Run · Voynich Manuscript

T44 generation 2, rung R1 PASSES: 80 hop rounds + trigram polish and decode; key 73.7 %, coverage 0.489 (bar 0.483), permutation p 0.005

t44_gen2_R1.zip holds the code as it ran, the json, the best bigram state (t44_g2r1_control_best.npz), the polished trigram state (t44_g2r1_control_best3.npz), every restart's likelihood and the combined log. R1 is not inside the T42 posterior (K 50 has mass 0.007, lam 0 has 0.039), so no manuscript decode follows from this rung.

R1 passes the control gate (coverage 0.489 >= 0.483 and key 0.737 >= 0.5; permuted keys p 0.005), the first learned-boundary pass in the programme, by a margin of 0.006 in coverage. The search itself did not improve on generation 1 (the bigram optimum is the same -40,675, 160 nats short of the true key's basin): the pass comes from reading the same 74 %-right key with the trigram decoder. Rung R2 (four homophones per consonant) starts with the same effort. The key-accuracy half of the gate is doing the work: a key 11 % right reaches coverage 0.52 under this decoder.restarts (5,000, seeds 200000+): -40,772.8 (key 0.687); hopping 80 rounds x 1,024: -40,675.9 (key 0.737; stalled after round 55); tempering 20 rounds: -40,724.4 (key 0.687). Trigram polish of the 5 best states (30 iterations): trigram lls -39,848 / -39,831 / -39,868 / -39,850 / -39,838; the chosen state's key 0.737. Trigram decode: coverage 0.489 (permuted keys mean 0.339, max 0.432, p 0.005), character similarity 0.673, null words 0.142, held-out ll/glyph -1.8916. The same state decoded by the bigram Viterbi: coverage 0.413. 'ecereporisercusacundenticipunaciliqueiammalispirimaudatisimaeprigideseodemtratumgenuitercuspinumacie' for 'aberenoncontigitcumteporisarboresabundentibipunicaeficiqueiammalietpirilaudatisimaefrigidaseodemtrac'0

Result

Run	Measured	Result	Against	Decision	Date
Run	Best training log-likelihood per search (bigram), trigram likelihood after polish; held-out key accuracy by use, dictionary coverage (bar 0.7 x plaintext's = 0.483), character similarity, key-permutation p (200 permutations, trigram decoder)	restarts (5,000, seeds 200000+): -40,772.8 (key 0.687); hopping 80 rounds x 1,024: -40,675.9 (key 0.737; stalled after round 55); tempering 20 rounds: -40,724.4 (key 0.687). Trigram polish of the 5 best states (30 iterations): trigram lls -39,848 / -39,831 / -39,868 / -39,850 / -39,838; the chosen state's key 0.737. Trigram decode: coverage 0.489 (permuted keys mean 0.339, max 0.432, p 0.005), character similarity 0.673, null words 0.142, held-out ll/glyph -1.8916. The same state decoded by the bigram Viterbi: coverage 0.413. 'ecereporisercusacundenticipunaciliqueiammalispirimaudatisimaeprigideseodemtratumgenuitercuspinumacie' for 'aberenoncontigitcumteporisarboresabundentibipunicaeficiqueiammalietpirilaudatisimaefrigidaseodemtrac'	Generation 1 (RUN0DCMW01CAK37): -40,674.8, key 0.736, bigram-decoded coverage 0.440 · true key: trigram-decoded coverage 0.584, key 0.778 · session 12's best: key 0.691, coverage 0.407	R1 passes the control gate (coverage 0.489 >= 0.483 and key 0.737 >= 0.5; permuted keys p 0.005), the first learned-boundary pass in the programme, by a margin of 0.006 in coverage. The search itself did not improve on generation 1 (the bigram optimum is the same -40,675, 160 nats short of the true key's basin): the pass comes from reading the same 74 %-right key with the trigram decoder. Rung R2 (four homophones per consonant) starts with the same effort. The key-accuracy half of the gate is doing the work: a key 11 % right reaches coverage 0.52 under this decoder.

What it used and found

Lattice EM on CUDA with batched restarts, basin hopping and parallel tempering, run up a ladder of planted controls (T44)

Method

MTH

Herbal A and Herbal B paragraph text: training and held-out pages

Dataset

DAT

Latin genre texts

Dataset

DAT

Naibbe cipher tables and example plaintexts (greshko/naibbe-cipher, commit 719f2f4c)

Dataset

DAT

Token table

Dataset

DAT

Parameters

pw = 0.25, rung = R1, topk = 16, alpha = 0.05, signs = 871, trigram = full, 71 history classes, elements = 71, restarts = 5000, settings = {'K': 50, 'h_c': 1, 'h_v': 1, 'lam': 0, 'Ssyl': 0, 'abbrev': 0, 'p_copy': 0, 'p_stay': 0.9, 'window': 5, 'novowel': 0, 'p_break': 0.5, 'spacing': 'stream', 'simplify': 1, 'positional': 0}, hop_pairs = 3, pt_levels = 8, pt_rounds = 20, hop_rounds = 80, permutations = 200, em_iterations = 60, restart_seeds = 200000-204999, PYTHONHASHSEED = 0, hop_em_iterations = 30, trigram_candidates = 5, pt_chains_per_level = 128, hop_proposals_per_round = 1024, trigram_polish_iterations = 30

Cite it

Mysteries Department. (2026). T44 generation 2, rung R1 PASSES: 80 hop rounds + trigram polish and decode; key 73.7 %, coverage 0.489 (bar 0.483), permutation p 0.005 [Run RUN0DCNEZ6RMXGR]. https://mysteriesdept.com/r/RUN0DCNEZ6RMXGR

@misc{mysteriesdept_run0dcnez6rmxgr,
  title     = {T44 generation 2, rung R1 PASSES: 80 hop rounds + trigram polish and decode; key 73.7 %, coverage 0.489 (bar 0.483), permutation p 0.005},
  author    = {{Mysteries Department}},
  year      = {2026},
  note      = {Run, catalog key RUN0DCNEZ6RMXGR},
  url       = {https://mysteriesdept.com/r/RUN0DCNEZ6RMXGR}
}