Positional Mimic Cipher (PM-Cipher)

[Jorge_Stolfi]

Vietnamese without special chars

In case you haven't noticed, those "special chars" are modifiers for the letters.  It makes no sense to exclude them.

I’ve been comparing full bigram distributions directly. For each text I build the 2D bigram probability matrix (word-reset, normalized), flatten it, and compute the Jensen–Shannon divergence (JSD) against the Voynich matrix.

First, this exercise is meaningless if the two texts use digraphs and trigraphs to encode single phonemes, or discard some phonetic information,  in different ways -  as is the case for all languages tested, including Voynichese.  

Second, IIUC, the JSD assumes that the two distributions P,Q are defined on the same set of elements, and compares the probabilities assigned by P and Q on each element.  Thus if P is the letter pair distribution of a text, and Q is the letter pair distribution of the same text encoded with a Caesar cipher, the JST should come out huge.  Do you take this into account, and try to vary the mapping between letters of the two languages?