The subject matter of this specification can be implemented in, among other things, a computer-implemented method including receiving audio data and a transcript of the audio data. The method further includes generating a language model including a factor automaton that includes automaton states and arcs, each of the automaton arcs corresponding to a language element from the transcript. The method further includes receiving language elements recognized from the received audio data and times at which each of the recognized language elements occur in the audio data. The method further includes comparing the recognized language elements to one or more of the language elements from the factor automaton to identify times at which the one or more of the language elements from the transcript occur in the audio data. The method further includes aligning a portion of the transcript with a portion of the audio data using the identified times.