Maybe try generating a TimeIndex with the HMM? And then using the TimeIndex to run a MIDIFileWithTimeIndex on your selected MIDI file (since it has all the continous controllers in it). In other words, the MIDIFileWithTimeIndex is generating the sound (the HMM is generating a timeIndex for that MIDIFileWithTimeIndex). There are some examples of this in the Kyma Sound LIbrary and in the Gallery that's generated from a MIDI file in the Sound Browser.
Let us know how it goes!