Run · Voynich Manuscript

T44 generation 1, rung R2 (four homophones per consonant): key 67 %, trigram-decoded coverage 0.468 under the bar of 0.487; hopping stalls 450 nats short of the true key

run_t44.py 6fcfbcf5 adds the MOVES option (default 'swap', which is what ran here) to the version that ran R1's generation 2. The archive holds the code as it ran, both best states, every restart's likelihood and the combined log.

Fails the control gate on coverage (0.468 < 0.487; key 0.673 passes its half). Homophones widen the search gap: the best state is 450 nats short of the true key's basin against 160 on R1, and the 3-pair row swap stops finding improvements after 50 rounds. Generation 2 of R2 drops tempering (worse than greedy hopping in all three runs so far), runs 150 hop rounds with a mixed move set (row swaps of 1-4 pairs, sign-column swaps between two elements, softened restarts) and polishes 8 states for 60 trigram iterations.1,205 signs. Restarts (5,000): -48,200.0 (key 0.624; median -48,753); hopping 80 rounds: -48,041.3 (key 0.656; stalled from round 50); tempering 20 rounds: -48,098.1 (key 0.608). Trigram polish of 5 states: -47,850.1 / -47,850.7 / -47,869.5 / -47,927.2 / -47,881.3; chosen state's key 0.673. Trigram decode: coverage 0.468 (permuted keys mean 0.320, max 0.409, p 0.005), character similarity 0.537, null words 0.175, held-out ll/glyph -2.021; bigram decode of the bigram-best state 0.392. 'namiceraeomneatraepictasagenimenumarelagonfueraperarinunto...' for 'nevitibusquidemxivceteraeomnesextrapraedictasetenimenumerarelongumestfoliadeperduntobservatumque...'0

Result

Run	Measured	Result	Against	Decision	Date
Run	Best training log-likelihood per search; trigram likelihood after polish; held-out key accuracy by use, dictionary coverage (bar 0.7 x plaintext's = 0.487), character similarity, key-permutation p (200 permutations, trigram decoder)	1,205 signs. Restarts (5,000): -48,200.0 (key 0.624; median -48,753); hopping 80 rounds: -48,041.3 (key 0.656; stalled from round 50); tempering 20 rounds: -48,098.1 (key 0.608). Trigram polish of 5 states: -47,850.1 / -47,850.7 / -47,869.5 / -47,927.2 / -47,881.3; chosen state's key 0.673. Trigram decode: coverage 0.468 (permuted keys mean 0.320, max 0.409, p 0.005), character similarity 0.537, null words 0.175, held-out ll/glyph -2.021; bigram decode of the bigram-best state 0.392. 'namiceraeomneatraepictasagenimenumarelagonfueraperarinunto...' for 'nevitibusquidemxivceteraeomnesextrapraedictasetenimenumerarelongumestfoliadeperduntobservatumque...'	True key on R2: bigram EM from truth -47,587 (key 0.845), trigram-decoded coverage 0.581 · R1 generation 2 passed at key 0.737, coverage 0.489	Fails the control gate on coverage (0.468 < 0.487; key 0.673 passes its half). Homophones widen the search gap: the best state is 450 nats short of the true key's basin against 160 on R1, and the 3-pair row swap stops finding improvements after 50 rounds. Generation 2 of R2 drops tempering (worse than greedy hopping in all three runs so far), runs 150 hop rounds with a mixed move set (row swaps of 1-4 pairs, sign-column swaps between two elements, softened restarts) and polishes 8 states for 60 trigram iterations.

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 = R2, topk = 16, alpha = 0.05, moves = swap, trigram = full, 71 history classes, elements = 71, restarts = 5000, settings = {'K': 50, 'h_c': 4, '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 = 300000-304999, 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 1, rung R2 (four homophones per consonant): key 67 %, trigram-decoded coverage 0.468 under the bar of 0.487; hopping stalls 450 nats short of the true key [Run RUN0DCP774CN9D7]. https://mysteriesdept.com/r/RUN0DCP774CN9D7

@misc{mysteriesdept_run0dcp774cn9d7,
  title     = {T44 generation 1, rung R2 (four homophones per consonant): key 67 %, trigram-decoded coverage 0.468 under the bar of 0.487; hopping stalls 450 nats short of the true key},
  author    = {{Mysteries Department}},
  year      = {2026},
  note      = {Run, catalog key RUN0DCP774CN9D7},
  url       = {https://mysteriesdept.com/r/RUN0DCP774CN9D7}
}