The techniques of Bayesian inference have been applied with great success to many problems in neural computing including evaluation of regression functions, determination of error bars on predictions, and the treatment of hyper-parameters. However, the problem of model comparison is a much more challenging one for which current techniques have significant limitations. In this paper we show how an extended form of Markov chain Monte Carlo, called chaining, is able to provide effective estimates of the relative probabilities of different models. We present results from the robot arm problem and compare them with the corresponding results obtained using the standard Gaussian approximation framework.