Run · Voynich Manuscript

T44 generation 3, rung R2 abandoned: resumed search reaches -47,651 (64 nats from the true key) and trigram hopping -47,157, key 70 %, coverage 0.471 still under the bar of 0.487

run_t44.py bbce360d adds the trigram-objective hop (TRI_HOPS) to the version of generation 2. The archive holds the code as it ran, the json, the bigram best state, the trigram best state after hopping (t44_g3r2_control_best3.npz), every fresh restart's likelihood and the combined log.

Fails the control gate for the third generation (0.471 < 0.487; key 0.698 passes its half), each generation having improved the search (bigram -48,041 -> -47,740 -> -47,651; key 0.673 -> 0.694 -> 0.698), so rung R2 is abandoned and the programme stops under the brief's rule. The bigram likelihood is now within 64 nats of the true key's basin, yet 30 % of the sign uses still map to the wrong element and coverage has moved only 0.005 over three generations: closing the last nats of likelihood does not buy coverage, which says the remaining errors are between elements the bigram and trigram Latin models hardly separate (homophones of similar consonants). R3-R5 were not started and the manuscript was not decoded.resumed from generation 2's best (-47,740.4) plus 5,000 fresh restarts (best -48,176.6, seeds 500000+); 150 mixed-move hop rounds: -47,651.2 (key 0.695; -47,685 at round 70, -47,663 at 100, flat from 121). Trigram polish of 8 states: best -47,338.5 (keys 0.575-0.715; the state with key 0.715 had trigram ll -47,726 and was not chosen). Trigram-objective hopping, 20 rounds x 8 proposals x 8 iterations: 12 accepted, -47,336.8 -> -47,156.6, key 0.694 -> 0.698. Decode: coverage 0.471 (permuted keys mean 0.327, max 0.419, p 0.005), character similarity 0.601, null words 0.155, held-out ll/glyph -2.0039; bigram decode 0.389. 'nateraeomnosquisuntraedinfecetenimenumerarelonpumatetineaerinuntobseretum...' for 'nevitibusquidemxivceteraeomnesextrapraedictasetenimenumerarelongumestfoliadeperduntobservatumque...'0

Result

Run	Measured	Result	Against	Decision	Date
Run	Best training log-likelihood (bigram), trigram likelihood after polish and trigram-objective hopping; held-out key accuracy by use, dictionary coverage (bar 0.487), character similarity, key-permutation p (200 permutations, trigram decoder)	resumed from generation 2's best (-47,740.4) plus 5,000 fresh restarts (best -48,176.6, seeds 500000+); 150 mixed-move hop rounds: -47,651.2 (key 0.695; -47,685 at round 70, -47,663 at 100, flat from 121). Trigram polish of 8 states: best -47,338.5 (keys 0.575-0.715; the state with key 0.715 had trigram ll -47,726 and was not chosen). Trigram-objective hopping, 20 rounds x 8 proposals x 8 iterations: 12 accepted, -47,336.8 -> -47,156.6, key 0.694 -> 0.698. Decode: coverage 0.471 (permuted keys mean 0.327, max 0.419, p 0.005), character similarity 0.601, null words 0.155, held-out ll/glyph -2.0039; bigram decode 0.389. 'nateraeomnosquisuntraedinfecetenimenumerarelonpumatetineaerinuntobseretum...' for 'nevitibusquidemxivceteraeomnesextrapraedictasetenimenumerarelongumestfoliadeperduntobservatumque...'	Generations 1 and 2 of R2 (RUN0DCP774CN9D7, RUN0DCQ48MV18VH): coverage 0.468 and 0.466, key 0.673 and 0.694, bigram -48,041 and -47,740 · true key: bigram -47,587, key 0.845, trigram-decoded coverage 0.581	Fails the control gate for the third generation (0.471 < 0.487; key 0.698 passes its half), each generation having improved the search (bigram -48,041 -> -47,740 -> -47,651; key 0.673 -> 0.694 -> 0.698), so rung R2 is abandoned and the programme stops under the brief's rule. The bigram likelihood is now within 64 nats of the true key's basin, yet 30 % of the sign uses still map to the wrong element and coverage has moved only 0.005 over three generations: closing the last nats of likelihood does not buy coverage, which says the remaining errors are between elements the bigram and trigram Latin models hardly separate (homophones of similar consonants). R3-R5 were not started and the manuscript was not decoded.

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, signs = 1205, resume = t44_g2r2_control_best.npz, 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_rounds = 150, permutations = 200, em_iterations = 60, restart_seeds = 500000-504999, PYTHONHASHSEED = 0, hop_em_iterations = 30, trigram_candidates = 8, trigram_hop_rounds = 20, trigram_hop_proposals = 8, hop_proposals_per_round = 1024, trigram_hop_em_iterations = 8, trigram_polish_iterations = 60

Cite it

Mysteries Department. (2026). T44 generation 3, rung R2 abandoned: resumed search reaches -47,651 (64 nats from the true key) and trigram hopping -47,157, key 70 %, coverage 0.471 still under the bar of 0.487 [Run RUN0DCR391F3RA3]. https://mysteriesdept.com/r/RUN0DCR391F3RA3

@misc{mysteriesdept_run0dcr391f3ra3,
  title     = {T44 generation 3, rung R2 abandoned: resumed search reaches -47,651 (64 nats from the true key) and trigram hopping -47,157, key 70 %, coverage 0.471 still under the bar of 0.487},
  author    = {{Mysteries Department}},
  year      = {2026},
  note      = {Run, catalog key RUN0DCR391F3RA3},
  url       = {https://mysteriesdept.com/r/RUN0DCR391F3RA3}
}