v1.0.1

[1.0.1]

Fixed

• Fix bug on CI pipeline to publish on PyPI

v1.0.0

[1.0.0]

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.
• 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
• Extended experiment set to match Ontology Embeddings Survey paper.
• Added mOWL format of GO and FoodOn datasets from OWL2VecStar repository
• Added PPI Human dataset (String v12.0)
• Added ontology_extended.owl version to PPI Yeast and PPI Human datasets. This extensions are required for CatE.
• Added PPIEvaluator, PPICatEEvaluator, GDAEvaluator and SubsumptionEvaluator

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.
• Updated CatE projection method based on latest version of paper (Nesy 2024 submission) ([#59][i59])

Deprecated

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

Removed

• End of support for Python 3.8 based on https://endoflife.date/python

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

v0.3.0

[0.3.0]

Added

• Implemented CategoricalProjector based on https://arxiv.org/abs/2305.07163. ([#59][i59])

Removed

• Removed redundant class based_models.EmbeddingModel

v0.2.1

Fixed

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

v0.2.0

[0.2.0]

Added

• BoxSquaredEL module added to mowl.nn
• Implemented model.from_pretrained method. Related to issue [#43][i43]
• Implemented model.add_axioms method. Related to issue [#43][i43]
• 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][i42])

Changed

• Bug fixed in corpus generation methods. Issue [#36][i36].
• Updated dependencies to work with Python 3.8 and 3.9. Issue [#42][i42]

v0.1.1

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

What's Changed

• CVE-2007-4559 Patch by @TrellixVulnTeam in #32
• Develop by @ferzcam in #35

New Contributors

• @TrellixVulnTeam made their first contribution in #32

v0.1.0

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.

v0.0.30

This is the first release of mOWL on GitHub. Previous and future releases can be found in PyPi. Some of the last updates are described below.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Added

• #19 - Added matplotlib and tqdm as dependencies of the package.

Fixed

• #20 - Walking methods accept optional outfile parameter and corpus extraction methods do not append by default.
• #21 - Documentation issue fixed.