Merge pull request #86 from bio-ontology-research-group/develop

Develop
bio-ontology-research-group · Nov 18, 2024 · 32f6a30 · 32f6a30
2 parents 9c26543 + 6e32dc5
commit 32f6a30
Show file tree

Hide file tree

Showing 95 changed files with 5,538 additions and 1,621 deletions.
diff --git a/.github/workflows/python-package_3_11.yml b/.github/workflows/python-package_3_11.yml
@@ -31,7 +31,7 @@ jobs:
         environment-file: envs/environment_3_11.yml
         auto-activate-base: false
         channels: conda-forge
-        use-mambda: true
+        use-mamba: true
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

diff --git a/.github/workflows/python-package_3_12.yml b/.github/workflows/python-package_3_12.yml
@@ -31,7 +31,7 @@ jobs:
         environment-file: envs/environment_3_12.yml
         auto-activate-base: false
         channels: conda-forge
-        use-mambda: true
+        use-mamba: true
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

diff --git a/.github/workflows/python-package_3_8.yml b/.github/workflows/python-package_3_8.yml
diff --git a/.gitignore b/.gitignore
@@ -40,4 +40,6 @@ dist/
 *.zip
 *.log
 
-docs/source/api/mowl.*
+docs/source/api/mowl.*
+
+**/wandb
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,16 +11,22 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - 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](https://github.com/bio-ontology-research-group/gda_analysis)
+- Extended experiment set to match [Ontology Embeddings Survey paper](https://arxiv.org/html/2406.10964v1).
+- Added mOWL format of GO and FoodOn datasets from [OWL2VecStar repository](https://github.com/KRR-Oxford/OWL2Vec-Star)
+- 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.

diff --git a/README.md b/README.md
@@ -21,7 +21,6 @@ mainly in Python, but we have integrated the functionalities of [OWLAPI](https:/
 
 ## Table of contents
   - [Installation](#installation)
-  - [List of contributors](#list-of-contributors)
   - [License](#license)
   - [Documentation](#documentation)
   - [Changelog](#changelog)
@@ -31,15 +30,17 @@ mainly in Python, but we have integrated the functionalities of [OWLAPI](https:/
 
 ### System dependencies
 
-  - JDK version >= 11
-  - Python version: 3.8, 3.9, 3.10, 3.11
-  - Conda version >= 4.x.x
+  - JDK version >= 22.x.x
+  - Python version: 3.9, 3.10, 3.11, 3.12
+  - Conda version >= 24.x.x
 
 ### Python requirements
 
-  - Gensim >= 4.x.x
-  - PyTorch >= 1.12.x
-  - PyKEEN >= 1.10.1
+  - torch
+  - gensim >= 4.3.0
+  - JPype1 == 1.5.0
+  - pykeen == 1.10.2
+  - scipy < 1.15.0
 
 ### Install from PyPi
 
@@ -61,19 +62,15 @@ pip install git+https://github.com/bio-ontology-research-group/mowl
 * [Evaluating Different Methods for Semantic Reasoning Over Ontologies](https://ceur-ws.org/Vol-3592/paper9.pdf)
 * [Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning](https://doi.org/10.1093/bioinformatics/btae301)
 
+### Authors
 
+**mOWL** is a project initiated and developed by the [Bio-Ontology Research Group](https://cemse.kaust.edu.sa/borg) from KAUST.
+Furthermore, mOWL had other collaboration by being part of:
 
-## List of contributors
-* [Fernando Zhapa](https://github.com/ferzcam)
-* [Maxat Kulmanov](https://github.com/coolmaksat)
-* [Sarah Alghamdi](https://github.com/smalghamdi)
-* [Robert Hoehndorf](https://github.com/leechuck)
-* [Carsten Jahn](https://github.com/carsten-jahn)
-* [Sonja Katz](https://github.com/sonjakatz)
-* [Marco Anteghini](https://github.com/MarcoAnteghini)
-* Francesco Gualdi
-* [luis-sribeiro](https://github.com/luis-sribeiro)
-* [Leduin Cuenca](https://github.com/leduin) (logo)
+* [Biohackathon Japan 2024](http://2024.biohackathon.org/)
+* [Biohackathon MENA 2023](https://biohackathon-europe.org/) as project ``#20``.
+* [Biohackathon Europe 2022](https://2022.biohackathon-europe.org/) as project ``#18``.
+* [Biohackathon Europe 2021](https://2021.biohackathon-europe.org/) as project ``#27``.
 
 ## License
 This software library is distributed under the [BSD-3-Clause license](https://github.com/bio-ontology-research-group/mowl/blob/main/LICENSE)

diff --git a/build_jars.sh b/build_jars.sh
@@ -1,9 +1,10 @@
 set -e
 cd gateway
-rm -f build/distributions/gateway/lib/*
+rm -r -f build/
 gradle distZip
 cd build/distributions
 yes | unzip gateway.zip
 cd ../../../
 rm -f mowl/lib/*.jar
 cp -r gateway/build/distributions/gateway/lib mowl
+
diff --git a/docs/environment.yml b/docs/environment.yml
@@ -1,7 +1,7 @@
 channels:
   - conda-forge
 dependencies:
-  - python=3.8
+  - python=3.9
   - click
   - deprecated
   - gensim>=4.3.0

diff --git a/docs/source/appendix/references.rst b/docs/source/appendix/references.rst
@@ -18,3 +18,5 @@ References
 .. [jackermeier2023] Jackermeier, M., Chen, J., & Horrocks, I. (2023). `Box2EL: Concept and Role Box Embeddings for the Description Logic EL++ <https://arxiv.org/abs/2301.11118>`_. ArXiv, abs/2301.11118.
 
 .. [xiong2022] Xiong, B., Potyka, N., Tran, TK., Nayyeri, M., Staab, S. (2022). Faithful Embeddings for EL++ Knowledge Bases. In: Sattler, U., et al. The Semantic Web – ISWC 2022. ISWC 2022. Lecture Notes in Computer Science, vol 13489. Springer, Cham. https://doi.org/10.1007/978-3-031-19433-7_2
+
+.. [brieulle2022] Ludovic Brieulle, Chan Le Duc, & Pascal Vaillant (2022). Reasoning in the Description Logic ALC under Category Semantics (Extended Abstract). In Proceedings of the 35th International Workshop on Description Logics (DL 2022) co-located with Federated Logic Conference (FLoC 2022), Haifa, Israel, August 7th to 10th, 2022. CEUR-WS.org.
diff --git a/docs/source/install/index.rst b/docs/source/install/index.rst
@@ -1,38 +1,29 @@
 Installation and Setup
 ===================================
 
-System requirements
--------------------
-
-- JDK version 17
-- Python version 3.8, 3.9, 3.10, 3.11, 3.12
-- Conda version >= 4.x.x
+System dependencies
+---------------------
 
+- JDK version >= 22.x.x
+- Python version: 3.9, 3.10, 3.11, 3.12
+- Conda version >= 24.x.x
 
 Python requirements
-----------------------
+-----------------------
 
-- Gensim >= 4.x.x
-- PyTorch >= 1.12.x
-- PyKEEN >= 1.10.1
+- torch
+- gensim >= 4.3.0
+- JPype1 == 1.5.0
+- pykeen == 1.10.2
+- scipy < 1.15.0
 
 
-
 Install from source code
 --------------------------
 
-Before installing from source, make sure to meet the dependencies.
-
-
-Installation can be done with the following commands:
-
 .. code:: bash
-	  
-   git clone https://github.com/bio-ontology-research-group/mowl.git
-   
-   cd mowl
 
-   pip install .
+   pip install git+https://github.com/bio-ontology-research-group/mowl
 
 Install from PyPi
 ------------------------------

diff --git a/envs/environment_3_10.yml b/envs/environment_3_10.yml
@@ -5,19 +5,19 @@ dependencies:
   - python=3.10
   - click
   - deprecated
-  - gensim>=4.3.0
   - gradle
   - JPype1=1.5.0
   - pandas
   - pytorch
   - pyyaml
   - requests
   - scikit-learn
-  - scipy<1.13.0  
   - tqdm
   - urllib3
   - pip
   - pip:
+    - gensim>=4.3.0
+    - scipy<1.15.0	    
     - pykeen==1.10.2
     - temp
 
diff --git a/envs/environment_3_11.yml b/envs/environment_3_11.yml
@@ -5,19 +5,19 @@ dependencies:
   - python=3.11
   - click
   - deprecated
-  - gensim>=4.3.0
   - gradle
   - JPype1=1.5.0
   - pandas
   - pytorch
   - pyyaml
   - requests
   - scikit-learn
-  - scipy<1.13.0  
   - tqdm
   - urllib3
   - pip
   - pip:
+    - gensim>=4.3.0
+    - scipy<1.15.0	    
     - pykeen==1.10.2
     - temp
 
diff --git a/envs/environment_3_12.yml b/envs/environment_3_12.yml
@@ -5,19 +5,19 @@ dependencies:
   - python=3.12
   - click
   - deprecated
-  - gensim>=4.3.0
   - gradle
   - JPype1=1.5.0
   - pandas
   - pytorch
   - pyyaml
   - requests
   - scikit-learn
-  - scipy<1.13.0  
   - tqdm
   - urllib3
   - pip
   - pip:
+    - gensim>=4.3.0
+    - scipy<1.15.0	    
     - pykeen==1.10.2
     - temp
 
diff --git a/envs/environment_3_8.yml → envs/environment_3_13.yml b/envs/environment_3_8.yml → envs/environment_3_13.yml
@@ -1,8 +1,8 @@
-name: mowl38
+name: mowl313
 channels:
   - conda-forge
 dependencies:
-  - python=3.8
+  - python=3.13
   - click
   - deprecated
   - gensim>=4.3.0
@@ -13,7 +13,7 @@ dependencies:
   - pyyaml
   - requests
   - scikit-learn
-  - scipy<1.13.0  
+  - scipy<1.15.0  
   - tqdm
   - urllib3
   - pip

diff --git a/envs/environment_3_9.yml b/envs/environment_3_9.yml
@@ -5,19 +5,19 @@ dependencies:
   - python=3.9
   - click
   - deprecated
-  - gensim>=4.3.0
   - gradle
   - JPype1=1.5.0
   - pandas
   - pytorch
   - pyyaml
   - requests
   - scikit-learn
-  - scipy<1.13.0  
   - tqdm
   - urllib3
   - pip
   - pip:
+    - gensim>=4.3.0
+    - scipy<1.15.0	    
     - pykeen==1.10.2
     - temp
 
diff --git a/envs/environment_dev_3_10.yml b/envs/environment_dev_3_10.yml
@@ -7,7 +7,6 @@ dependencies:
   - python=3.10
   - cairo
   - deprecated
-  - numpy
   - networkx
   - click
   - grpcio
@@ -16,17 +15,18 @@ dependencies:
   - protobuf
   - pyyaml
   - requests
-  - scipy<1.13.0
   - scikit-learn
   - urllib3
   - pytorch
-  - gensim>=4.3.0
   - openjdk
   - gradle
   - pip
   - pip:
+    - gensim>=4.3.0
+    - scipy<1.15.0	    
     - build
     - pykeen==1.10.2
+    - numpy
     - sphinx-rtd-theme
     - pytest
     - pytest-faulthandler
Original file line number	Diff line number	Diff line change
Expand Up		@@ -18,3 +18,5 @@ References
		.. [jackermeier2023] Jackermeier, M., Chen, J., & Horrocks, I. (2023). `Box2EL: Concept and Role Box Embeddings for the Description Logic EL++ <https://arxiv.org/abs/2301.11118>`_. ArXiv, abs/2301.11118.

		.. [xiong2022] Xiong, B., Potyka, N., Tran, TK., Nayyeri, M., Staab, S. (2022). Faithful Embeddings for EL++ Knowledge Bases. In: Sattler, U., et al. The Semantic Web – ISWC 2022. ISWC 2022. Lecture Notes in Computer Science, vol 13489. Springer, Cham. https://doi.org/10.1007/978-3-031-19433-7_2

		.. [brieulle2022] Ludovic Brieulle, Chan Le Duc, & Pascal Vaillant (2022). Reasoning in the Description Logic ALC under Category Semantics (Extended Abstract). In Proceedings of the 35th International Workshop on Description Logics (DL 2022) co-located with Federated Logic Conference (FLoC 2022), Haifa, Israel, August 7th to 10th, 2022. CEUR-WS.org.