I will add Ion Dissonance, War From A Harlots Mouth, Burnt By The Sun, Architects, Johnny Truant, The Arusha Accord, Burst and The Ocean to these, not prog in the standard sense of the word, but these are all math-ish metalcore bands that play with demented time-signatures and unusual sounds.
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Dead Letter Circus is quite similiar to this so I hear (never heard Karnivool but DLC is really dope), nice proggy/atmospheric alt rock, totally recommend it.