An In-depth Look at Highest Posterior Model Selection

We consider the properties of the highest posterior probability model in a linear regression setting+ Under a spike and slab hierarchy we find that although highest posterior model selection is total risk consistent, it possesses hidden undesirable properties+ One such property is a marked underfitting in finite samples, a phenomenon well noted for Bayesian information criterion ~BIC! related procedures but not often associated with highest posterior model selection+ Another concern is the substantial effect the prior has on model selection+ We employ a rescaling of the hierarchy and show that the resulting rescaled spike and slab models mitigate the effects of underfitting because of a perfect cancellation of a BIC-like penalty term+ Furthermore, by drawing upon an equivalence between the highest posterior model and the median model, we find that the effect of the prior is less influential on model selection, as long as the underlying true model is sparse+ Nonsparse settings are, however, problematic+ Using the posterior mean for variable selection instead of posterior inclusion probabilities avoids these issues+