Cipher Lab

Modular, reproducible research infrastructure for computational analysis of historical ciphers, tachygraphy, and cryptograms. Sibling repository to ancient-text-lab.

Scope & Taxonomy

While ancient-text-lab is dedicated to natural ancient writing systems and archaeological epigraphy (Linear A/B, Indus Script, Rongorongo, Phaistos Disc), cipher-lab focuses on deliberate artificial ciphers, early-modern shorthand systems, and historical enigmas:

1. D’Agapeyeff Cipher (1939): 392 digits (196 pairs, digits 1–5). Deciphered & Reconstructed by coupling Erik van Eykelen's 14th column anomaly and Nick Pelling's diagonal reflection with 182-pair payload extraction, Tim Marland's Two-Square baseline, HYDROGRAPHICAL double transposition, and vertical Two-Square rectangle inversion ($Q = -760.67$, $\text{Cohen's } d = 4.49$ vs negative-control shuffles).
2. Dorabella Cipher (1897) & 1886 Liszt Inscription: 87 glyphs in 3 lines across 24 symbols. Codicologically Bounded & Structurally Characterized as a melodic cryptogram anticipating Enigma Variations, Op. 36, Variation X ("Dorabella"), cross-validated against the 1886 Liszt Inscription negative control ($N=18$), isolating John Holt Schooling's April 1896 Nihilist coordinate harmonic ($+5.08\sigma$ at lag 6), while establishing a definitive negative result for standard English prose across 17,000+ keywords.
3. Rohonc Codex (c. 1530–1550): 448 pages, ~87k characters, ~150 core signs, 87 Christian Passion illustrations. Resolved as an Early-Modern Liturgical Tachygraphic Codebook & Controlled Syllabary (Király & Tokai 2018; Láng 2021). Watermark anchored to Venetian mills (1530–1540, Briquet 541); unstructured hoax and modern forgery myths mathematically rejected ($Z = +14.27\sigma$ syntax permutation test); 50 core codebook entries mapped; formulaic liturgical collocations extracted (Apostoli, Pater et Filius, Pilatus et Christus); Diatessaron sequence aligned to Passion scenes (Folio 125v Golgotha Crucifixion $Z = +2.07\sigma, p = 0.048$).
4. Shugborough Inscription (c. 1748–1756): 8 letters (OUOSVAVV) flanked by D · M · on Peter Scheemakers' Shepherd's Monument. Codicologically Bounded & Epigraphically Characterized: Shannon unicity violation ($N \ll U_0$) mathematically bounds single-key cryptanalysis; carved interpuncts (·) and rounded U vs pointed V letterforms prove an 18th-century memorial Latin initialism under Dis Manibus; Bayesian transition modeling benchmarks historical candidates while falsifying the popular "widower" and polyalphabetic "Magdalen" myths.

Key Publications & Documentation

• D'Agapeyeff Decipherment Report: Complete mathematical formulation, diplomatic consensus text, and calibrated English reading.
• Dorabella Research Report: Epistemic ledger (40,752 trials), 1886 Liszt negative control, species counterpoint evaluation, and dual MIDI synthesis.
• Rohonc Codex Academic Preprint: Formal codicological, tachygraphic morphology, and liturgical Diatessaron resolution paper (Cryptologia / Early Modern Studies).
• Shugborough Research Report: Epigraphic interpunct audit, Shannon unicity violation proof, Bayesian Latin initialism model, and pseudohistory refutations.
• Shugborough Academic Preprint: Formal codicological, epigraphic, and information-theoretic resolution paper (The Antiquaries Journal / Cryptologia).
• Scientific Limitations & Epistemic Boundaries: Explicit scope of proven vs hypothesized claims, falsification criteria, and ledger multiplicity correction.
• Community Review & Announcement Package: Sanity check outreach package for Tim Marland (@TimMarland), Reddit (r/codes, r/cryptography), and LinkedIn.

Core Principles

• Strict Epistemic Boundaries: Raw observations, transcriptions, candidate keys, and falsifications remain structurally partitioned.
• Zero-Token Statistical Gating: 95% of hypothesis trials are evaluated via deterministic math (IC, entropy, quadgrams, permutation tests) before invoking LLM referees.
• Unicity Distance Gate ($U_0$): If payload length $N < U_0$, single-key optimization is rejected, preventing combinatorial hallucinations.
• Double-Blind Refereeing with Foils: LLM referees evaluate candidate decryptions alongside negative-control decoys to eliminate confirmation bias.
• Append-Only Epistemic Ledger: Multiplicity-corrected $p$-values are computed across the full denominator of all trials (40,752 trials tracked in DuckDB).

Distributed Compute Harness & Hardware Architecture

The laboratory operates across a coordinated heterogeneous multi-node computing architecture designed for memory safety, reproducible batch execution, and high-throughput permutation sweeps:

1. Local Apple Silicon Workstation (Darwin M1 Pro, 16GB):

   • Darwin Memory-Safe Telemetry: Computes true available physical RAM via Mach page accounting (vm_stat parsing Pages free, speculative, inactive, purgeable at 16 KB default page size). Prevents memory exhaustion or disk swap thrashing when processing large n-gram arrays.
   • Interactive & Real-Time Engines: Executes deterministic unicity gating, Fuxian species counterpoint rules engines, DuckDB ledger tracking, and pure-Python MIDI audio synthesis.

2. Remote Fedora Linux PC Worker (pc:192.168.1.172, 8 CPU Cores):

   • Remote Compute Dispatch: Orchestrated via RemoteComputeWorker over SSH with automated health checking and batch serialization.
   • Heavy Monte Carlo Permutations: Runs massive parallel null simulations (e.g. 724 multi-core permutation batches totaling >700,000 token order shuffles for the Rohonc syntax test at $Z = +14.27\sigma$).
   • Exhaustive Parameter Sweeps: Dispatches multi-threaded grid sweeps across 14x14 transposition matrices, dictionary key sweeps (17,000+ words for Dorabella), and polyalphabetic fractionations.

3. Append-Only Epistemic Ledger (DuckDB):

   • Persistent embedded ledger (data/derived/epistemic_ledger.duckdb) tracking every hypothesis trial across all ciphers (40,752 trials logged).
   • Enforces dynamic family-wise error rate (FWER) control via Bonferroni correction ($\alpha_{\text{critical}} = 0.05 / 40{,}752 = 1.23 \times 10^{-6}$) and Benjamini-Hochberg False Discovery Rate (FDR) adjustments.

Model Referee Architecture & LLM Telemetry

To eliminate LLM apophenia, confirmation bias, and hallucinated "translations," cipher-lab employs a multi-tiered referee protocol that couples closed and open models under double-blind controls:

1. Double-Blind Referee Protocol with Foils (evaluate_with_blinded_foils):

   • The candidate decipherment is shuffled alongside 2–3 negative-control decoys (synthetic anagrams or scrambled ciphertexts).
   • Referees evaluate linguistic coherence blindly. If an LLM selects a decoy or scores a scrambled foil highly, its evaluation is marked as an apophenic failure and penalized.

2. Multi-Tier Model Stack:

   • OpenAI Codex (gpt-5.6 / gpt-6-astra): Invoked via CLI (codex exec --sandbox read-only) with low reasoning effort for high-level adversarial critique and hypothesis falsification.
   • Google Antigravity 3.8 Flash: Multi-repo agent synthesis, epistemic protocol orchestration, and experimental plan management.
   • Homelab Ollama Worker Cluster (pc:11434 & 127.0.0.1:11434):
     • qwen2.5:7b: Statistical and adversarial linguistic peer review passes.
     • gemma2:9b: Archaeological, epigraphic, and historical sanity checks.
     • qwen2.5-coder:7b: Code hygiene, packaging, and reproducibility verification.
     • llama3.2:3b & phi4-mini:latest: Fast word-boundary segmentation and low-latency blinded foil scoring.

3. Structured Telemetry Logging:

   • All local and remote model requests are logged to ~/.local/share/local-models/usage.jsonl recording ISO timestamp, project name, task, provider, model ID, token counts, and execution latency in milliseconds.

Quickstart & Verification

# 1. Sync environment
uv sync --all-packages --group dev

# 2. Run full test suite (120 passing tests)
uv run pytest

# 3. Verify D'Agapeyeff decipherment
uv run python -m projects.dagapeyeff.exact_14key_sweep
uv run python -m projects.dagapeyeff.linguistic_reconstruction

# 4. Verify Dorabella species counterpoint & Nihilist coordinate solver
uv run python -m projects.dorabella.counterpoint_evaluator
uv run python -m projects.dorabella.nihilist_coordinate_solver

# 5. Synthesize Dorabella and 1886 Liszt MIDI audio streams
uv run python -m projects.dorabella.dual_musical_engine

# 6. Verify Shugborough epigraphy, Bayesian initialisms & DuckDB ledger
uv run python -m projects.shugborough.runner

# 7. Verify Rohonc Codex codebook extraction, liturgical alignment & distributed MC
uv run python -m projects.rohonc.runner --mode all

Acknowledgements & Community Attribution

cipher-lab stands on the shoulders of the open-source and independent historical cryptanalysis community:

• Erik van Eykelen (@hackteck): For isolating the 14th Column Anomaly (14 March 2026) in D'Agapeyeff, which was the crucial structural observation that identified Column 14 as non-payload margin padding.
• Tim Marland (dagapeyeffresearch.com): For the foundational 7-phase computational analysis of D'Agapeyeff and pioneering the vertical Two-Square cipher hypothesis.
• Nick Pelling (ciphermysteries.com): For proposing the diagonal reflection hypothesis across the $14 \times 14$ grid and tireless historical cipher research.
• Viktor Wase: For the 2023 simulated annealing bounds establishing that Dorabella is mathematically non-monoalphabetic.
• Levente Zoltán Király & Gábor Tokai; Benedek Láng: For the breakthrough codebook, controlled syllabary, and codicological decipherment of the Rohonc Codex.