Ontolearn: Learning OWL Class Expressions
Ontolearn is an open-source software library for learning owl class expressions at large scale.
Given positive and negative OWL named individual examples
$E^+$ and $E^-$, learning OWL Class expression problem refers to the following supervised Machine Learning problem
$$\forall p \in E^+\ \mathcal{K} \models H(p) \wedge \forall n \in E^-\ \mathcal{K} \not \models H(n).$$
To tackle this supervised learning problem, ontolearn offers many symbolic, neuro-symbolic and deep learning based Learning algorithms:
Find more in the Documentation.
Installation
pip install ontolearn
or
git clone https://github.com/dice-group/Ontolearn.git
# To create a virtual python env with conda
conda create -n venv python=3.10.14 --no-default-packages && conda activate venv && pip install -e .
# To download knowledge graphs
wget https://files.dice-research.org/projects/Ontolearn/KGs.zip -O ./KGs.zip && unzip KGs.zip
# To download learning problems
wget https://files.dice-research.org/projects/Ontolearn/LPs.zip -O ./LPs.zip && unzip LPs.zip
Learning OWL Class Expression
from ontolearn.learners import TDL
from ontolearn.triple_store import TripleStore
from ontolearn.knowledge_base import KnowledgeBase
from ontolearn.learning_problem import PosNegLPStandard
from owlapy.owl_individual import OWLNamedIndividual
from owlapy import owl_expression_to_sparql, owl_expression_to_dl
# (1) Initialize Triplestore or KnowledgeBase
# sudo docker run -p 3030:3030 -e ADMIN_PASSWORD=pw123 stain/jena-fuseki
# Login http://localhost:3030/#/ with admin and pw123 and upload KGs/Family/family.owl
# kb = TripleStore(url="http://localhost:3030/family")
kb = KnowledgeBase(path="KGs/Family/father.owl")
# (2) Initialize a learner.
model = TDL(knowledge_base=kb, use_nominals=True)
# (3) Define a description logic concept learning problem.
lp = PosNegLPStandard(pos={OWLNamedIndividual("http://example.com/father#stefan")},
neg={OWLNamedIndividual("http://example.com/father#heinz"),
OWLNamedIndividual("http://example.com/father#anna"),
OWLNamedIndividual("http://example.com/father#michelle")})
# (4) Learn description logic concepts best fitting (3).
h = model.fit(learning_problem=lp).best_hypotheses()
print(h)
print(owl_expression_to_dl(h))
print(owl_expression_to_sparql(expression=h))
"""
OWLObjectSomeValuesFrom(property=OWLObjectProperty(IRI('http://example.com/father#','hasChild')),filler=OWLObjectOneOf((OWLNamedIndividual(IRI('http://example.com/father#','markus')),)))
∃ hasChild.{markus}
SELECT
DISTINCT ?x WHERE {
?x <http://example.com/father#hasChild> ?s_1 .
FILTER ( ?s_1 IN (
<http://example.com/father#markus>
) )
}
"""
print(model.classification_report)
"""
Classification Report: Negatives: -1 and Positives 1
precision recall f1-score support
Negative 1.00 1.00 1.00 3
Positive 1.00 1.00 1.00 1
accuracy 1.00 4
macro avg 1.00 1.00 1.00 4
weighted avg 1.00 1.00 1.00 4
"""
Learning OWL Class Expression over DBpedia
from ontolearn.learners import TDL
from ontolearn.triple_store import TripleStore
from ontolearn.learning_problem import PosNegLPStandard
from owlapy.owl_individual import OWLNamedIndividual
from owlapy import owl_expression_to_sparql, owl_expression_to_dl
from ontolearn.utils.static_funcs import save_owl_class_expressions
# (1) Initialize Triplestore
kb = TripleStore(url="http://dice-dbpedia.cs.upb.de:9080/sparql")
# (3) Initialize a learner.
model = TDL(knowledge_base=kb)
# (4) Define a description logic concept learning problem.
lp = PosNegLPStandard(pos={OWLNamedIndividual("http://dbpedia.org/resource/Angela_Merkel")},
neg={OWLNamedIndividual("http://dbpedia.org/resource/Barack_Obama")})
# (5) Learn description logic concepts best fitting (4).
h = model.fit(learning_problem=lp).best_hypotheses()
print(h)
print(owl_expression_to_dl(h))
print(owl_expression_to_sparql(expression=h))
save_owl_class_expressions(expressions=h,path="owl_prediction")
Fore more please refer to the examples folder.
ontolearn-webservice
Click me!
Load an RDF knowledge graph
```shell
ontolearn-webservice --path_knowledge_base KGs/Mutagenesis/mutagenesis.owl
```
or launch a Tentris instance https://github.com/dice-group/tentris over Mutagenesis.
```shell
ontolearn-webservice --endpoint_triple_store http://0.0.0.0:9080/sparql
```
The below code trains DRILL with 6 randomly generated learning problems
provided that **path_to_pretrained_drill** does not lead to a directory containing pretrained DRILL.
Thereafter, trained DRILL is saved in the directory **path_to_pretrained_drill**.
Finally, trained DRILL will learn an OWL class expression.
```python
import json
import requests
with open(f"LPs/Mutagenesis/lps.json") as json_file:
learning_problems = json.load(json_file)["problems"]
for str_target_concept, examples in learning_problems.items():
response = requests.get('http://0.0.0.0:8000/cel',
headers={'accept': 'application/json', 'Content-Type': 'application/json'},
json={"pos": examples['positive_examples'],
"neg": examples['negative_examples'],
"model": "Drill",
"path_embeddings": "mutagenesis_embeddings/Keci_entity_embeddings.csv",
"path_to_pretrained_drill": "pretrained_drill",
# if pretrained_drill exists, upload, otherwise train one and save it there
"num_of_training_learning_problems": 2,
"num_of_target_concepts": 3,
"max_runtime": 60000, # seconds
"iter_bound": 1 # number of iterations/applied refinement opt.
})
print(response.json()) # {'Prediction': '∀ hasAtom.(¬Nitrogen-34)', 'F1': 0.7283582089552239, 'saved_prediction': 'Predictions.owl'}
```
TDL (a more scalable learner) can also be used as follows
```python
import json
import requests
with open(f"LPs/Mutagenesis/lps.json") as json_file:
learning_problems = json.load(json_file)["problems"]
for str_target_concept, examples in learning_problems.items():
response = requests.get('http://0.0.0.0:8000/cel',
headers={'accept': 'application/json', 'Content-Type': 'application/json'},
json={"pos": examples['positive_examples'],
"neg": examples['negative_examples'],
"model": "TDL"})
print(response.json())
```
Benchmark Results
To see the results
```shell
# To download learning problems. # Benchmark learners on the Family benchmark dataset with benchmark learning problems.
wget https://files.dice-research.org/projects/Ontolearn/LPs.zip -O ./LPs.zip && unzip LPs.zip
```
### 10-Fold Cross Validation Family Benchmark Results
Here we apply 10-fold cross validation technique on each benchmark learning problem with max runtime of 60 seconds to measure the training and testing performance of learners.
In the evaluation, from a given single learning problem (a set of positive and negative examples), a learner learns an OWL Class Expression (H) on a given 9 fold of positive and negative examples.
To compute the training performance, We compute F1-score of H train positive and negative examples.
To compute the test performance, we compute F1-score of H w.r.t. test positive and negative examples.
```shell
# To download learning problems and benchmark learners on the Family benchmark dataset with benchmark learning problems.
python examples/concept_learning_cv_evaluation.py --kb ./KGs/Family/family-benchmark_rich_background.owl --lps ./LPs/Family/lps_difficult.json --path_of_nces_embeddings ./NCESData/family/embeddings/ConEx_entity_embeddings.csv --path_of_clip_embeddings ./CLIPData/family/embeddings/ConEx_entity_embeddings.csv --max_runtime 60 --report family_results.csv
```
In the following python script, the results are summarized and the markdown displayed below generated.
```python
import pandas as pd
df=pd.read_csv("family_results.csv").groupby("LP").mean()
print(df[[col for col in df if col.startswith('Test-F1') or col.startswith('RT')]].to_markdown(floatfmt=".3f"))
```
**Note that DRILL is untrained and we simply used accuracy driven heuristics to learn an OWL class expression.**
Below, we report the average test F1 score and the average runtimes of learners.
| LP | Test-F1-OCEL | RT-OCEL | Test-F1-CELOE | RT-CELOE | Test-F1-Evo | RT-Evo | Test-F1-DRILL | RT-DRILL | Test-F1-TDL | RT-TDL | Test-F1-NCES | RT-NCES | Test-F1-CLIP | RT-CLIP |
|:------------------:|-------------:|--------:|--------------:|---------:|------------:|-------:|--------------:|---------:|------------:|-------:|-------------:|--------:|-------------:|--------:|
| Aunt | 0.614 | 13.697 | 0.855 | 13.697 | 0.978 | 5.278 | 0.811 | 60.351 | 0.956 | 0.118 | 0.812 | 1.168 | 0.855 | 14.059 |
| Cousin | 0.712 | 10.846 | 0.789 | 10.846 | 0.993 | 3.311 | 0.701 | 60.485 | 0.820 | 0.176 | 0.677 | 1.050 | 0.779 | 9.050 |
| Grandgranddaughter | 1.000 | 0.013 | 1.000 | 0.013 | 1.000 | 0.426 | 0.980 | 17.486 | 1.000 | 0.050 | 1.000 | 0.843 | 1.000 | 0.639 |
| Grandgrandfather | 1.000 | 0.897 | 1.000 | 0.897 | 1.000 | 0.404 | 0.947 | 55.728 | 0.947 | 0.059 | 0.927 | 0.902 | 1.000 | 0.746 |
| Grandgrandmother | 1.000 | 4.173 | 1.000 | 4.173 | 1.000 | 0.442 | 0.893 | 50.329 | 0.947 | 0.060 | 0.927 | 0.908 | 1.000 | 0.817 |
| Grandgrandson | 1.000 | 1.632 | 1.000 | 1.632 | 1.000 | 0.452 | 0.931 | 60.358 | 0.911 | 0.070 | 0.911 | 1.050 | 1.000 | 0.939 |
| Uncle | 0.876 | 16.244 | 0.891 | 16.244 | 0.964 | 4.516 | 0.876 | 60.416 | 0.933 | 0.098 | 0.891 | 1.256 | 0.928 | 17.682 |
| LP | Train-F1-OCEL | Train-F1-CELOE | Train-F1-Evo | Train-F1-DRILL | Train-F1-TDL | Train-F1-NCES | Train-F1-CLIP |
|:------------------:|--------------:|---------------:|-------------:|---------------:|-------------:|----------------:|----------------:|
| Aunt | 0.835 | 0.918 | 0.995 | 0.837 | 1.000 | 0.804 | 0.918 |
| Cousin | 0.746 | 0.796 | 1.000 | 0.732 | 1.000 | 0.681 | 0.798 |
| Grandgranddaughter | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
| Grandgrandfather | 1.000 | 1.000 | 1.000 | 0.968 | 1.000 | 0.973 | 1.000 |
| Grandgrandmother | 1.000 | 1.000 | 1.000 | 0.975 | 1.000 | 0.939 | 1.000 |
| Grandgrandson | 1.000 | 1.000 | 1.000 | 0.962 | 1.000 | 0.927 | 1.000 |
| Uncle | 0.904 | 0.907 | 0.996 | 0.908 | 1.000 | 0.884 | 0.940 |
### 10-Fold Cross Validation Mutagenesis Benchmark Results
```shell
python examples/concept_learning_cv_evaluation.py --kb ./KGs/Mutagenesis/mutagenesis.owl --lps ./LPs/Mutagenesis/lps.json --path_of_nces_embeddings ./NCESData/mutagenesis/embeddings/ConEx_entity_embeddings.csv --path_of_clip_embeddings ./CLIPData/mutagenesis/embeddings/ConEx_entity_embeddings.csv --max_runtime 60 --report mutagenesis_results.csv
```
| LP | Train-F1-OCEL | Test-F1-OCEL | RT-OCEL | Train-F1-CELOE | Test-F1-CELOE | RT-CELOE | Train-F1-Evo | Test-F1-Evo | RT-Evo | Train-F1-DRILL | Test-F1-DRILL | RT-DRILL | Train-F1-TDL | Test-F1-TDL | RT-TDL | Train-F1-NCES | Test-F1-NCES | RT-NCES | Train-F1-CLIP | Test-F1-CLIP | RT-CLIP |
|:---------|--------------:|-------------:|--------:|---------------:|--------------:|---------:|-------------:|------------:|-------:|---------------:|--------------:|---------:|-------------:|------------:|-------:|--------------:|-------------:|--------:|--------------:|-------------:|--------:|
| NotKnown | 0.916 | 0.918 | 60.705 | 0.916 | 0.918 | 60.705 | 0.975 | 0.970 | 51.870 | 0.809 | 0.804 | 60.140 | 1.000 | 0.852 | 13.569 | 0.717 | 0.718 | 3.784 | 0.916 | 0.918 | 26.312|
### 10-Fold Cross Validation Carcinogenesis Benchmark Results
```shell
python examples/concept_learning_cv_evaluation.py --kb ./KGs/Carcinogenesis/carcinogenesis.owl --lps ./LPs/Carcinogenesis/lps.json --path_of_nces_embeddings ./NCESData/carcinogenesis/embeddings/ConEx_entity_embeddings.csv --path_of_clip_embeddings ./CLIPData/carcinogenesis/embeddings/ConEx_entity_embeddings.csv --max_runtime 60 --report carcinogenesis_results.csv
```
| LP | Train-F1-OCEL | Test-F1-OCEL | RT-OCEL | Train-F1-CELOE | Test-F1-CELOE | RT-CELOE | Train-F1-Evo | Test-F1-Evo | RT-Evo | Train-F1-DRILL | Test-F1-DRILL | RT-DRILL | Train-F1-TDL | Test-F1-TDL | RT-TDL | Train-F1-NCES | Test-F1-NCES | RT-NCES | Train-F1-CLIP | Test-F1-CLIP | RT-CLIP |
|:---------|--------------:|-------------:|--------:|---------------:|--------------:|---------:|-------------:|------------:|-------:|---------------:|--------------:|---------:|-------------:|------------:|-------:|--------------:|-------------:|--------:|--------------:|-------------:|--------:|
| NOTKNOWN | 0.737 | 0.711 | 62.048 | 0.740 | 0.701 | 62.048 | 0.822 | 0.628 | 64.508 | 0.740 | 0.707 | 60.120 | 1.000 | 0.616 | 5.196 | 0.705 | 0.704 | 4.157 | 0.740 | 0.701 | 48.475|
Development
To see the results
Creating a feature branch **refactoring** from development branch
```shell
git branch refactoring develop
```
Each feature branch must be merged to develop branch. To this end, the tests must run without a problem:
```shell
# To download knowledge graphs
wget https://files.dice-research.org/projects/Ontolearn/KGs.zip -O ./KGs.zip && unzip KGs.zip
# To download learning problems
wget https://files.dice-research.org/projects/Ontolearn/LPs.zip -O ./LPs.zip && unzip LPs.zip
# Download weights for some model for few tests
wget https://files.dice-research.org/projects/NCES/NCES_Ontolearn_Data/NCESData.zip -O ./NCESData.zip && unzip NCESData.zip && rm NCESData.zip
wget https://files.dice-research.org/projects/Ontolearn/CLIP/CLIPData.zip && unzip CLIPData.zip && rm CLIPData.zip
pytest -p no:warnings -x # Running 76 tests takes ~ 17 mins
```
References
Currently, we are working on our manuscript describing our framework.
If you find our work useful in your research, please consider citing the respective paper:
# DRILL
@inproceedings{demir2023drill,
author = {Demir, Caglar and Ngomo, Axel-Cyrille Ngonga},
booktitle = {The 32nd International Joint Conference on Artificial Intelligence, IJCAI 2023},
title = {Neuro-Symbolic Class Expression Learning},
url = {https://www.ijcai.org/proceedings/2023/0403.pdf},
year={2023}
}
# NCES2
@inproceedings{kouagou2023nces2,
author={Kouagou, N'Dah Jean and Heindorf, Stefan and Demir, Caglar and Ngonga Ngomo, Axel-Cyrille},
title={Neural Class Expression Synthesis in ALCHIQ(D)},
url = {https://papers.dice-research.org/2023/ECML_NCES2/NCES2_public.pdf},
booktitle={Machine Learning and Knowledge Discovery in Databases},
year={2023},
publisher={Springer Nature Switzerland},
address="Cham"
}
# NCES
@inproceedings{kouagou2023neural,
title={Neural class expression synthesis},
author={Kouagou, N’Dah Jean and Heindorf, Stefan and Demir, Caglar and Ngonga Ngomo, Axel-Cyrille},
booktitle={European Semantic Web Conference},
pages={209--226},
year={2023},
publisher={Springer Nature Switzerland}
}
# EvoLearner
@inproceedings{heindorf2022evolearner,
title={Evolearner: Learning description logics with evolutionary algorithms},
author={Heindorf, Stefan and Bl{\"u}baum, Lukas and D{\"u}sterhus, Nick and Werner, Till and Golani, Varun Nandkumar and Demir, Caglar and Ngonga Ngomo, Axel-Cyrille},
booktitle={Proceedings of the ACM Web Conference 2022},
pages={818--828},
year={2022}
}
# CLIP
@inproceedings{kouagou2022learning,
title={Learning Concept Lengths Accelerates Concept Learning in ALC},
author={Kouagou, N’Dah Jean and Heindorf, Stefan and Demir, Caglar and Ngonga Ngomo, Axel-Cyrille},
booktitle={European Semantic Web Conference},
pages={236--252},
year={2022},
publisher={Springer Nature Switzerland}
}
In case you have any question, please contact: caglar.demir@upb.de
or caglardemir8@gmail.com