Merge pull request #64 from bio-ontology-research-group/cate

CatE Implementation (#59) and Docs update.

.github/ISSUE_TEMPLATE/bug.yml

@@ -0,0 +1,33 @@
+name: Report a bug
+description: Describe any wrong or unexpected behavior of mOWL
+labels: [ "bug" ]
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Describe the bug
+      description: Please provide a clear and concise description of the unexpected or erroneous behavior in mOWL that you experienced and what you expected to happen instead.
+    validations:
+      required: true
+  - type: textarea
+    id: reproduction
+    attributes:
+      label: How to reproduce
+      description: Please provide a example of the code that you ran to encounter the bug. This is a crucial aspect in order to find the source of error.
+    validations:
+      required: true
+  - type: textarea
+    id: environment
+    attributes:
+      label: Environment
+      description: Please, describe the OS, the Python version, mOWL version and JDK version where you ran the code.
+    validations:
+      required: true
+  - type: textarea
+    id: extras
+    attributes:
+      label: Additional information
+      description: Add any other information about the problem here.
+    validations:
+      required: false
+

.github/ISSUE_TEMPLATE/model.yml

@@ -0,0 +1,45 @@
+name: Add a new model
+description: Suggest a new model for mOWL
+labels: [ "model" ]
+body:
+  - type: dropdown
+    id: models
+    attributes:
+      label: mOWL support different types of models. Select which type fits better for your suggestion.
+      multiple: false
+      options:
+        - Ontology graph projection
+        - Random walker
+        - Syntactic model
+        - Model-theoretic model
+        - Other
+  - type: input
+    id: arxiv
+    attributes:
+      label: Publication Link
+      description: Link to the academic text of record where the model was first proposed (e.g., from _arXiv_)
+      placeholder: e.g., https://arxiv.org/abs/1902.10499
+    validations:
+      required: true
+  - type: input
+    id: reference_implementation
+    attributes:
+      label: Reference Implementation
+      description: Link to the publicly available reference implementation, preferrably from the authors of the publication
+      placeholder: e.g., https://github.com/bio-ontology-research-group/el-embeddings
+    validations:
+      required: false
+  - type: textarea
+    id: additional_implementations
+    attributes:
+      label: Additional Implementations
+      description: Links to any additional publicly available implementations
+    validations:
+      required: false
+  - type: textarea
+    id: context
+    attributes:
+      label: Additional Information
+      description: Additional information related to this model.
+    validations:
+        required: false

.gitignore

@@ -39,4 +39,6 @@ dist/
 .coverage
 *.pickle
 *.zip
-*.log
+*.log
+
+docs/source/api/mowl.*

CHANGELOG.md

@@ -13,6 +13,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 ### Security
 
+## [0.3.0]
+### Added
+- Implemented `CategoricalProjector` based on [https://arxiv.org/abs/2305.07163](https://arxiv.org/abs/2305.07163). ([#59][i59])
+
+### 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][i60])
@@ -78,7 +86,9 @@ Fixed issue related to importing graph-based models due to missing `__init__.py`
 - Walking methods accept optional `outfile` parameter and corpus extraction methods do not append by default.
 - Documentation updated and fixed some typos.
 
-[unreleased]: https://github.com/bio-ontology-research-group/mowl/compare/v0.2.0...HEAD
+[unreleased]: https://github.com/bio-ontology-research-group/mowl/compare/v0.3.0...HEAD
+[0.3.0]: https://github.com/bio-ontology-research-group/mowl/releases/tag/v0.3.0
+[0.2.1]: https://github.com/bio-ontology-research-group/mowl/releases/tag/v0.2.1
 [0.2.0]: https://github.com/bio-ontology-research-group/mowl/releases/tag/v0.2.0
 [0.1.1]: https://github.com/bio-ontology-research-group/mowl/releases/tag/v0.1.1
 [0.1.0]: https://github.com/bio-ontology-research-group/mowl/releases/tag/v0.1.0
@@ -89,4 +99,6 @@ Fixed issue related to importing graph-based models due to missing `__init__.py`
 [i36]: https://github.com/bio-ontology-research-group/mowl/issues/36
 [i42]: https://github.com/bio-ontology-research-group/mowl/issues/42
 [i43]: https://github.com/bio-ontology-research-group/mowl/issues/43
-[i43]: https://github.com/bio-ontology-research-group/mowl/issues/60
+[i59]: https://github.com/bio-ontology-research-group/mowl/issues/59
+[i60]: https://github.com/bio-ontology-research-group/mowl/issues/60
+

README.md

@@ -20,7 +20,7 @@ mainly in Python, but we have integrated the functionalities of [OWLAPI](https:/
 
 ### System dependencies
 
-  - JDK version 17
+  - JDK version >= 11
   - Python version: 3.8, 3.9, 3.10, 3.11
   - Conda version >= 4.x.x
 

docs/environment.yml

@@ -4,13 +4,9 @@ dependencies:
   - python=3.8
   - click
   - deprecated
-  - gensim
+  - gensim>=4.3.0
   - gradle
-  - JPype1=1.3.0
-  - matplotlib
-  - networkx
-  - numpy
-  - openjdk
+  - JPype1=1.4.1
   - pandas
   - pytorch
   - pyyaml
@@ -21,10 +17,14 @@ dependencies:
   - urllib3
   - pip
   - pip:
-    - pykeen==1.9.0
+    - pykeen>=1.10.1
     - temp
     - deprecated
     - nbsphinx
     - sphinx-gallery
+    - sphinx-rtd-theme
     - ipython
-    - memory-profiler
+    - memory-profiler
+    - matplotlib
+    - sphinx-automodapi
+    - mock

docs/source/api/base_models/index.rst

@@ -1,20 +1,9 @@
 mowl.base_models
 =====================
 
-* :doc:`base`
-* :doc:`base_graph`
-* :doc:`base_syntactic`
-* :doc:`base_el`
-
+.. automodapi:: mowl.base_models
+   :no-heading:
+   :headings: --
 
-.. toctree::
-   :maxdepth: 0
-   :hidden:
-   :glob:
-
-   base
-   base_graph
-   base_syntactic
-   base_el
 
 

docs/source/api/datasets/index.rst

@@ -1,22 +1,20 @@
 mowl.datasets
 =====================
 
-Base dataset
--------------------------
+Dataset constructors
+----------------------
 
-.. automodule:: mowl.datasets.base
-   :members:
-   :show-inheritance:
+.. automodapi:: mowl.datasets
+   :no-heading:
+   :headings: --
+
+|
+|
 
 Built-in datasets
 -------------------
-.. automodule:: mowl.datasets.builtin
-   :members:
-   :show-inheritance:
 
-Dataset for :math:`\mathcal{EL}` language
-------------------------------------------
-.. automodule:: mowl.datasets.el
-   :members:
-   :show-inheritance:
+.. automodapi:: mowl.datasets.builtin
+   :no-heading:
+   :headings: --
 

docs/source/api/evaluation/index.rst

@@ -1,13 +1,6 @@
 mowl.evaluation
 ============================
 
-.. automodule:: mowl.evaluation.base
-   :members:
-   :show-inheritance:
-
-
-
-.. automodule:: mowl.evaluation.rank_based
-   :members:
-   :show-inheritance:
-
+.. automodapi:: mowl.evaluation
+   :no-heading:
+   :headings: --

docs/source/api/projection/dl2vec.rst → docs/source/api/extra/dl2vec.rst

@@ -1,5 +1,4 @@
-
-The DL2Vec graph follows the rules described in the paper `Predicting candidate genes from phenotypes, functions, and anatomical site of expression (2020) <https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa879/5922810>`__. The parsing rules are shown in the table below:
+The parsing rules are shown in the table below:
 
 
 +-------------------------------------------------------+---------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
@@ -14,3 +13,17 @@ The DL2Vec graph follows the rules described in the paper `Predicting candidate
 | :math:`A \equiv B`					|											| :math:`\left\langle A, EquivalentTo, B \right\rangle`						|
 +-------------------------------------------------------+---------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------+
 
+Initially, DL2Vec projection rules are intended to parse TBox axioms. However, for some cases, useful information might be present as ABox axioms of the form :math:`C(a)`, :math:`\exists R.C (a)` and :math:`R(a,b)` where :math:`C` is an atomic concept, :math:`R` is a role and :math:`a, b` are individuals. The extended rules are the following:
+
+
++---------------------------+-----------------------------------------------------------+
+| Condition		    | Triple     						|
++===========================+===========================================================+
+| :math:`C(a)`	            | :math:`\left\langle a, http://type, C \right\rangle`	|
++---------------------------+-----------------------------------------------------------+
+| :math:`\exists R.C (a)`   | :math:`\left\langle a, R, C \right\rangle`		|
++---------------------------+-----------------------------------------------------------+
+| :math:`R(a,b)`	    | :math:`\left\langle a, R, b \right\rangle`		|
++---------------------------+-----------------------------------------------------------+
+
+

docs/source/api/models/index.rst

@@ -1,19 +1,6 @@
 mowl.models
 ============
 
-* :doc:`graphs`
-* :doc:`syntactic`
-* :doc:`elembeddings`
-* :doc:`elboxembeddings`
-
-
-.. toctree::
-   :maxdepth: 0
-   :hidden:
-   :glob:
-
-   graphs
-   syntactic
-   elembeddings
-   elboxembeddings
-
+.. automodapi:: mowl.models
+   :no-heading:
+   :headings: --