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Best Python Packages (Tools) For Knowledge Graphs

Best Python Packages (Tools) For Knowledge Graphs

By Memgraph
5 min readMay 23, 2022

A Knowledge Graph is a reusable data layer that is used to answer sophisticated queries across multiple data silos. With contextualized data displayed and organized in the form of tables and graphs, they achieve pinnacle connectivity. They can quickly accept new information, classifications, and criteria since they were designed to capture the ever-changing nature of the data. There are different libraries for performing knowledge graphs in Python. Let's check out a few of them.

Python Packages for Knowledge Graphs

1. Pykg2vec

Pykg2vec is a Python package that implements knowledge graph embedding algorithms and flexible embedding pipeline building elements. This library seeks to assist academics and programmers in fast testing algorithms with their knowledge base, or adapting the package for their algorithms using modular blocks.

Pykg2vec was built using TensorFlow, but because more authors utilized Pytorch to create their KGE models, it was switched with Pytorch. The TF version is still available in the tf2-master branch. In addition to the primary model training procedure, pykg2vec uses multi-processing to generate mini-batches and conduct an assessment to minimize the overall completion time.


  • Bayesian hyperparameter optimization
  • Inspection techniques for the learned embeddings
  • Support cutting-edge KGE model variants as well as evaluation datasets
  • Allow for the export of learned embeddings in TSV or Pandas-compatible formats
  • KPI overview visualization depending on TSNE (mean rank, hit ratio) in multiple formats


  • Interactive visualizations
  • Personalized datasets


PyKEEN (Python Knowledge Embeddings) is a Python library that builds and evaluates knowledge graphs and embedding models. In PyKEEN 1.0, we can estimate the aggregation measures directly for all frequent rank categories. Such as mean, optimistic, and pessimistic, allowing comparison of their differences.

It can identify instances where the model precisely forecasts identical scores for various triples, which is typically undesirable behavior. The PyTorch module is used to implement it for Python 3.7+. It includes a set of comprehensive testing processes performed with PyTest and Tox. You can execute in Travis-continuous CI's integration environment.


  • Training Approaches: LCWA and sLCWA
  • Uniform and Bernoulli negative samplers
  • Optimization of hyper-parameters using optuna
  • Early stopping
  • Evaluation metrics: adjusted mean rank, mean rank, ROC-AUC score


  • It is the only library that uses automatic memory optimization to verify that memory limits are not surpassed during testing and training.
  • Users can replicate and maintain graphs due to several community-driven tools.

3. AmpliGraph

Knowledge graph embeddings can be used for various tasks, including knowledge graph completion, information retrieval, and link-based categorization, to name a few. AmpliGraph is the first open-source toolkit to democratize graph representation learning, allowing for discovering whole new knowledge from existing graphs.

The AmpliGraph package includes machine learning models that can generate knowledge graph embeddings (KGEs), low-level vector representations of the items, and relationships that make up a knowledge graph.

These models use low-dimensional vectors to encode nodes and relationships of a graph. As a result, subsequent systems that depend on those graphs, such as question-answering software, improve efficiency.

It reduces the entry barriers for knowledge graph embeddings, making such models available to even the most unskilled users and establishing a community of professionals who can benefit from the freeware API for learning on knowledge graphs.


Customization: You can enhance AmpliGraph-based estimators to create your custom knowledge graph embeddings framework.

Support: It can run on both CPUs and GPUs to accelerate the training procedure.

Less Code: Its APIs cut down on the code needed to anticipate code in knowledge graphs.


  • Open Source API
  • It can predict the missing relationships between graphs.
  • The curation of graphs produced automatically from text, which are typically messy and imprecise, is also considerably improved by link prediction.

4. LibKGE

LibKGE's primary purpose is to promote repeatable study into KGE models and training techniques. The training approach and hyperparameters selected significantly impact simulation results than the model class alone.

The goal of LibKGE is to provide simple training, hyperparameter optimization, and assessment procedures that can be used with any model. Every possible knob or heuristic in the platform is available explicitly through well-documented configuration files. The most common KGE models are included in LibKGE, and you can introduce new models. A thorough logging mechanism and equipment facilitate in-depth examination.


  • Early termination
  • Checkpointing
  • High parallelism potential
  • You can pause and restart at any moment
  • With or without mutual interactions, all models can be employed.
  • Automated Memory management for huge batch sizes


  • LIBKGE is well-structured. Individual modules can be combined and matched, and additional components can be incorporated quickly.
  • The present configuration of the test is saved alongside the model to increase evaluation and consistency.
  • During tests, LIBKGE logs a lot of data and keeps track of performance measures like runtime, memory utilization, training attrition, and evaluation methods.

5. GraphVite

The main library and the Python wrapper comprise the GraphVite platform. Python wrapper enables automatic packaging procedures for core library classes. It also provides an implementation for data sets and various applications.

The core library is written in C+11 and CUDA, and pybind11 is used to link it to Python. It encompasses all GraphVite's calculation-related classes, such as graphs, analyzers, and optimization algorithms. Developers can bundle all of these components into classes that resemble Python interfaces.

The architecture allows dynamic data types in the Python interface and optimizes compile time for optimal efficiency. It also includes nine major models and their comparisons to standard data sets. Users can quickly practice complicated graphics embedding methods and get results in a short amount of time using the Python interface. Users can utilize the core interface to develop visual deep learning methods without worrying about scheduling.


  • Node embedding
  • Knowledge Graph embedding
  • High-dimensional data visualization
  • Replication of learning algorithm on a unified platform


  • High speed
  • You can learn from large scale graphs
  • Visualize charts or high-dimensional information effectively
  • Enhance working prototype and model modification effectiveness
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