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Just chiming in to say I’ve been using NONSENSEWORD => list of PHONES for this purpose for a while now and it’s been working well :) Here’s a concrete example for the benefit of anyone googling this discussion at some point in the future — if your utterance is word1 word2 word1, and your phonetic transcript is pron1 pron2 pron3, then you need a pronunciation dictionary which looks something like this:
word1_pron1 p r o n 1
word2_pron2 p r o n 2
word1_pron3 p r o n 3
In other words, NONSENSEWORD should be a unique identifier for the given word + pronunciation combination. It can be anything, but it can be helpful to make it human-readable, in which case concatenating the basic and phonetic transcript is a good choice imho.
Before running the aligner, you should also remember to convert the utterance from word1 word2 word1 to word1_pron1 word2_pron2 word1_pron3 — your utterances need to consist of words which can actually be found in the dictionary.
Best,
David