| # 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 |
| ``` |
|
|
|
|
