title: hmm transition matrix estimation
body: <p>In the context of a quantum physics experiment, I am interested in estimating some parameters of the hidden Markov model describing my experiments. I am aware of the Baum-Welch algorithm for estimating all parameters of a hmm. I am, however, only interested in estimating the transition matrix as I have additional data for estimating the emission matrix. 
  What is the best way to proceed? Can I use the Baum-Welch algorithm for updating only the transition matrix while keeping the emission matrix fixed or is there a better approach?</p>
  
  <p>[the hmm I am interested one, has only two hidden states and two (or four) output states.]</p>