Merge pull request #52 from Sujit-O/development

Development

README.md

@@ -236,14 +236,15 @@ We intend to provide the libraries to test the knowledge graph algorithms agains
 * [SSL: CERTIFICATE_VERIFY_FAILED with urllib](https://stackoverflow.com/questions/49183801/ssl-certificate-verify-failed-with-urllib)
 
 ## Cite
- Please kindly cite us if you found the library helpful. 
+ Please kindly cite the paper corresponding to the library. 
+
  ```
- @online{pykg2vec,
- author = {Rokka Chhetri, Sujit and Yu, Shih-Yuan and Salih Aksakal, Ahmet and Goyal, Palash and Canedo, Arquimedes},
- title = {pykg2vec: Python Knowledge Graph Embedding Library},
- year = 2019,
- url = {https://pypi.org/project/pykg2vec/}
- }
+ @article{yu2019pykg2vec,
+ title={Pykg2vec: A Python Library for Knowledge Graph Embedding},
+ author={Yu, Shih Yuan and Rokka Chhetri, Sujit and Canedo, Arquimedes and Goyal, Palash and Faruque, Mohammad Abdullah Al},
+ journal={arXiv preprint arXiv:1906.04239},
+ year={2019}
+}
  
  ```
  [__***Back to Top***__](#table-of-contents)

pykg2vec/config/hyperparams.py

@@ -446,8 +446,8 @@ def __init__(self):
  self.lr_decay = [0.95, 0.9, 0.8]
  self.learning_rate = [0.00001, 0.0001, 0.001, 0.01, 0.1, 1]
  self.L1_flag = [True, False]
- self.hidden_size = [8, 16, 32, 64, 128, 256]
- self.batch_size = [128, 256, 512]
+ self.hidden_size = [8, 16]
+ self.batch_size = [256, 512]
  self.epochs = [2, 5, 10]
  self.margin = [0.4, 1.0, 2.0]
  self.optimizer = ["adam", "sgd", 'rms']

pykg2vec/utils/kgcontroller.py

@@ -5,7 +5,7 @@
 """
 
 
-import shutil, tarfile, pickle
+import shutil, tarfile, pickle, time
 import urllib.request
 from pathlib import Path
 from collections import defaultdict
@@ -42,19 +42,12 @@ def __init__(self, h, r, t):
  self.h = None
  self.r = None
  self.t = None
- self.h_string = None
- self.r_string = None
- self.t_string = None
 
- if type(h) is int and type(r) is int and type(t) is int:
- self.h = h
- self.r = r
- self.t = t
+ assert type(h) is str and type(r) is str and type(t) is str, "h, r, t should be strings."
 
- else:
- self.h_string = h
- self.r_string = r
- self.t_string = t
+ self.h_string = h
+ self.r_string = r
+ self.t_string = t
 
  self.hr_t = None
  self.tr_h = None
@@ -71,18 +64,18 @@ def set_ids(self, h, r, t):
  self.r = r
  self.t = t
 
- def set_strings(self, h, r, t):
- """This function assigns the head, relation and tail in string format.
+ # def set_strings(self, h, r, t):
+ #  """This function assigns the head, relation and tail in string format.
 
- Args:
- h (str): String head entity.
- r (str): String relation entity.
- t (str): String tail entity.
+ #  Args:
+ #  h (str): String head entity.
+ #  r (str): String relation entity.
+ #  t (str): String tail entity.
 
- Todo:
- * Assing the strings.
- """
- pass
+ #  Todo:
+ #  * Assing the strings.
+ #  """
+ #  pass
 
  def set_hr_t(self, hr_t):
  """This function assigns the tails list for the given h,r pair.
@@ -173,8 +166,8 @@ class KnownDataset:
 
  Examples:
  >>> from pykg2vec.config.global_config import KnownDataset
- >>> name = "dLmL50"
- >>> url = "https://dl.dropboxusercontent.com/s/awoebno3wbgyrei/dLmL50.tgz?dl=0"
+ >>> name = "dL50a"
+ >>> url = "https://github.com/louisccc/KGppler/raw/master/datasets/dL50a.tgz"
  >>> prefix = 'deeplearning_dataset_50arch-'
  >>> kgdata = KnownDataset(name, url, prefix)
  >>> kgdata.download()
@@ -199,9 +192,11 @@ def __init__(self, name, url, prefix):
  self.download()
  self.extract()
 
+ path_eq_root = ['YAGO3_10', 'WN18RR', 'FB15K_237', 'Kinship',
+ 'Nations', 'UMLS']
  if self.name == 'WN18':
  self.dataset_path = self.root_path / 'wordnet-mlj12'
- elif self.name == 'YAGO3_10' or self.name == 'WN18RR':
+ elif self.name in path_eq_root:
  self.dataset_path = self.root_path
  else:
  self.dataset_path = self.root_path / self.name
@@ -294,8 +289,8 @@ class DeepLearning50a(KnownDataset):
 
  """
  def __init__(self):
- name = "dLmL50"
- url = "https://dl.dropboxusercontent.com/s/awoebno3wbgyrei/dLmL50.tgz?dl=0"
+ name = "dL50a"
+ url = "https://github.com/louisccc/KGppler/raw/master/datasets/dL50a.tgz"
  prefix = 'deeplearning_dataset_50arch-'
 
  KnownDataset.__init__(self, name, url, prefix)
@@ -335,7 +330,7 @@ class WordNet18_RR(KnownDataset):
  """
  def __init__(self):
  name = "WN18RR"
- url = "https://github.com/TimDettmers/ConvE/raw/master/WN18RR.tar.gz"
+ url = "https://github.com/louisccc/KGppler/raw/master/datasets/WN18RR.tar.gz"
  prefix = ''
 
  KnownDataset.__init__(self, name, url, prefix)
@@ -355,7 +350,87 @@ class YAGO3_10(KnownDataset):
  """
  def __init__(self):
  name = "YAGO3_10"
- url = "https://github.com/TimDettmers/ConvE/raw/master/YAGO3-10.tar.gz"
+ url = "https://github.com/louisccc/KGppler/raw/master/datasets/YAGO3-10.tar.gz"
+ prefix = ''
+
+ KnownDataset.__init__(self, name, url, prefix)
+
+
+class FreebaseFB15k_237(KnownDataset):
+ """This data structure defines the necessary information for downloading FB15k-237 dataset.
+
+ FB15k-237 module inherits the KnownDataset class for processing
+ the knowledge graph dataset.
+
+ Attributes:
+ name (str): Name of the datasets
+ url (str): The full url where the dataset resides.
+ prefix (str): The prefix of the dataset given the website.
+
+ """
+ def __init__(self):
+ name = "FB15K_237"
+ url = "https://github.com/louisccc/KGppler/raw/master/datasets/fb15k-237.tgz"
+ prefix = ''
+
+ KnownDataset.__init__(self, name, url, prefix)
+
+
+class Kinship(KnownDataset):
+ """This data structure defines the necessary information for downloading Kinship dataset.
+
+ Kinship module inherits the KnownDataset class for processing
+ the knowledge graph dataset.
+
+ Attributes:
+ name (str): Name of the datasets
+ url (str): The full url where the dataset resides.
+ prefix (str): The prefix of the dataset given the website.
+
+ """
+ def __init__(self):
+ name = "Kinship"
+ url = "https://github.com/louisccc/KGppler/raw/master/datasets/kinship.tar.gz"
+ prefix = ''
+
+ KnownDataset.__init__(self, name, url, prefix)
+
+
+class Nations(KnownDataset):
+ """This data structure defines the necessary information for downloading Nations dataset.
+
+ Nations module inherits the KnownDataset class for processing
+ the knowledge graph dataset.
+
+ Attributes:
+ name (str): Name of the datasets
+ url (str): The full url where the dataset resides.
+ prefix (str): The prefix of the dataset given the website.
+
+ """
+ def __init__(self):
+ name = "Nations"
+ url = "https://github.com/louisccc/KGppler/raw/master/datasets/nations.tar.gz"
+ prefix = ''
+
+ KnownDataset.__init__(self, name, url, prefix)
+
+
+class UMLS(KnownDataset):
+ """This data structure defines the necessary information for downloading UMLS dataset.
+
+ UMLS module inherits the KnownDataset class for processing
+ the knowledge graph dataset.
+
+ Attributes:
+ name (str): Name of the datasets
+ url (str): The full url where the dataset resides.
+ prefix (str): The prefix of the dataset given the website.
+
+ """
+ def __init__(self):
+ name = "UMLS"
+ url = "https://github.com/louisccc/KGppler/raw/master/datasets/umls.tar.gz"
  prefix = ''
 
  KnownDataset.__init__(self, name, url, prefix)
@@ -444,7 +519,7 @@ class KnowledgeGraph(object):
  negative_sample (str): Sampling technique to be used for generating negative triples (bern or uniform).
 
  Attributes:
- dataset_name (str): The name of the dataset. 
+ dataset_name (str): The name of the dataset.
  dataset (object): The dataset object isntance.
  negative_sample (str): negative_sample
  triplets (dict): dictionary with three list of training, testing and validation triples.
@@ -467,19 +542,27 @@ class KnowledgeGraph(object):
  >>> knowledge_graph.prepare_data()
  """
  def __init__(self, dataset='Freebase15k', negative_sample='uniform'):
- 
+
  self.dataset_name = dataset
 
- if dataset.lower() == 'freebase15k':
+ if dataset.lower() == 'freebase15k' or dataset.lower() == 'fb15k':
  self.dataset = FreebaseFB15k()
- elif dataset.lower() == 'deeplearning50a':
+ elif dataset.lower() == 'deeplearning50a' or dataset.lower() == 'dl50a':
  self.dataset = DeepLearning50a()
- elif dataset.lower() == 'wordnet18':
+ elif dataset.lower() == 'wordnet18' or dataset.lower() == 'wn18':
  self.dataset = WordNet18()
- elif dataset.lower() == 'wordnet18_rr':
+ elif dataset.lower() == 'wordnet18_rr' or dataset.lower() == 'wn18_rr':
  self.dataset = WordNet18_RR()
- elif dataset.lower() == 'yago3_10':
+ elif dataset.lower() == 'yago3_10' or dataset.lower() == 'yago':
  self.dataset = YAGO3_10()
+ elif dataset.lower() == 'freebase15k_237' or dataset.lower() == 'fb15k_237':
+ self.dataset = FreebaseFB15k_237()
+ elif dataset.lower() == 'kinship' or dataset.lower() == 'ks':
+ self.dataset = Kinship()
+ elif dataset.lower() == 'nations':
+ self.dataset = Nations()
+ elif dataset.lower() == 'umls':
+ self.dataset = UMLS()
  else:
  # if the dataset does not match with existing one, check if it exists in user's local space.
  # if it still can't find corresponding folder, raise exception in UserDefinedDataset.__init__()
@@ -511,10 +594,13 @@ def __init__(self, dataset='Freebase15k', negative_sample='uniform'):
  self.kg_meta = KGMetaData()
 
  def force_prepare_data(self):
- if self.dataset.is_meta_cache_exists():
- self.dataset.cache_metadata_path.unlink()
+ shutil.rmtree(str(self.dataset.root_path))
+
+ time.sleep(1)
+
+ self.__init__(dataset=self.dataset_name, negative_sample=self.negative_sample)
  self.prepare_data()
- 
+
  def prepare_data(self):
  """Function to prepare the dataset"""
  if self.dataset.is_meta_cache_exists():
@@ -778,4 +864,4 @@ def dump(self):
  print("Total validation Triples :", len(self.triplets['valid']))
  print("Total Entities :", self.kg_meta.tot_entity)
  print("Total Relations :", self.kg_meta.tot_relation)
- print("---------------------------------------------")
+ print("---------------------------------------------")