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Merged
merged 65 commits into from
Jun 1, 2022
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52874eb
before pulling
ferzcam Feb 22, 2022
db43f4e
fix conflicts
ferzcam Feb 22, 2022
1949f2d
update
ferzcam Mar 12, 2022
61be61c
:art: update taxonomy parser to parse with transitve closure (subclass)
ferzcam Mar 13, 2022
7ce50de
:bug: fix bug in DL2Vec model. Now it accepts empty test set
ferzcam Mar 14, 2022
c6ce270
:bug: fix missing _testing attribute error
ferzcam Mar 14, 2022
452465e
:art: catEmbeddings: fix nf1loss
ferzcam Mar 16, 2022
dc78163
:sparkles: beginning evaluation framework
ferzcam Mar 26, 2022
5a18afa
:bug: support empty testing dataset
ferzcam Mar 27, 2022
10b89d6
:bug: translational model supports empty testing dataset
ferzcam Mar 27, 2022
71e179e
:bug: translational model supports empty testing dataset
ferzcam Mar 27, 2022
687d45d
:art: CatEmbeddings new notebooks and updates
ferzcam Apr 12, 2022
a5733c3
:sparkles: New functions to add annotations to ontologies
ferzcam Apr 18, 2022
872b2fd
:memo: update docs
ferzcam Apr 18, 2022
1ca8b61
Merge branch 'docs' of https://github.com/bio-ontology-research-group…
ferzcam Apr 18, 2022
708865f
:memo: update docs
ferzcam Apr 18, 2022
b04a5d5
:memo: update docs
ferzcam Apr 18, 2022
51cf60c
.
ferzcam Apr 18, 2022
dbae9aa
Merge branch 'develop' of https://github.com/bio-ontology-research-gr…
ferzcam Apr 18, 2022
007fa7a
:memo: Added list of contributors
ferzcam Apr 18, 2022
9abf7b4
:memo: Added list of contributors
ferzcam Apr 18, 2022
f5b9b7e
:bug: fix name of annotations
ferzcam Apr 20, 2022
4882f0b
Merge branch 'develop' of https://github.com/bio-ontology-research-gr…
ferzcam Apr 20, 2022
c11ab7d
:bug: enable dl2vec model to save walks
ferzcam Apr 20, 2022
74ca79a
:bug: enable dl2vec model to save walks
ferzcam Apr 20, 2022
6343dbb
Merge branch 'develop' into docs
ferzcam Apr 20, 2022
7054f5e
:bug: enable owl2vec model to save walks
ferzcam Apr 20, 2022
c0c7c32
:bug: fix owl2vec parsing for complex subclasses
ferzcam Apr 20, 2022
abc138d
:memo: Updated docs
ferzcam Apr 24, 2022
b752a34
:memo: updated tutorial section
ferzcam Apr 25, 2022
72ec014
:bug: Fixed minor bug in DL2VecParser method
ferzcam Apr 26, 2022
929131c
renaming class
ferzcam Apr 26, 2022
902fe18
renaming class
ferzcam Apr 26, 2022
e84dccb
:art: :sparkles: modifications in insert_annotations method
ferzcam Apr 26, 2022
82aba7c
.
ferzcam Apr 26, 2022
9e23814
Merge branch 'develop' into docs
ferzcam Apr 26, 2022
f141c25
tmp
ferzcam Apr 27, 2022
c2dd076
:bug: insert_annotations method:allow prefixes in document
ferzcam Apr 27, 2022
37b008f
Merge branch 'docs' into develop
ferzcam Apr 27, 2022
0d6133d
:art: Changed name Parsers to Projectors
ferzcam May 10, 2022
61e7007
:art: updated dl2vec model
ferzcam May 11, 2022
f80b6e2
:art: :sparkles: user can define amount of jvm memory
ferzcam May 11, 2022
5f52417
:art: update create_from_triples method
ferzcam May 11, 2022
603a84f
:art: updated Model class
ferzcam May 11, 2022
5faed41
:art: :sparkles: :bug: fixed evaluation bugs, added rank based evaluator
ferzcam May 11, 2022
c6c0cea
:art: :recycle: updated onto2vec using the new reasoning module
ferzcam May 11, 2022
a0ba8d6
:art: :recycle: updated elembeddings using the new reasoning module
ferzcam May 11, 2022
78817ca
:alembic: update notebooks
ferzcam May 11, 2022
a57aa01
:sparkles: :necktie: create reasoning, visualization and corpus modules
ferzcam May 11, 2022
6f2a1b1
:construction: fixing deepwalk and node2vec to include edge labels
ferzcam May 14, 2022
9143b2c
:art: :white_check_mark: Finished update of DeepWalk and Node2Vec to …
ferzcam May 14, 2022
63e95a3
:construction: redesigning Model class
ferzcam May 16, 2022
5dbf5e9
:art:
ferzcam May 18, 2022
aabebcf
:construction: updating Translational Embeddings
ferzcam May 19, 2022
9706d27
:fire: removed walkRdfAndOwl as walking method as now it is equivalen…
ferzcam May 19, 2022
57f8e76
:art: added zipping method in Edge class
ferzcam May 19, 2022
f2a64af
.
ferzcam May 22, 2022
0da8096
Merge branch 'develop' of https://github.com/bio-ontology-research-gr…
ferzcam May 22, 2022
3abbfcf
:art: updated models
ferzcam May 22, 2022
1f644c3
:art: update on methods for creating datasets
ferzcam Jun 1, 2022
d09f822
:sparkles: extend EL normalization to 7 normal forms
ferzcam Jun 1, 2022
c9cb0fb
:art: update model class
ferzcam Jun 1, 2022
fdac893
:art: :construction: update evaluation module. Working but still on d…
ferzcam Jun 1, 2022
f3bf2a0
:art: update elembeddings model to make it compatible with the evalua…
ferzcam Jun 1, 2022
86e4695
:art: update elembeddings model to make it compatible with the evalua…
ferzcam Jun 1, 2022
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🎨 updated Model class
  • Loading branch information
ferzcam committed May 11, 2022
commit 603a84f42524f6357db007ebc7c4f95980cca0df
30 changes: 30 additions & 0 deletions mowl/model.py
Original file line number Diff line number Diff line change
@@ -2,15 +2,45 @@ class Model(object):

def __init__(self, dataset):
self.dataset = dataset
self._testing_set = None



@property
def testing_set(self):
return self._testing_set

@property
def training_set(self):
return self._training_set

@property
def head_entities(self):
return self._head_entities
@property
def tail_entities(self):
return self._tail_entities

def train(self):
'''Trains the model
'''
raise NotImplementedError()

def eval_method():
raise NotImplementedError()

def evaluate(self):
'''Evaluates the model
'''
raise NotImplementedError()


class EmbeddingModel(Model):

def __init__(self, dataset):
super().__init__(dataset)


def get_entities_index_dict(self):
return self.class_index_dict, self.relation_index_dict