ontolearn 0.8.1

Ontolearn is an open-source software library for structured machine learning in Python. Ontolearn includes modules for processing knowledge bases, inductive logic programming and ontology engineering.

 

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:

• Drill → Neuro-Symbolic Class Expression Learning
• EvoLearner → EvoLearner: Learning Description Logics with Evolutionary Algorithms
• NCES2 → (soon) Neural Class Expression Synthesis in ALCHIQ(D)
• NCES → Neural Class Expression Synthesis
• NERO → (soon) Learning Permutation-Invariant Embeddings for Description Logic Concepts
• CLIP → Learning Concept Lengths Accelerates Concept Learning in ALC
• CELOE → Class Expression Learning for Ontology Engineering
• OCEL → A limited version of CELOE

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

ontolearn-webservice --path_knowledge_base KGs/Mutagenesis/mutagenesis.owl

or launch a Tentris instance https://github.com/dice-group/tentris over Mutagenesis.

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.

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

import json
import requests
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())

NCES (another scalable learner). The following will first train NCES if the provided path path_to_pretrained_nces does not exist

import json
import requests
with open(f"LPs/Mutagenesis/lps.json") as json_file:
    learning_problems = json.load(json_file)["problems"]
## This trains NCES before solving the provided learning problems. Expect poor performance for this number of epochs, and this training data size.
## If GPU is available, set `num_of_training_learning_problems` t0 10_000 or more. Set `nces_train_epochs` to 300 or more, and increase `nces_batch_size`.
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": "NCES",
                                  "path_embeddings": "mutagenesis_embeddings/Keci_entity_embeddings.csv",
                                  "path_to_pretrained_nces": None,
                                  # if pretrained_nces exists, load weghts, otherwise train one and save it
                                  "num_of_training_learning_problems": 100,
                                  "nces_train_epochs": 5,
                                  "nces_batch_size": 16
                                  })
    print(response.json())

Now this will use pretrained weights for NCES

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": "NCES",
                                  "path_embeddings": "./NCESData/mutagenesis/embeddings/ConEx_entity_embeddings.csv",
                                  "path_to_pretrained_nces": "./NCESData/mutagenesis/trained_models/",
                                  # if pretrained_nces exists, load weghts, otherwise train one and save it
                                  "num_of_training_learning_problems": 100,
                                  "nces_train_epochs": 5,
                                  "nces_batch_size": 16
                                  })
    print(response.json())

Benchmark Results

To see the results

# 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.

# 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.

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

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

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

git branch refactoring develop

Each feature branch must be merged to develop branch. To this end, the tests must run without a problem:

# 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: [e-mail] or [e-mail]