I used Jahmm to train an HMM using my input sequence. After the training is complete, I have learnt HMM model and my initial input sequence. How do I generate the output states for the input sequence using the learnt HMM model?
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I assume you are looking for the most likely state sequence for a given input sequence.
This can be retrieved using
ViterbiCalculator.stateSequence()in the jahmm package, see the Javadoc.