Benchmark Datasets for Knowledge Graph Generation

IntelliGraphs is a collection of benchmark datasets specifically for use in benchmarking generative models for knowledge graphs. You can learn more about it in our preprint: IntelliGraphs: Datasets for Benchmarking Knowledge Graph Generation. The intelligraphs Python package provides easy access to the datasets, along with pre- and post-processing functions, baseline models, and evaluation tools for benchmarking new models.

Table of Contents

• Installation
• Downloading IntelliGraphs datasets
• Data Loader
• Generator
• Verifier
• Baseline Models
• Data Validation
• Reporting Issues
• License Information

Installation

IntelliGraphs can be installed using either pip or conda, depending on your preferred package management system. The IntelliGraphs python package requires a number of dependencies which will also be installed during the installation process.

Installing with pip

pip is the Python package installer, and it's commonly used for installing Python packages from the Python Package Index (PyPI). To install IntelliGraphs using pip, open your terminal or command prompt and run the following command:

pip install intelligraphs

This command will automatically download and install the IntelliGraphs package along with any dependencies required for it to function properly.

Installing with conda

If you prefer to use conda, you can install IntelliGraphs by running the following command in your terminal or command prompt:

conda install -c thiv intelligraphs

Verifying the Installation

After installation, you can verify that IntelliGraphs has been successfully installed by running the following command in your Python environment:

import intelligraphs

print(intelligraphs.__version__)

Platform Compatibility

This package has been and developed and tested on MacOS and Linux operating systems. Users on Windows may encounter issues. If you experience any problems on Windows, please raise an issue on the project's GitHub repository.

Downloading the Datasets

The datasets required for this project can be obtained either manually or automatically through IntelliGraphs Python package.

Manual Download

The datasets are hosted on Zenodo and can be downloaded directly from the following link:

Zenodo Download Link: https://doi.org/10.5281/zenodo.7824818

To manually download the datasets:

1. Click on the provided link above.
2. You will be redirected to the Zenodo page hosting the datasets.
3. On the Zenodo page, click the Download button or select specific files to download as needed.
4. Once downloaded, extract the files (if compressed) to a directory of your choice on your local machine.

Automatic Download with IntelliGraphs

Alternatively, you can use the IntelliGraphsDataLoader class to download and prepare the datasets automatically. This method is convenient if you want to streamline the process and ensure that all required data is correctly organized.

To download datasets automatically:

1. Ensure you have the necessary dependencies installed, including intelligraphs.

2. Use the following code snippet to download and load the dataset:

from intelligraphs import IntelliGraphsDataLoader  

# Initialize the data loader with the desired dataset name
dataset_name = 'syn-paths'  # Example dataset name, replace with the dataset you want to download
data_loader = IntelliGraphsDataLoader(dataset_name)

# Load data into PyTorch DataLoader objects
train_loader, valid_loader, test_loader = data_loader.load_torch(batch_size=32)

3. The dataset will be automatically downloaded and extracted to the .data directory if it does not already exist.

4. The data will be loaded into PyTorch DataLoader objects (train_loader, valid_loader, test_loader) for easy use in training and evaluation.

5. If you prefer to download the dataset only (without loading into PyTorch), simply instantiate the IntelliGraphsDataLoader class and it will handle the download and extraction automatically:

from intelligraphs import IntelliGraphsDataLoader  # Replace with the actual import path

# Initialize the data loader to download the dataset
dataset_name = 'syn-paths'  # Example dataset name, replace with the dataset you want to download
data_loader = IntelliGraphsDataLoader(dataset_name)

The dataset will be saved in the .data directory by default.

IntelliGraphs Data Loader

The IntelliGraphsDataLoader class is a utility for loading IntelliGraphs datasets, simplifying the process of accessing and organizing the data for machine learning tasks. It provides functionalities to download, extract, and load the datasets into PyTorch tensors.

Features and Benefits

• PyTorch Integration: Seamless integration with PyTorch for graph-based machine learning tasks.
• Configuration Options: Customizable options for batch size, padding, and shuffling.
• Data Preprocessing: Simplifies dataset preprocessing with automated download, extraction, and conversion.

Usage

1. Instantiate the DataLoader:

from intelligraphs import IntelliGraphsDataLoader
data_loader = IntelliGraphsDataLoader(dataset_name='syn-paths')

2. Load the Data:

train_loader, valid_loader, test_loader = data_loader.load_torch(
    batch_size=32,
    padding=True,
    shuffle_train=False,
    shuffle_valid=False,
    shuffle_test=False
)

3. Access the Data:

for batch in train_loader:
    # Perform training steps with the batch

for batch in valid_loader:
    # Perform validation steps with the batch

for batch in test_loader:
    # Perform testing steps with the batch

IntelliGraphs Synthetic KG Generator

SynPathsGenerator

This generator creates path graphs where each node represents a city in the Netherlands and each edge represents a mode of transport (cycle_to, drive_to, train_to).

• Entities: Dutch cities
• Relations: Modes of transport between cities
• Use case: Structural learning

SynTIPRGenerator

This generator creates graphs representing academic roles, timelines, and people. The nodes represent individuals, roles, and years, and the edges represent relationships like has_name, has_role, start_year, and end_year.

• Entities: Names, roles, years
• Relations: Relationships between academic roles and timeframes
• Use case: Basic temporal reasoning and type checking

SynTypesGenerator

This generator creates graphs where nodes represent countries, languages, and cities, and edges represent relationships like spoken_in, part_of, and same_as.

• Entities: Countries, languages, cities
• Relations: Geographical and linguistic relationships
• Use case: Type checking

Customization

Each generator class inherits from BaseSyntheticDatasetGenerator and can be customized by overriding methods or adjusting parameters. The base class provides utility methods for splitting datasets, checking for unique graphs, and visualizing graphs.

Extending Functionality

To create a new dataset generator, simply create a new class that inherits from BaseSyntheticDatasetGenerator and implement the sample_synthetic_data method to define your dataset's logic.

class MyCustomDatasetGenerator(BaseSyntheticDatasetGenerator):
    def sample_synthetic_data(self, num_graphs):
        # Implement your custom logic here
        pass

Data Generation

You can generate synthetic datasets by running the corresponding script for each generator. Each generator allows customization of dataset size, random seed, and other parameters.

python intelligraphs/generator/synthetic/synpaths_generator.py --train_size 60000 --val_size 20000 --test_size 20000 --num_edges 3 --random_seed 42 --dataset_name "syn-paths"
python intelligraphs/generator/synthetic/syntypes_generator.py  --train_size 60000 --val_size 20000 --test_size 20000 --num_edges 3 --random_seed 42 --dataset_name "syn-types"
python intelligraphs/generator/synthetic/syntipr_generator.py --train_size 50000 --val_size 10000 --test_size 10000 --num_edges 3 --random_seed 42 --dataset_name "syn-tipr"

IntelliGraphs Verifier

Rules

Every dataset comes with a set of rules that describe the nature of the graphs. The ConstraintVerifier class includes a convenient method called print_rules() that allows you to view all the rules and their descriptions in a clean and organized format.

To use the print_rules() method, simply instantiate a subclass of ConstraintVerifier, such as SynPathsVerifier, and then call the print_rules() method on that instance to list the logical rules for a given dataset.

Example Usage

from intelligraphs.verifier.synthetic import SynPathsVerifier

# Initialize the verifier for the syn-paths dataset
verifier = SynPathsVerifier()

# Print the rules and their descriptions for the syn-paths dataset
verifier.print_rules()

When you call print_rules(), you'll get a formatted list of all the rules along with their corresponding descriptions. For example:

List of Rules and Descriptions:
        -> Rule 1:
           FOL: ∀x, y, z: connected(x, y) ∧ connected(y, z) ⇒ connected(x, z)
           Description: Ensures transitivity. If x is connected to y, and y is connected to z, then x should be connected to z.
        -> Rule 2:
           FOL: ∀x, y: edge(x, y) ⇒ connected(x, y)
           Description: If there's an edge between two nodes x and y, then x should be connected to y.
        ...

Baseline Models

Importing Baseline Models

Our baseline models are also available through the Python API. You can find them inside baseline_models class.

To import the Uniform Baseline model:

from intelligraphs.baseline_models import UniformBaseline

To import the Knowledge Graph Embedding (KGE) models:

from intelligraphs.baseline_models.knowledge_graph_embedding_model import KGEModel

Setup

To recreate our experiments, you will need to recreate the virtual environments with the required dependencies.

1. Create and activate a new conda environment:

• First, create a dedicated environment named intelligraph_baseline with Python 3.10:

  conda create -n intelligraph_baseline python=3.10

• Activate the newly created environment:

  conda activate intelligraph_baseline

2. Install the intelligraphs package:

• To install the intelligraphs package, choose one of the following methods:

  pip install -e .

  pip install intelligraphs

  conda install -c thiv intelligraphs

3. Install additional dependencies for running baselines:

• The baseline experiments require some extra Python packages. These packages include popular libraries such as PyTorch (for machine learning), PyYAML (for configuration file management), tqdm (for progress bars), Weights & Biases (for experiment tracking), NumPy, and SciPy. Install them using:

  pip install torch pyyaml tqdm wandb numpy scipy

4. Set up Weights & Biases (wandb) for experiment tracking:

• We use Weights & Biases (wandb) to track experiments, log metrics, and visualize results.
• To start using wandb, create an account on their platform and log in from the command line:

  wandb login

• If you prefer not to use wandb for tracking, you can disable it by setting wandb to offline mode:

  wandb offline

• When set to offline, wandb will not sync any data to the cloud, but you can still run experiments locally.

Uniform Baseline Model

The uniform baseline model is designed to serve as a simple reference baseline. It applies a random compression strategy for the synthetic and real-world datasets. You can run this baseline using the following commands:

python benchmark/experiments/uniform_baseline_compression_test.py

It should complete in about a minute without any GPU-acceleration.

To run the graph sampling experiment using the uniform sampler, run the command:

python benchmark/experiments/uniform_baseline_graph_sampling.py

Probabilistic KGE Models

We have developed three probabilistic Knowledge Graph Embedding (KGE) models based on TransE, DistMult, and ComplEx. These models are CUDA-compatible and can take advantage of multiple GPUs for accelerated training and inference.

The following commands allow you to run baseline experiments on various synthetic and real-world datasets. Each experiment is configured through a YAML file, which specifies the model and dataset parameters.

For the syn-paths dataset:

python benchmark/experiments/probabilistic_kge_baselines.py  --config benchmark/configs/syn-paths-transe.yaml
python benchmark/experiments/probabilistic_kge_baselines.py  --config benchmark/configs/syn-paths-complex.yaml
python benchmark/experiments/probabilistic_kge_baselines.py  --config benchmark/configs/syn-paths-distmult.yaml

For the syn-tipr dataset:

python experiments/train_baseline.py  --config benchmark/configs/syn-tipr-transe.yaml
python experiments/train_baseline.py  --config benchmark/configs/syn-tipr-complex.yaml
python experiments/train_baseline.py  --config benchmark/configs/syn-tipr-distmult.yaml

For the syn-types dataset:

python benchmark/experiments/probabilistic_kge_baselines.py  --config benchmark/configs/syn-types-transe.yaml
python benchmark/experiments/probabilistic_kge_baselines.py  --config benchmark/configs/syn-types-complex.yaml
python benchmark/experiments/probabilistic_kge_baselines.py  --config benchmark/configs/syn-types-distmult.yaml

For the wd-articles dataset:

python benchmark/experiments/probabilistic_kge_baselines.py  --config benchmark/configs/wd-articles-transe.yaml
python benchmark/experiments/probabilistic_kge_baselines.py  --config benchmark/configs/wd-articles-complex.yaml
python benchmark/experiments/probabilistic_kge_baselines.py  --config benchmark/configs/wd-articles-distmult.yaml

For the wd-movies dataset:

python benchmark/experiments/probabilistic_kge_baselines.py  --config benchmark/configs/wd-movies-transe.yaml
python benchmark/experiments/probabilistic_kge_baselines.py  --config benchmark/configs/wd-movies-complex.yaml
python benchmark/experiments/probabilistic_kge_baselines.py  --config benchmark/configs/wd-movies-distmult.yaml

Dataset Verification

We have written test functions to check the graphs in the datasets against the list of rules. It can be run using:

python intelligraphs/data_validation/validate_data.py

If there are any errors in the data, it will raise a DataError exception and the error message will look similar to this:

intelligraphs.errors.custom_error.DataError: Violations found in a graph from the training dataset: 
        - Rule 6: An academic's tenure end year cannot be before its start year. The following violation(s) were found: (_time, start_year, 1996), (_time, end_year, 1994).

How to Cite

If you use IntelliGraphs in your research, please cite the following paper:

@article{thanapalasingam2023intelligraphs,
  title={IntelliGraphs: Datasets for Benchmarking Knowledge Graph Generation},
  author={Thanapalasingam, Thiviyan and van Krieken, Emile and Bloem, Peter and Groth, Paul},
  journal={arXiv preprint arXiv:2307.06698},
  year={2023}
}

Reporting Issues

If you encounter any bugs or have any feature requests, please file an issue here.

License

IntelliGraphs datasets and the python package is licensed under CC-BY License. See LICENSE for more information.

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Unit tests

Make sure to activate the virtual environment with the installation of the intelligraphs package.

To run the unit tests, install pytest and verify installation:

pip install pytest
pytest --version

Execute the units tests using:

pytest