running MCMC for too long…
Here is an excerpt from an email I just received from a young astronomer with whom I have had many email exchanges about the nature and implementation of MCMC algorithms, not making my point apparently:
The acceptance ratio turn to be good if I used (imposed by me) smaller numbers of iterations. What I think I am doing wrong is the convergence criteria. I am not stopping when I should stop.
To which I replied he should come (or Skype) and talk with me as I cannot get into enough details to point out his analysis is wrong… It may be the case that the MCMC algorithm finds a first mode, explores its neighbourhood (hence a good acceptance rate and green signals for convergence), then wanders away, attracted by other modes. It may also be the case the code has mistakes. Anyway, you cannot stop a (basic) MCMC algorithm too late or let it run for too long! (Disclaimer: the picture of an observatory seen from across Brunel’s suspension bridge in Bristol is unrelated to the young astronomer!)