Run · Voynich Manuscript

T44 generation 2, rung R2: mixed hop moves gain 300 nats of likelihood (-47,740) and key 69 %, but trigram-decoded coverage stays at 0.466 (bar 0.487)

The archive holds the code as it ran, the json, both best states, every restart's likelihood and the combined log. The restart-stage key of 0.403 (against 0.62-0.69 in the other runs) shows how little the best-of-5,000 bigram restart constrains the key on this rung.

Fails the control gate on coverage (0.466 < 0.487; key 0.694 passes its half). The mixed move set is a real search improvement (301 nats, two thirds of the remaining gap to the true key's basin, and the key rose from 0.673 to 0.694), yet coverage did not move: with four homophones per consonant the decoded text already reads in stretches ('etenimenumerarelon[g]um', 'observatum') while the remaining wrong rows break enough words to hold coverage under the bar. Generation 3 resumes from this best state, adds fresh restarts, 150 more mixed-move rounds, a longer trigram polish and 20 rounds of hopping under the trigram likelihood itself; it is the third and last generation for R2 under the stopping rule.restarts (5,000, seeds 400000+): -48,119.1 (key 0.403); hopping with the mixed move set, 150 rounds x 1,024: -47,740.4 (key 0.694; still moving at round 149: -47,866 at 70, -47,772 at 80, -47,752 at 120). Trigram polish of 8 states (60 iterations): best -47,429.4 (from the bigram best; the others -47,542 to -47,944). Trigram decode: coverage 0.466 (permuted keys mean 0.326, max 0.417, p 0.005), character similarity 0.591, null words 0.173, held-out ll/glyph -2.0159; bigram decode 0.388. 'nateraeomneaedinfecetenimenumerarelonpumatroineaerinuntobseretum...' for 'nevitibusquidemxivceteraeomnesextrapraedictasetenimenumerarelongumestfoliadeperduntobservatumque...'0

Result

Run	Measured	Result	Against	Decision	Date
Run	Best training log-likelihood (bigram) and trigram likelihood after polish; held-out key accuracy by use, dictionary coverage (bar 0.487), character similarity, key-permutation p (200 permutations, trigram decoder)	restarts (5,000, seeds 400000+): -48,119.1 (key 0.403); hopping with the mixed move set, 150 rounds x 1,024: -47,740.4 (key 0.694; still moving at round 149: -47,866 at 70, -47,772 at 80, -47,752 at 120). Trigram polish of 8 states (60 iterations): best -47,429.4 (from the bigram best; the others -47,542 to -47,944). Trigram decode: coverage 0.466 (permuted keys mean 0.326, max 0.417, p 0.005), character similarity 0.591, null words 0.173, held-out ll/glyph -2.0159; bigram decode 0.388. 'nateraeomneaedinfecetenimenumerarelonpumatroineaerinuntobseretum...' for 'nevitibusquidemxivceteraeomnesextrapraedictasetenimenumerarelongumestfoliadeperduntobservatumque...'	Generation 1 of R2 (RUN0DCP774CN9D7): -48,041.3, key 0.673, coverage 0.468 · true key: -47,587 (bigram), key 0.845, trigram-decoded coverage 0.581	Fails the control gate on coverage (0.466 < 0.487; key 0.694 passes its half). The mixed move set is a real search improvement (301 nats, two thirds of the remaining gap to the true key's basin, and the key rose from 0.673 to 0.694), yet coverage did not move: with four homophones per consonant the decoded text already reads in stretches ('etenimenumerarelon[g]um', 'observatum') while the remaining wrong rows break enough words to hold coverage under the bar. Generation 3 resumes from this best state, adds fresh restarts, 150 more mixed-move rounds, a longer trigram polish and 20 rounds of hopping under the trigram likelihood itself; it is the third and last generation for R2 under the stopping rule.

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 = mix (row swaps of 1-4 pairs, sign-column swaps of 1-8 signs, softened restarts), signs = 1205, 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}, pt_rounds = 0, hop_rounds = 150, permutations = 200, em_iterations = 60, restart_seeds = 400000-404999, PYTHONHASHSEED = 0, hop_em_iterations = 30, trigram_candidates = 8, hop_proposals_per_round = 1024, trigram_polish_iterations = 60

Cite it

Mysteries Department. (2026). T44 generation 2, rung R2: mixed hop moves gain 300 nats of likelihood (-47,740) and key 69 %, but trigram-decoded coverage stays at 0.466 (bar 0.487) [Run RUN0DCQ48MV18VH]. https://mysteriesdept.com/r/RUN0DCQ48MV18VH

@misc{mysteriesdept_run0dcq48mv18vh,
  title     = {T44 generation 2, rung R2: mixed hop moves gain 300 nats of likelihood (-47,740) and key 69 %, but trigram-decoded coverage stays at 0.466 (bar 0.487)},
  author    = {{Mysteries Department}},
  year      = {2026},
  note      = {Run, catalog key RUN0DCQ48MV18VH},
  url       = {https://mysteriesdept.com/r/RUN0DCQ48MV18VH}
}