tda-graph-network-analysis

Constructs and analyzes Mapper graphs, transition graphs, and network metrics for topological data analysis.

1|Updated Dec 13, 2025
One-click install
npx skills add https://github.com/ZK-Theory/TDL --skill tda-graph-network-analysis-zk-theory
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: tda-graph-network-analysis
Source: https://github.com/ZK-Theory/TDL/tree/main/.agents/skills/tda-graph-network-analysis
Command: npx skills add https://github.com/ZK-Theory/TDL --skill tda-graph-network-analysis-zk-theory

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires networkx.

What problem does it solve? Graph summaries like Mapper graphs and transition networks are often misused as substitutes for persistent homology or built with undocumented parameters, producing unreproducible and overclaimed results. This Skill enforces a disciplined procedure for defining, constructing, and reporting graph analyses in TDL research. ## Core Features & Use Cases - Graph Construction Discipline: Requires explicit node semantics, edge semantics, directionality, weighting, and construction thresholds before any metric is computed. - Question-Matched Metrics: Computes only the network metrics that answer a named scientific question, avoiding unfocused metric dumps. - Reproducibility Controls: Mandates recording layout seeds, thresholds, and component handling in a structured output record. - Use Case: When building a Mapper graph over a UMAP embedding of employment trajectories, the Skill routes the embedding choice through representation diagnostics first, then records all construction parameters so the graph result can support a paper claim. ## Quick Start Ask the assistant to construct a Mapper graph from trajectory clusters and record the full graph construction output record for a TDL paper.

Frequently Asked Questions about tda-graph-network-analysis

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I build a Mapper graph for trajectory data?

Define node semantics as clusters of trajectories and edge semantics as overlap counts or probabilities, then specify thresholds, directionality, and weighting before computing metrics. Record all construction parameters in the required output record for reproducibility.

Should I use NetworkX or torch-geometric for graph analysis?

NetworkX is the default for Mapper graphs, transition graphs, and network metrics. torch-geometric is reserved for later graph-learning papers and is an optional dependency, so verify it is installed before importing it.

Can a graph metric confirm a persistent homology result?

No. A graph metric such as modularity can corroborate but never substitute for a topological result. Equivalence claims between graph summaries and persistent homology must be routed through the topology lane for validation.

Why is my graph visualization not reproducible?

Graph layout algorithms are stochastic, so an unseeded layout produces different results each run. Always record the layout algorithm and its random seed in the output record to make figures reproducible.

When should graph construction thresholds trigger a sensitivity analysis?

When changing overlap, edge cutoff, or binning thresholds materially changes the conclusion, that is a sensitivity analysis requiring dedicated review, not a footnote. Escalate to the sensitivity-comparison-review workflow.