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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

Added

  • Added load_corpus to mowl.base_models.SyntacticModel
  • Added .jar files to enable pip install from GitHub
  • Tested with Python 3.12
  • Refactored Evaluation module.
  • Added PPIEvaluator, GDAEvaluator, SubsumptionEvaluator
  • Refactored model object and introduced model.train() and model.evaluate() methods.
  • Added GDADatasetV2 and GDADatasetV2EL. Datasets were introduced in https://github.com/bio-ontology-research-group/gda_analysis

Changed

  • Removed .mean() for GCI losses in BoxSquaredELModule
  • Property evaluation_classes in mowl.datasets.builtin.PPIYeastDataset returns a pair of OWLClasses objects instead of a single OWLClasses object.

Deprecated

  • mowl.nn.ELBoxModule changed name to mowl.nn.ELBEModule

Removed

Fixed

  • Fix bug in GCI2 score for ELEmbeddings
  • Fix bottleneck in ELBE example for PPI.
  • Fix bugs in BoxSquaredEL model.
  • Fix bug on OWL2VecStarProjector about projecting with literals

Security

0.3.0

Added

Removed

  • Removed redundant class based_models.EmbeddingModel

0.2.1

Fixed

Fixed issue related to importing graph-based models due to missing __init__.py files. (#60)

0.2.0

Added

  • BoxSquaredEL module added to mowl.nn
  • Implemented model.from_pretrained method. Related to issue #43
  • Implemented model.add_axioms method. Related to issue #43
  • Added models RandomWalkPlusW2VModel, GraphPlusPyKEENModel, SyntacticPlusW2VModel,
  • Updated dependencies: JPype-1.3.0 --> JPype-1.4.1, pykeen-1.9.0 --> pykeen-1.10.1
  • Support for Python 3.8, 3.9, 3.10, 3.11. (#42)

Changed

  • Bug fixed in corpus generation methods. Issue #36.
  • Updated dependencies to work with Python 3.8 and 3.9. Issue #42

0.1.1

Added

  • Family dataset: a small ontology containing 12 axioms.
  • Unit tests up to 88% of coverage
  • DL2VecProjector includes assertion axioms with named individuals
  • FastTensorDataLoader is part of mOWL in the module mowl.utils.data
  • DeepGOZero implementation in mOWL
  • Module mowl.owlapi with shortcuts to the OWLAPI
  • Extended Dataset class.

Security

  • Added Patch for bug CVE-2007-4559. Based on pull request #32

0.1.0

Added

  • Modules mowl.ontology.extend and mowl.ontology.create created including insert_annotations and create_from_triples methods, respectively.
  • Package deprecated as dependency.
  • ELEmbeddingModel abstract class that contains basic functionality for models embedding the EL language.
  • Implementation of ELBoxEmbeddings
  • ELDataset class to work with EL models.
  • Module mowl.nn where torch.nn-based modules will reside. The first module existing there is the abstract module for EL models.
  • Module mowl.models where implementation of ELEmbeddings and ELBoxEmbeddings reside.
  • PyKEEN as dependency
  • GDAHumanELDataset and GDAMouseELDataset, which are reduced versions of GDAHumanDataset and GDAMouseDataset, respectively. The new datasets can be normalized into the EL language using the jcel library.
  • Started implementation of unit tests for datasets and walking modules.

Changed

  • All builtin datasets can be imported from mowl.datasets.builtin module.
  • Updated implementation of ELEmbeddings
  • Changed method mowl.datasets.PathDataset.get_evaluation_classes to property mowl.datasets.PathDataset.evaluation_classes
  • #25 Walking methods now accept an optional parameter for a list of nodes to filter the random walks.

Deprecated

  • Modules mowl.datasets.ppi_yeast and mowl.datasets.gda.
  • File mowl.datasets.build_ontology.
  • Class mowl.embeddings.elembeddings.ELEmbeddings. Future versions will point to mowl.models.ELEmbeddings
  • Method mowl.corpus.base.extract_annotation_corpus. Future versions will split this method into two: mowl.corpus.base.extract_annotation_corpus and mowl.corpus.base.extract_and_save_annotation_corpus.
  • Method mowl.datasets.PathDataset.get_evaluation_classes.

0.0.30 - 2022-07-03

Added

  • Added matplotlib and tqdm as dependencies of the package.

Fixed

  • Walking methods accept optional outfile parameter and corpus extraction methods do not append by default.
  • Documentation updated and fixed some typos.