activeinferenceinstitute/gnn-visualization
src/visualization/SKILL.md
GNN graph and matrix visualization generation. Use when creating network graph plots, matrix heatmaps, state space diagrams, or other visual representations of GNN models.
$ install --global
skillsauthnpx skillsauth add activeinferenceinstitute/generalizednotationnotation gnn-visualizationInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- name:
- gnn-visualization
- description:
- GNN graph and matrix visualization generation. Use when creating network graph plots, matrix heatmaps, state space diagrams, or other visual representations of GNN models.
GNN Visualization (Step 8)
Purpose
Generates static visualizations of GNN models including network graphs, matrix heatmaps, state space diagrams, and connection maps using matplotlib and networkx.
Key Commands
# Run visualization
python src/8_visualization.py --target-dir input/gnn_files --output-dir output --verbose
# As part of pipeline
python src/main.py --only-steps 8 --verbose
API
from pathlib import Path
from visualization import (
GNNVisualizer, MatrixVisualizer, GraphVisualizer,
generate_graph_visualization, generate_matrix_visualization,
generate_visualizations, process_visualization,
)
# Use the GNNVisualizer class
viz = GNNVisualizer(output_dir="output/")
viz.generate_graph_visualization(graph_data)
viz.generate_matrix_visualization(matrix_data)
# Standalone functions
generate_graph_visualization(graph_data, output_dir="output/")
generate_matrix_visualization(matrix_data, output_dir="output/")
# Run full visualization step (used by pipeline)
process_visualization(Path("input/gnn_files"), Path("output/8_visualization_output"), verbose=True)
Key Exports
GNNVisualizer/GraphVisualizer— main visualization classesMatrixVisualizer— matrix-specific visualizationgenerate_graph_visualization— network graph plotsgenerate_matrix_visualization— matrix heatmapsprocess_visualization— pipeline processing (JSON-first when step-3*_parsed.jsonexists)
Safe-to-Fail Pattern
Visualization uses a four-tier recovery system:
- Full visualizer with all dependencies
- Matrix-only visualizer
- Basic plots
- HTML recovery report
Dependencies
# matplotlib + networkx (included in core)
uv sync
# For additional viz backends
uv sync --extra visualization
Output
- PNG/SVG images in
output/8_visualization_output/ - HTML recovery reports when matplotlib unavailable
MCP Tools
This module registers tools with the GNN MCP server (see mcp.py):
process_visualizationget_visualization_optionslist_visualization_artifactsget_visualization_module_info
References
- AGENTS.md — Module documentation
- README.md — Usage guide
- SPEC.md — Module specification
Documentation
- README: Module Overview
- AGENTS: Agentic Workflows
- SPEC: Architectural Specification
- SKILL: Capability API
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