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Graph-Based Data Science Masterclass

A Talk by Paco Nathan
Managing Partner, Derwen, Inc.

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About this talk

Slides available at "Media" section on the right

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Paco's Masterclass sneak peak

Graph-Based Data Science Workshop

Python has excellent libraries for working with graphs which provide: semantic technologies, graph queries, interactive visualizations, graph algorithms, probabilistic graph inference, as well as embedding and other integrations with deep learning.

However, almost none of these have integration paths other than writing lots of custom code, and most do not share common file formats. Moreover, few of these libraries integrate effectively with popular data science tools (e.g., pandas, scikit-learn, PyTorch, spaCy, etc.) or with popular infrastructure for scale-out (Apache Spark, Ray, RAPIDS, Apache Parquet, fsspec, etc.) on cloud computing.

This workshop uses kglab – an open source project that integrates RDFlib, OWL-RL, pySHACL, NetworkX, iGraph, pslpython, node2vec, PyVis, and more – to show how to use a wide range of graph-based approaches, blending smoothly into data science workflows, and working efficiently with popular data engineering practices.

The material emphasizes hands-on coding examples which you can reuse; best practices for integrating and leveraging other useful libraries; history and bibliography (e.g., links to primary sources); accessible, detailed API documentation; a detailed glossary of terminology; plus links to many helpful resources, such as online "playgrounds".

Meanwhile, overall we keep a practical focus on use cases.


  • Python developers who need to work with KGs
  • Data Scientists, Data Engineers, Machine Learning Engineers
  • Technical Leaders who want hands-on KG implementation experience
  • Executives working on data strategy who need to learn about KG capabilities
  • People interested in developing personal knowledge graphs

Key Takeaways

  • Hands-on experience with popular open source libraries in Python for building KGs, including rdflib, pyshacl, networkx, owlrl, pslpython, and more.
  • Coding examples that can be used as starting points for your own KG projects
  • How to blend different graph-based approaches within a data science workflow to complement each other's strengths: for data quality checks, inference, human-in-the-loop, etc.
  • Integrating with popular data science tools, such as pandas, scikit-learn, matplotlib, etc.
  • Graph-based practices that fit well with Big Data tools such as Spark, Parquet, Ray, RAPIDS, and so on


  • Some coding experience in Python (you can read a 20-line program)
  • Interest in use cases that require knowledge graph representation

Additionally, if you've completed Algebra 2 in secondary school and have some business experience working with data analytics – both can come in handy.


See the installation instructions at

  1. Git clone
  2. Install required libraries using pip or conda
  3. Install JupyterLab


  1. Sources for data and controlled vocabularies: using a progressive example based on a Kaggle dataset for food/recipes
  2. KG Construction in rdflib and Serialization in TTL, JSON-LD, Parquet, etc.
  3. Transformations between RDF graphs and algebraic objects
  4. Interactive Visualization with PyVis
  5. Querying with SPARQL, with results in pandas
  6. Graph-based validation with SHACL constraint rules
  7. Graph Algorithms in networkx and igraph
  8. Inference based on semantic closures
  9. Inference and data quality checks based on probabilistic soft logic
  10. Embedding (deep learning) for data preparation and KG construction

Categories covered by this talk

Paco Nathan

Known as a "player/coach", with core expertise in data science, natural language, machine learning, cloud computing; 38+ years tech industry experience, ranging from Bell Labs to early-stage start-ups.

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