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Visualizing and Debugging Your Knowledge Graph

The following step-by-step guide walks through the process to visualize a knowledge graph after it's been constructed by graphrag. Note that some of the settings recommended below are based on our own experience of what works well. Feel free to change and explore other settings for a better visualization experience!

1. Run the Pipeline

Before building an index, please review your settings.yaml configuration file and ensure that graphml snapshots is enabled. 

snapshots:
  graphml: true
(Optional) To support other visualization tools and exploration, additional parameters can be enabled that provide access to vector embeddings. 
embed_graph:
  enabled: true # will generate node2vec embeddings for nodes
umap:
  enabled: true # will generate UMAP embeddings for nodes
After running the indexing pipeline over your data, there will be an output folder (defined by the storage.base_dir setting).

  • Output Folder: Contains artifacts from the LLM’s indexing pass.

2. Locate the Knowledge Graph

In the output folder, look for a file named merged_graph.graphml. graphml is a standard file format supported by many visualization tools. We recommend trying Gephi.

3. Open the Graph in Gephi

  1. Install and open Gephi
  2. Navigate to the output folder containing the various parquet files.
  3. Import the merged_graph.graphml file into Gephi. This will result in a fairly plain view of the undirected graph nodes and edges.

A basic graph visualization by Gephi

4. Install the Leiden Algorithm Plugin

  1. Go to Tools -> Plugins.
  2. Search for "Leiden Algorithm".
  3. Click Install and restart Gephi.

5. Run Statistics

  1. In the Statistics tab on the right, click Run for Average Degree and Leiden Algorithm.

A view of Gephi's network overview settings

  1. For the Leiden Algorithm, adjust the settings:
  2. Quality function: Modularity
  3. Resolution: 1

6. Color the Graph by Clusters

  1. Go to the Appearance pane in the upper left side of Gephi.

A view of Gephi's appearance pane

  1. Select Nodes, then Partition, and click the color palette icon in the upper right.
  2. Choose Cluster from the dropdown.
  3. Click the Palette... hyperlink, then Generate....
  4. Uncheck Limit number of colors, click Generate, and then Ok.
  5. Click Apply to color the graph. This will color the graph based on the partitions discovered by Leiden.

7. Resize Nodes by Degree Centrality

  1. In the Appearance pane in the upper left, select Nodes -> Ranking
  2. Select the Sizing icon in the upper right.
  3. Choose Degree and set:
  4. Min: 10
  5. Max: 150
  6. Click Apply.

8. Layout the Graph

  1. In the Layout tab in the lower left, select OpenORD.

A view of Gephi's layout pane

  1. Set Liquid and Expansion stages to 50, and everything else to 0.
  2. Click Run and monitor the progress.

9. Run ForceAtlas2

  1. Select Force Atlas 2 in the layout options.

A view of Gephi's ForceAtlas2 layout pane

  1. Adjust the settings:
  2. Scaling: 15
  3. Dissuade Hubs: checked
  4. LinLog mode: uncheck
  5. Prevent Overlap: checked
  6. Click Run and wait.
  7. Press Stop when it looks like the graph nodes have settled and no longer change position significantly.

10. Add Text Labels (Optional)

  1. Turn on text labels in the appropriate section.
  2. Configure and resize them as needed.

Your final graph should now be visually organized and ready for analysis!