Networkx
by eyadsibai
Use when "NetworkX", "graph analysis", "network analysis", "graph algorithms", "shortest path", "centrality", "PageRank", "community detection", "social network", "knowledge graph
Skill Details
Repository Files
1 file in this skill directory
name: networkx description: Use when "NetworkX", "graph analysis", "network analysis", "graph algorithms", "shortest path", "centrality", "PageRank", "community detection", "social network", "knowledge graph" version: 1.0.0
NetworkX Graph Analysis
Python library for creating, analyzing, and visualizing networks and graphs.
When to Use
- Social network analysis
- Knowledge graphs and ontologies
- Shortest path problems
- Community detection
- Citation/reference networks
- Biological networks (protein interactions)
Graph Types
| Type | Edges | Multiple Edges |
|---|---|---|
Graph |
Undirected | No |
DiGraph |
Directed | No |
MultiGraph |
Undirected | Yes |
MultiDiGraph |
Directed | Yes |
Key Algorithms
Centrality Measures
| Measure | What It Finds | Use Case |
|---|---|---|
| Degree | Most connections | Popular nodes |
| Betweenness | Bridge nodes | Information flow |
| Closeness | Fastest reach | Efficient spreaders |
| PageRank | Importance | Web pages, citations |
| Eigenvector | Influential connections | Who knows important people |
Path Algorithms
| Algorithm | Purpose |
|---|---|
| Shortest path | Minimum hops |
| Weighted shortest | Minimum cost |
| All pairs shortest | Full distance matrix |
| Dijkstra | Efficient weighted paths |
Community Detection
| Method | Approach |
|---|---|
| Louvain | Modularity optimization |
| Greedy modularity | Hierarchical merging |
| Label propagation | Fast, scalable |
Graph Generators
| Generator | Model |
|---|---|
| Erdős-Rényi | Random edges |
| Barabási-Albert | Preferential attachment (scale-free) |
| Watts-Strogatz | Small-world |
| Complete | All connected |
Layout Algorithms
| Layout | Best For |
|---|---|
| Spring | General purpose |
| Circular | Regular structure |
| Kamada-Kawai | Aesthetics |
| Spectral | Clustered graphs |
I/O Formats
| Format | Preserves Attributes | Human Readable |
|---|---|---|
| GraphML | Yes | Yes (XML) |
| Edge list | No | Yes |
| JSON | Yes | Yes |
| Pandas | Yes | Via DataFrame |
Performance Considerations
| Scale | Approach |
|---|---|
| < 10K nodes | Any algorithm |
| 10K - 100K | Use approximate algorithms |
| > 100K | Consider graph-tool or igraph |
Key concept: NetworkX is pure Python - great for prototyping, may need alternatives for production scale.
Best Practices
- Set random seeds for reproducibility
- Choose correct graph type upfront
- Use pandas integration for data exchange
- Consider memory for large graphs
Resources
- NetworkX docs: https://networkx.org/documentation/latest/
- Tutorial: https://networkx.org/documentation/latest/tutorial.html
Related Skills
Attack Tree Construction
Build comprehensive attack trees to visualize threat paths. Use when mapping attack scenarios, identifying defense gaps, or communicating security risks to stakeholders.
Grafana Dashboards
Create and manage production Grafana dashboards for real-time visualization of system and application metrics. Use when building monitoring dashboards, visualizing metrics, or creating operational observability interfaces.
Matplotlib
Foundational plotting library. Create line plots, scatter, bar, histograms, heatmaps, 3D, subplots, export PNG/PDF/SVG, for scientific visualization and publication figures.
Scientific Visualization
Create publication figures with matplotlib/seaborn/plotly. Multi-panel layouts, error bars, significance markers, colorblind-safe, export PDF/EPS/TIFF, for journal-ready scientific plots.
Seaborn
Statistical visualization. Scatter, box, violin, heatmaps, pair plots, regression, correlation matrices, KDE, faceted plots, for exploratory analysis and publication figures.
Shap
Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap), debugging models, analyzing model bias or fairness, comparing models, or implementing explainable AI. Works with tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model
Pydeseq2
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
Query Writing
For writing and executing SQL queries - from simple single-table queries to complex multi-table JOINs and aggregations
Pydeseq2
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
Scientific Visualization
Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journal formatting (Nature, Science, Cell). Orchestrates matplotlib/seaborn/plotly with publication styles. For quick exploration use seaborn or plotly directly.
