns, embedding_columns,
+        super().__init__(embedding_size, embedding_dict,ner_df, chemical_property_columns, embedding_columns,
                          ner_columns, **kwargs)
 
         # kwargs = {'index_path': str(HERE.joinpath('indexes'))}

{ddi_fw-0.0.35.dist-info → ddi_fw-0.0.37.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ddi_fw
-Version: 0.0.35
+Version: 0.0.37
 Summary: Do not use :)
 Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
 Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>

{ddi_fw-0.0.35.dist-info → ddi_fw-0.0.37.dist-info}/RECORD

@@ -1,12 +1,12 @@
 ddi_fw/datasets/__init__.py,sha256=gkzHCU9-BL_bOU-RvvwdOIp_DhKRfXKU5SvgfQLVTds,505
-ddi_fw/datasets/core.py,sha256=DbNTZmGxn4oeSSAPdhH8zf6g-5VgoPivfQwAtBYdcAg,18090
+ddi_fw/datasets/core.py,sha256=uIoYKEaMXDGUwkYp6uwgKBa-wsNXPt6Py46-h_M6AMo,18312
 ddi_fw/datasets/db_utils.py,sha256=OTsa3d-Iic7z3HmzSQK9UigedRbHDxYChJk0s4GfLnw,6191
 ddi_fw/datasets/embedding_generator.py,sha256=Jqrlv88RCu0Lg812KsA12X0cSaZuxbckJ4LNRKNy_qw,2173
 ddi_fw/datasets/embedding_generator_new.py,sha256=GExjmBysPWkmFxTZQPs2yEmDdFllZ-qC9lhZeRQAfbQ,4320
 ddi_fw/datasets/feature_vector_generation.py,sha256=dxTHvp6uTkao9PdThs116Q3bWw_WTo9T8WigVL4G01s,3245
 ddi_fw/datasets/idf_helper.py,sha256=_Gd1dtDSLaw8o-o0JugzSKMt9FpeXewTh4wGEaUd4VQ,2571
 ddi_fw/datasets/setup_._py,sha256=khYVJuW5PlOY_i_A16F3UbSZ6s6o_ljw33Byw3C-A8E,1047
-ddi_fw/datasets/ddi_mdl/base.py,sha256=zKwxVXI-vVB2FcSHcgiXH-vfVjFPJsbm6c_ZZ1tqyvg,2473
+ddi_fw/datasets/ddi_mdl/base.py,sha256=iBA-ZbpPswj0K2is3ptCGo-ylz2CZvtTxEnZLh19kp4,2505
 ddi_fw/datasets/ddi_mdl/readme.md,sha256=WC6lpmsEKvIISnZqENY7TWtzCQr98HPpE3oRsBl8pIw,625
 ddi_fw/datasets/ddi_mdl/data/event.db,sha256=cmlSsf9MYjRzqR-mw3cUDnTnfT6FkpOG2yCl2mMwwew,30580736
 ddi_fw/datasets/ddi_mdl/indexes/test_indexes.txt,sha256=XVlDqYATckrQwNSXqMSKVBqyoN_Hg8SK6CL-XMdLADY,102176
@@ -80,7 +80,7 @@ ddi_fw/utils/enums.py,sha256=19eJ3fX5eRK_xPvkYcukmug144jXPH4X9zQqtsFBj5A,671
 ddi_fw/utils/py7zr_helper.py,sha256=rWhz3Trj6bk6B24hMuff1fKdRbC0yuvaHFlL8-eaAhg,4450
 ddi_fw/utils/utils.py,sha256=Na6Y8mY-CFbQjrgd9xC8agcrjVvTj_7KIXqFm1H_3qU,3549
 ddi_fw/utils/zip_helper.py,sha256=YRZA4tKZVBJwGQM0_WK6L-y5MoqkKoC-nXuuHK6CU9I,5567
-ddi_fw-0.0.35.dist-info/METADATA,sha256=_VVWhz49MppA95FRWQctsYfT8koX9VF2xnNBqrphL3w,1563
-ddi_fw-0.0.35.dist-info/WHEEL,sha256=5Mi1sN9lKoFv_gxcPtisEVrJZihrm_beibeg5R6xb4I,91
-ddi_fw-0.0.35.dist-info/top_level.txt,sha256=PMwHICFZTZtcpzQNPV4UQnfNXYIeLR_Ste-Wfc1h810,7
-ddi_fw-0.0.35.dist-info/RECORD,,
+ddi_fw-0.0.37.dist-info/METADATA,sha256=-3OgsCF56D6cF71EcF7ha7EiJ2e5Cr_qwDzk96tTyB0,1563
+ddi_fw-0.0.37.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+ddi_fw-0.0.37.dist-info/top_level.txt,sha256=PMwHICFZTZtcpzQNPV4UQnfNXYIeLR_Ste-Wfc1h810,7
+ddi_fw-0.0.37.dist-info/RECORD,,

{ddi_fw-0.0.35.dist-info → ddi_fw-0.0.37.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.0.0)
+Generator: setuptools (75.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any