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Repository Map

This file maps the paper claims to concrete directories and entry points.

Top-level Layout

  • README.md — front-door summary and links.
  • CLAIMS_AND_EVIDENCE.md — claim-by-claim evidence table.
  • docs/experiments/ — per-phase reproducibility docs.
  • paper/ — manuscript (main.tex), PDF, figure pipeline.
  • artifacts/ — committed run outputs used in analysis.
  • outputs/ — additional generated outputs from legacy runs.
  • repro/ — environment lock and rebuild notes.
  • scripts/ — active analysis/generation scripts for Phases A/B/C.
  • phase_a_global_h0_topology/scripts/ — legacy original root scripts (moved for clarity).
  • phase_a_global_h0_topology/figures_archive/ — preserved visuals from the original Phase A direction.

Experiment Phases

Phase A: Global Topology (Negative)

  • Doc: docs/experiments/01_global_h0_topology/README.md
  • Legacy scripts: phase_a_global_h0_topology/scripts/
  • Main artifacts:
    • artifacts/paired_dynamic_qwen35/
    • artifacts/qwen35_2b_window_corrected/

Phase B: Convergence Failure (Fixed Decoding)

  • Doc: docs/experiments/02_convergence_failure/README.md
  • Main scripts:
    • scripts/run_multi_sample_questions.py
    • scripts/analyze_within_question_basins.py
    • scripts/run_cap_sensitivity.py
    • scripts/analyze_cap_sensitivity.py
  • Main artifacts:
    • artifacts/qwen35_2b_within_question/
    • artifacts/qwen35_2b_cap_sensitivity_640/

Phase C: Micro-World Semantics (Main Result)

  • Doc: docs/experiments/03_micro_world_semantics/README.md
  • Main scripts:
    • scripts/generate_micro_world_dataset.py
    • scripts/run_micro_world_inference.py
    • scripts/analyze_micro_world_geometry.py
    • scripts/run_micro_world_probe.py
    • scripts/analyze_micro_world_label_logits.py
    • scripts/run_micro_world_layer_sweep_probe.py
    • scripts/run_readout_intervention.py
    • scripts/run_latent_readout_steering.py
    • scripts/run_mlp_probe_sensitivity.py
  • Main artifacts:
    • artifacts/micro_world_v1/dataset/
    • artifacts/micro_world_v1/generations/
    • artifacts/micro_world_v1/comparison_*.csv
    • artifacts/micro_world_v1/layer_sweep_*
    • artifacts/micro_world_v1/label_logits_*
    • artifacts/micro_world_v1/readout_intervention/
    • artifacts/micro_world_v1/latent_readout_steering/
    • artifacts/micro_world_v1/probe_mlp_sensitivity/

Paper Assets

  • TeX source: paper/main.tex
  • Compiled PDF: paper/paper.pdf
  • Figure script: paper/scripts/make_figures.py
  • Generated figures: paper/figures/
  • CI workflow: .github/workflows/paper.yml
  • Release bundler: scripts/package_release_bundle.py

Legacy Script Location

Legacy first-direction scripts previously kept at repo root are now under:

  • phase_a_global_h0_topology/scripts/

This includes:

  • audit_report.py
  • trace_generator.py
  • batch_verifier.py
  • topological_engine.py
  • analyze_results.py
  • visualizer.py
  • visualize_comparisons.py