Index

A

add_axioms() (mowl.base_models.EmbeddingELModel method) (mowl.base_models.Model method) (mowl.datasets.Dataset method) (mowl.models.GraphPlusPyKEENModel method) (mowl.models.RandomWalkPlusW2VModel method) (mowl.models.SyntacticPlusW2VModel method)

ALCDataset (class in mowl.datasets) as_pykeen() (mowl.projection.Edge static method) astuple() (mowl.projection.Edge method) Axiom (class in mowl.ontology.normalize)

B

BaseRankingEvaluator (class in mowl.evaluation) BoxEL (class in mowl.models) BoxELGDA (class in mowl.models)

BoxELModule (class in mowl.nn) BoxELPPI (class in mowl.models) BoxSquaredEL (class in mowl.models) BoxSquaredELModule (class in mowl.nn)

C

CategoricalProjector (class in mowl.projection) check_owl_type() (mowl.datasets.OWLClasses method) (mowl.datasets.OWLIndividuals method) (mowl.datasets.OWLObjectProperties method) class_ (mowl.ontology.normalize.ClassAssertion property) class_assertion_dataset (mowl.datasets.ELDataset attribute) class_assertion_loss() (mowl.nn.BoxELModule method) (mowl.nn.BoxSquaredELModule method) (mowl.nn.ELBEModule method) (mowl.nn.ELEmModule method) (mowl.nn.ELModule method) class_embeddings (mowl.base_models.EmbeddingELModel attribute) (mowl.base_models.Model attribute) (mowl.models.GraphPlusPyKEENModel attribute) (mowl.models.RandomWalkPlusW2VModel attribute) (mowl.models.SyntacticPlusW2VModel attribute) class_index_dict (mowl.base_models.Model attribute) (mowl.datasets.ELDataset attribute) class_to_id (mowl.datasets.ALCDataset attribute) (mowl.datasets.Dataset attribute) ClassAssertion (class in mowl.ontology.normalize) classes (mowl.datasets.Dataset attribute) compute_loss() (mowl.base_models.EmbeddingELModel method) (mowl.models.ELBE method)

compute_ranking_metrics() (mowl.evaluation.BaseRankingEvaluator method) corpus (mowl.base_models.SyntacticModel attribute) corpus_filepath (mowl.base_models.SyntacticModel attribute) create_class() (mowl.owlapi.adapter.OWLAPIAdapter method) create_class_assertion() (mowl.owlapi.adapter.OWLAPIAdapter method) create_complement_of() (mowl.owlapi.adapter.OWLAPIAdapter method) create_disjoint_classes() (mowl.owlapi.adapter.OWLAPIAdapter method) create_equivalent_classes() (mowl.owlapi.adapter.OWLAPIAdapter method) create_from_triples() (in module mowl.ontology.create) create_individual() (mowl.owlapi.adapter.OWLAPIAdapter method) create_object_all_values_from() (mowl.owlapi.adapter.OWLAPIAdapter method) create_object_intersection_of() (mowl.owlapi.adapter.OWLAPIAdapter method) create_object_property() (mowl.owlapi.adapter.OWLAPIAdapter method) create_object_property_assertion() (mowl.owlapi.adapter.OWLAPIAdapter method) create_object_some_values_from() (mowl.owlapi.adapter.OWLAPIAdapter method) create_object_union_of() (mowl.owlapi.adapter.OWLAPIAdapter method) create_ontology() (mowl.owlapi.adapter.OWLAPIAdapter method) create_subclass_of() (mowl.owlapi.adapter.OWLAPIAdapter method) create_tuples() (mowl.evaluation.Evaluator method) (mowl.evaluation.GDAEvaluator method) (mowl.evaluation.PPIEvaluator method) (mowl.evaluation.RankingEvaluator method) (mowl.evaluation.SubsumptionEvaluator method)

D

data_factory (mowl.owlapi.adapter.OWLAPIAdapter property) Dataset (class in mowl.datasets) deductive_closure_tuples (mowl.evaluation.Evaluator attribute)

DeepWalk (class in mowl.walking) DL2VecProjector (class in mowl.projection) dst (mowl.projection.Edge attribute)

E

Edge (class in mowl.projection) edges (mowl.base_models.GraphModel attribute) ELBE (class in mowl.models) ELBEGDA (class in mowl.models) ELBEModule (class in mowl.nn) ELBEPPI (class in mowl.models) ELDataset (class in mowl.datasets) ELEmbeddings (class in mowl.models) ELEmGDA (class in mowl.models) ELEmModule (class in mowl.nn) ELEmPPI (class in mowl.models) ELModule (class in mowl.nn) ELNormalizer (class in mowl.ontology.normalize) EmbeddingELModel (class in mowl.base_models) eval_fn() (mowl.base_models.Model method) eval_gci_name (mowl.base_models.EmbeddingELModel attribute) eval_method() (mowl.base_models.EmbeddingELModel method) evaluate() (mowl.base_models.Model method) (mowl.evaluation.Evaluator method) (mowl.evaluation.RankingEvaluator method) evaluate_base() (mowl.evaluation.Evaluator method)

evaluate_ppi() (mowl.models.BoxELPPI method) (mowl.models.ELBEPPI method) (mowl.models.ELEmPPI method) evaluation_classes (mowl.datasets.builtin.FamilyDataset attribute) (mowl.datasets.builtin.GDADataset attribute) (mowl.datasets.builtin.GDADatasetV2 attribute) (mowl.datasets.builtin.HPIDataset attribute) (mowl.datasets.builtin.PPIHumanDataset attribute) (mowl.datasets.builtin.PPIYeastDataset attribute) (mowl.datasets.Dataset attribute) evaluation_model (mowl.base_models.EmbeddingELModel attribute) (mowl.base_models.Model attribute) (mowl.models.GraphPlusPyKEENModel attribute) (mowl.models.RandomWalkPlusW2VModel attribute) (mowl.models.SyntacticPlusW2VModel attribute) evaluation_object_property (mowl.datasets.builtin.GDADatasetV2 attribute) (mowl.datasets.builtin.HPIDataset attribute) Evaluator (class in mowl.evaluation) extract_and_save_annotation_corpus() (in module mowl.corpus.base) extract_and_save_axiom_corpus() (in module mowl.corpus.base) extract_annotation_corpus() (in module mowl.corpus.base) extract_axiom_corpus() (in module mowl.corpus.base)

F

FamilyDataset (class in mowl.datasets.builtin) filler (mowl.ontology.normalize.GCI2 property) (mowl.ontology.normalize.GCI3 property) FoodOnSubsumptionDataset (class in mowl.datasets.builtin) forward() (mowl.nn.ELModule method)

from_pretrained() (mowl.base_models.EmbeddingELModel method) (mowl.base_models.Model method) (mowl.models.GraphPlusPyKEENModel method) (mowl.models.RandomWalkPlusW2VModel method) (mowl.models.SyntacticPlusW2VModel method)

G

GCI (class in mowl.ontology.normalize) GCI0 (class in mowl.ontology.normalize) GCI0_BOT (class in mowl.ontology.normalize) gci0_bot_dataset (mowl.datasets.ELDataset attribute) gci0_bot_loss() (mowl.nn.BoxELModule method) (mowl.nn.BoxSquaredELModule method) (mowl.nn.ELBEModule method) (mowl.nn.ELEmModule method) (mowl.nn.ELModule method) gci0_dataset (mowl.datasets.ELDataset attribute) gci0_loss() (mowl.nn.BoxELModule method) (mowl.nn.BoxSquaredELModule method) (mowl.nn.ELBEModule method) (mowl.nn.ELEmModule method) (mowl.nn.ELModule method) GCI1 (class in mowl.ontology.normalize) GCI1_BOT (class in mowl.ontology.normalize) gci1_bot_dataset (mowl.datasets.ELDataset attribute) gci1_bot_loss() (mowl.nn.BoxELModule method) (mowl.nn.BoxSquaredELModule method) (mowl.nn.ELBEModule method) (mowl.nn.ELEmModule method) (mowl.nn.ELModule method) gci1_dataset (mowl.datasets.ELDataset attribute) gci1_loss() (mowl.nn.BoxELModule method) (mowl.nn.BoxSquaredELModule method) (mowl.nn.ELBEModule method) (mowl.nn.ELEmModule method) (mowl.nn.ELModule method) GCI2 (class in mowl.ontology.normalize) gci2_dataset (mowl.datasets.ELDataset attribute) gci2_loss() (mowl.nn.BoxELModule method) (mowl.nn.BoxSquaredELModule method) (mowl.nn.ELBEModule method) (mowl.nn.ELEmModule method) (mowl.nn.ELModule method) gci2_score() (mowl.nn.ELBEModule method) (mowl.nn.ELEmModule method) GCI3 (class in mowl.ontology.normalize) GCI3_BOT (class in mowl.ontology.normalize) gci3_bot_dataset (mowl.datasets.ELDataset attribute) gci3_bot_loss() (mowl.nn.BoxELModule method) (mowl.nn.BoxSquaredELModule method) (mowl.nn.ELBEModule method) (mowl.nn.ELEmModule method) (mowl.nn.ELModule method) gci3_dataset (mowl.datasets.ELDataset attribute) gci3_loss() (mowl.nn.BoxELModule method) (mowl.nn.BoxSquaredELModule method) (mowl.nn.ELBEModule method) (mowl.nn.ELEmModule method) (mowl.nn.ELModule method) GDADataset (class in mowl.datasets.builtin) GDADatasetV2 (class in mowl.datasets.builtin)

GDADatasetV2EL (class in mowl.datasets.builtin) GDAEvaluator (class in mowl.evaluation) GDAHumanDataset (class in mowl.datasets.builtin) GDAHumanELDataset (class in mowl.datasets.builtin) GDAMouseDataset (class in mowl.datasets.builtin) GDAMouseELDataset (class in mowl.datasets.builtin) generate_corpus() (mowl.base_models.SyntacticModel method) generate_negatives() (mowl.base_models.EmbeddingELModel method) (mowl.models.BoxELPPI method) (mowl.models.ELBEPPI method) (mowl.models.ELEmPPI method) generate_points() (mowl.visualization.base.TSNE method) get_axiom_pattern() (mowl.datasets.ALCDataset method) get_axiom_vector() (mowl.datasets.ALCDataset method) get_cache_path() (mowl.ontology.normalize.ELNormalizer method) get_datasets() (mowl.datasets.ALCDataset method) get_embeddings() (mowl.base_models.EmbeddingELModel method) get_entities() (mowl.ontology.normalize.Axiom static method) (mowl.ontology.normalize.ClassAssertion method) (mowl.ontology.normalize.GCI0 method) (mowl.ontology.normalize.GCI1 method) (mowl.ontology.normalize.GCI2 method) (mowl.ontology.normalize.GCI3 method) (mowl.ontology.normalize.ObjectPropertyAssertion method) get_entities_and_relations() (mowl.projection.Edge static method) get_evaluation_property() (mowl.datasets.builtin.GDADataset method) (mowl.datasets.builtin.PPIHumanDataset method) (mowl.datasets.builtin.PPIYeastDataset method) get_expanded_scores() (mowl.evaluation.BaseRankingEvaluator method) get_gci_datasets() (mowl.datasets.ELDataset method) get_grouped_axioms() (mowl.datasets.ALCDataset method) get_logits() (mowl.evaluation.Evaluator method) get_loss_function() (mowl.nn.ELModule method) get_negative_sampling_config() (mowl.base_models.EmbeddingELModel method) (mowl.models.BoxELGDA method) (mowl.models.BoxELPPI method) (mowl.models.ELBEGDA method) (mowl.models.ELBEPPI method) (mowl.models.ELEmGDA method) (mowl.models.ELEmPPI method) get_obj_prop_assertion_data() (mowl.datasets.ALCDataset method) get_optimizer() (mowl.base_models.EmbeddingELModel method) get_regularization_loss() (mowl.base_models.EmbeddingELModel method) get_scores() (mowl.evaluation.BaseRankingEvaluator method) (mowl.evaluation.GDAEvaluator method) (mowl.evaluation.PPIEvaluator method) (mowl.evaluation.SubsumptionEvaluator method) getEntitiesAndRelations() (mowl.projection.Edge static method) GOSubsumptionDataset (class in mowl.datasets.builtin) graph_node_to_id (mowl.base_models.GraphModel attribute) graph_relation_to_id (mowl.base_models.GraphModel attribute) GraphModel (class in mowl.base_models) GraphPlusPyKEENModel (class in mowl.models) grouped_axioms (mowl.datasets.ALCDataset attribute)

H

head_entities (mowl.base_models.EmbeddingELModel attribute)

HPIDataset (class in mowl.datasets.builtin)

I

individual (mowl.ontology.normalize.ClassAssertion property) individual_embeddings (mowl.base_models.EmbeddingELModel attribute) (mowl.base_models.Model attribute) (mowl.models.GraphPlusPyKEENModel attribute) (mowl.models.RandomWalkPlusW2VModel attribute) (mowl.models.SyntacticPlusW2VModel attribute) individual_index_dict (mowl.base_models.Model attribute) individual_to_id (mowl.datasets.ALCDataset attribute) (mowl.datasets.Dataset attribute) individuals (mowl.datasets.Dataset attribute)

infer_disjoint_class_axioms() (mowl.reasoning.base.MOWLReasoner method) infer_equivalent_class_axioms() (mowl.reasoning.base.MOWLReasoner method) infer_subclass_axioms() (mowl.reasoning.base.MOWLReasoner method) init_embeddings() (mowl.nn.BoxSquaredELModule method) init_entity_embedding() (mowl.nn.BoxELModule method) init_module() (mowl.base_models.EmbeddingELModel method) (mowl.models.BoxEL method) (mowl.models.BoxSquaredEL method) (mowl.models.ELBE method) (mowl.models.ELEmbeddings method) insert_annotations() (in module mowl.ontology.extend)

K

kge_method (mowl.base_models.KGEModel attribute)

KGEModel (class in mowl.base_models)

L

labels (mowl.datasets.Dataset attribute) left_subclass (mowl.ontology.normalize.GCI1 property) load() (mowl.datasets.ALCDataset method) (mowl.datasets.ELDataset method)

load_best_model() (mowl.base_models.EmbeddingELModel method) load_corpus() (mowl.base_models.SyntacticModel method) load_pairwise_eval_data() (mowl.base_models.EmbeddingELModel method)

M

metrics (mowl.base_models.Model attribute) Model (class in mowl.base_models) model_filepath (mowl.base_models.Model attribute) module mowl.base_models mowl.corpus.base mowl.datasets mowl.datasets.builtin mowl.evaluation mowl.models mowl.nn mowl.ontology.create mowl.ontology.extend mowl.ontology.normalize mowl.owlapi.adapter mowl.owlapi.defaults mowl.projection mowl.reasoning.base mowl.visualization.base mowl.walking mowl.base_models module mowl.corpus.base module mowl.datasets module

mowl.datasets.builtin module mowl.evaluation module mowl.models module mowl.nn module mowl.ontology.create module mowl.ontology.extend module mowl.ontology.normalize module mowl.owlapi.adapter module mowl.owlapi.defaults module mowl.projection module mowl.reasoning.base module mowl.visualization.base module mowl.walking module MOWLReasoner (class in mowl.reasoning.base)

N

neg_capable_gcis (mowl.nn.BoxELModule attribute) (mowl.nn.BoxSquaredELModule attribute) (mowl.nn.ELBEModule attribute) (mowl.nn.ELEmModule attribute) (mowl.nn.ELModule attribute)

Node2Vec (class in mowl.walking) normalize() (mowl.ontology.normalize.ELNormalizer method)

O

object_ (mowl.ontology.normalize.ObjectPropertyAssertion property) object_properties (mowl.datasets.Dataset attribute) object_property (mowl.ontology.normalize.GCI2 property) (mowl.ontology.normalize.GCI3 property) (mowl.ontology.normalize.ObjectPropertyAssertion property) object_property_assertion_dataset (mowl.datasets.ELDataset attribute) object_property_assertion_loss() (mowl.nn.BoxELModule method) (mowl.nn.BoxSquaredELModule method) (mowl.nn.ELBEModule method) (mowl.nn.ELEmModule method) (mowl.nn.ELModule method) object_property_embeddings (mowl.base_models.EmbeddingELModel attribute) (mowl.base_models.Model attribute) (mowl.models.GraphPlusPyKEENModel attribute) (mowl.models.RandomWalkPlusW2VModel attribute) (mowl.models.SyntacticPlusW2VModel attribute)

object_property_index_dict (mowl.base_models.Model attribute) (mowl.datasets.ELDataset attribute) object_property_to_id (mowl.datasets.ALCDataset attribute) (mowl.datasets.Dataset attribute) ObjectPropertyAssertion (class in mowl.ontology.normalize) ontology (mowl.datasets.Dataset attribute) OWL2VecStarProjector (class in mowl.projection) owl_axiom (mowl.ontology.normalize.Axiom property) owl_manager (mowl.owlapi.adapter.OWLAPIAdapter property) owl_subclass (mowl.ontology.normalize.GCI property) owl_superclass (mowl.ontology.normalize.GCI property) OWLAPIAdapter (class in mowl.owlapi.adapter) OWLClasses (class in mowl.datasets) OWLIndividuals (class in mowl.datasets) OWLObjectProperties (class in mowl.datasets)

P

PathDataset (class in mowl.datasets) PPIEvaluator (class in mowl.evaluation) PPIHumanDataset (class in mowl.datasets.builtin) PPIYeastDataset (class in mowl.datasets.builtin) PPIYeastSlimDataset (class in mowl.datasets.builtin) preprocess_ontology() (mowl.ontology.normalize.ELNormalizer method) process_axiom() (mowl.projection.CategoricalProjector method) project() (mowl.projection.CategoricalProjector method) (mowl.projection.DL2VecProjector method) (mowl.projection.OWL2VecStarProjector method) (mowl.projection.TaxonomyProjector method) (mowl.projection.TaxonomyWithRelationsProjector method)

projector (mowl.base_models.GraphModel attribute) projector_factory() (in module mowl.projection) protein_ids (mowl.models.BoxELPPI attribute) (mowl.models.ELBEPPI attribute) (mowl.models.ELEmPPI attribute)

R

RandomWalkModel (class in mowl.base_models) RandomWalkPlusW2VModel (class in mowl.models) RankingEvaluator (class in mowl.evaluation) regularization_loss() (mowl.nn.BoxELModule method) (mowl.nn.BoxSquaredELModule method) (mowl.nn.ELEmModule method)

rel (mowl.projection.Edge attribute) RemoteDataset (class in mowl.datasets) right_subclass (mowl.ontology.normalize.GCI1 property)

S

savefig() (mowl.visualization.base.TSNE method) score() (mowl.base_models.EmbeddingELModel method) (mowl.base_models.Model method) set_evaluator() (mowl.base_models.Model method) set_kge_method() (mowl.base_models.KGEModel method) (mowl.models.GraphPlusPyKEENModel method) set_projector() (mowl.base_models.GraphModel method) set_w2v_model() (mowl.models.RandomWalkPlusW2VModel method) (mowl.models.SyntacticPlusW2VModel method) set_walker() (mowl.base_models.RandomWalkModel method)

show() (mowl.visualization.base.TSNE method) src (mowl.projection.Edge attribute) subclass (mowl.ontology.normalize.GCI0 property) (mowl.ontology.normalize.GCI2 property) subject (mowl.ontology.normalize.ObjectPropertyAssertion property) SubsumptionEvaluator (class in mowl.evaluation) superclass (mowl.ontology.normalize.GCI0 property) (mowl.ontology.normalize.GCI1 property) (mowl.ontology.normalize.GCI3 property) SyntacticModel (class in mowl.base_models) SyntacticPlusW2VModel (class in mowl.models)

T

tail_entities (mowl.base_models.EmbeddingELModel attribute) TarFileDataset (class in mowl.datasets) TaxonomyProjector (class in mowl.projection) TaxonomyWithRelationsProjector (class in mowl.projection) testing (mowl.datasets.Dataset attribute) testing_dataloaders (mowl.base_models.EmbeddingELModel attribute) testing_datasets (mowl.base_models.EmbeddingELModel attribute) testing_set (mowl.base_models.EmbeddingELModel attribute) to_str() (mowl.datasets.OWLClasses method) (mowl.datasets.OWLIndividuals method) (mowl.datasets.OWLObjectProperties method)

train() (mowl.base_models.EmbeddingELModel method) (mowl.base_models.Model method) (mowl.base_models.RandomWalkModel method) (mowl.base_models.SyntacticModel method) (mowl.models.GraphPlusPyKEENModel method) (mowl.models.RandomWalkPlusW2VModel method) (mowl.models.SyntacticPlusW2VModel method) training_dataloaders (mowl.base_models.EmbeddingELModel attribute) training_datasets (mowl.base_models.EmbeddingELModel attribute) training_set (mowl.base_models.EmbeddingELModel attribute) triples_factory (mowl.models.GraphPlusPyKEENModel attribute) TSNE (class in mowl.visualization.base)

U

update_filtering_labels() (mowl.evaluation.BaseRankingEvaluator method)

V

validation (mowl.datasets.Dataset attribute)

validation_dataloaders (mowl.base_models.EmbeddingELModel attribute) validation_datasets (mowl.base_models.EmbeddingELModel attribute)

W

wait_for_all_walks() (mowl.walking.WalkingModel method) walk() (mowl.walking.DeepWalk method) (mowl.walking.Node2Vec method) (mowl.walking.WalkingModel method)

walker (mowl.base_models.RandomWalkModel attribute) walker_factory() (in module mowl.walking) WalkingModel (class in mowl.walking) weight (mowl.projection.Edge attribute)

Z

zip() (mowl.projection.Edge static method)