# Graph-analysis Supplementary Information data

This directory is the portable, machine-readable record behind the graph
sections of the main paper and Supplementary Information. It is copied from
the fingerprinted analysis at
`experiments/graph-topology-rigorous-2026-07-17/` so that the complete
`paper/` directory can be moved to Overleaf or archived independently.

The graph study is a post-hoc analysis of previously generated and inspected
Gemma states. The primary graph protocol was frozen before graph outputs were
calculated. Later falsification and ranking analyses were frozen in separate
amendments before their corresponding outputs. The graph evidence is
representational, not causal, and the signed-relation graph is stratified by
the supplied mechanism family.

## Prompts and primary edges

- `signed-relation-prompt-manifest.json`: all 72 exact prompts, mechanism and
  material-case identifiers, surface variants, physical directions, expected
  answers, and displayed answer orders.
- `primary_jacobian_edges_with_ids.csv`: all 144 primary frozen-band Jacobian
  edges with complete prompt IDs, case IDs, physical directions, expected
  outcomes, similarities, correctness, first-valid ranks, and pairwise AUCs.
- `all-method-selected-edges.csv`: all 1,440 selected-edge rows across matched
  state, lexical, answer-order, oracle, and layer-band configurations.
- `all-method-candidate-ranks.csv`: all 1,440 corresponding candidate-ranking
  rows.

The Supplementary Information prints every prompt and every primary edge in
human-readable form. Regenerate those LaTeX inputs from the repository root:

```bash
python scripts/build_graph_si_inventory.py
```

## Layer, robustness, and negative-control data

- `relation-layer-metrics.csv`: signed-relation edge precision by layer and
  representation.
- `mechanism-layer-metrics.csv`: 50-prompt cross-phrasing mechanism graph by
  layer and representation.
- `mechanism-residual-layer-metrics.csv`: mechanism graph after prompt-only
  similarity residualization.
- `mechanism-hard-negatives.csv`: all frozen lexical-competitor comparisons.
- `target-free-word-enrichment.csv`: all 523 target-free word-network tests;
  zero survives BH FDR 0.05.
- `statistics.json`: complete numerical output, including blocked
  permutations, the 46,656-assignment exact null, family results, ranking,
  leave-one-family-out checks, edge stability, and negative controls.
- `validation.json`: independent 11-check audit record.

## Frozen analysis record

- `protocol.json`: primary graph protocol.
- `protocol-amendment-v1.json`: answer-order and exact structured-null
  falsification plan.
- `protocol-amendment-v2.json`: ranking and robustness plan.
- `protocol-amendment-v2-correction.json`: preserved implementation
  correction.

The manuscript records SHA-256 fingerprints for these files. The authoritative
analysis and audit commands are:

```bash
python scripts/analyze_graph_topology_rigorous.py
python scripts/audit_graph_topology_rigorous.py
```