Maybe, I'm not thinking about the same 1D PPC graphs as you are, but I actually think they do have at least a bit of value. For me that value is actually as a substitute for computing the posterior predictive p-values. Rarely do I actually care what the precise value of one of the p-values is, so instead of computing them I'll just make a quick plot (e.g. T(y) as a vertical bar on a histogram of T(yrep)) and eyeball it. So I guess what I'm saying is that the 1D graphs and p-values aren't particularly useful, but if I'm going to pick one I'd prefer the graph.
The word "predictions" is important here.
> I want to say that
>
> 1. models need to be calibrated in the posterior interval coverage
> sense, and
I would write "posterior predictive" instead of just "posterior",
because most of the time we can check the calibration only with
respect to observations.
> 2. given two calibrated models, the one with narrower intervals
> makes better predictions.
>
> Is there a name for (2) other than "precision" (which is overused)?
Sharpness. See "Probabilistic forecasts, calibration and sharpness"
https://www.stat.washington.edu/raftery/Research/PDF/Gneiting2007jrssb.pdf
> I didn't see a direct discussion of (2) in BDA, either.
We refer to this paper, but don't mention the term sharpness. Maybe in
the next edition?
> I think (2) is closely related to
>
> 3. given two models, the one with higher posterior density for
> new data is better.
>
> Usually because to get higher density for the new data, you also
> get narrower intervals.
Again it would better to have "higher posterior *predictive* density"
instead of just "higher posterior density". I think it's better to be
explicit here.
Yes, you need sharpness, but you need to be also somewhat calibrated
to get high density for new data.
In baseball example we have separate independent test data, but often
we don't have that. Chapter 6 in BDA3 assumes mostly that we don't
have independent test data.
Short story of Posterior predictive checking vs. Cross-validation
- posterior predictive checking is good for joint predictive distribution checks, but there is no calibration in test statistics
- in cross-validation checking the test statistics are calibrated (given usual assumptions), but it can be used only for marginal predictive distributions (univariate or m-dimensional where m is the block size)
Longer explanation
Posterior predictive checking (as defined in BDA) compares posterior
predictive distribution conditioned on data to the same data and this
causes the problem that the posterior predictive p-values are not
calibrated (overfitting, double use of data, etc). This is seen
especially when the chosen test statistic is related to one of the
parameters in the model. For example, in the baseball example, the
mean test statistic is bad since the model has a parameter related to
that. In BDA light speed example, variance is also bad since the model
has variance term, too. Posterior predictive checking is good for
examining properties of joint predictive distribution, such as the
minimum or maximum observed value in the baseball and light speed
example, or number state changes in hot hand examples. In weather
prediction, we might be interested in knowing the probability that the
temperature drops below zero in any part of a specific road, and thus
we need again the joint predictive distribution. Another good
example, is population dynamic models, model generated population
sizes in time are plotted and the resulting curves are compared to
observed curves and they should have similar look. It is not so easy
to make test statistic for summarizing with a single value features of
connected prey-predator population dynamics.
Predictive checking with new data avoids the double use of data, but
before we have that data we need to do something else and
cross-validation is useful option for that (most information criteria
are close to some version of leave-one-out cross-validation, but loo
is more robust http://arxiv.org/abs/1507.04544,
http://arxiv.org/abs/1412.7461). In cross-validation the double use
of data is avoided and test statistic can be calibrated. In
leave-one-out cross-validation we examine (usually) univariate
posterior predictive distributions, and thus we can't examine
properties of the joint predictive distribution. To examine
specifically whether the model predictions are calibrated, the usual
test is to look at the leave-one-out cross-validation predictive
cumulative density function values, which are uniformly distributed if
the model is calibrated (BDA3, Ch 6, Section "Marginal predictive
checks"). If the model is calibrated based on cross-validation
predictive distributed tail area probabilities, then you could look at
the sharpness of the cross-validation predictive
distributions. Looking at the cross-validation predictive densities
directly combines the calibration and sharpness and "given two models,
the one with higher cross-validation predictive density is
better". This what the 'loo' package is doing. Furthermore, in
leave-one-block-out we can examine joint posterior predictive for
blocks, so that we could look for example joint predictions for
several patients in one hospital.
One problem in reporting log predictive densities is that people tend
to have difficulties on interpreting the values and differences
between the values (leading to attaching magical properties to
information criteria and model complexity). If possible, it is good to
report the predictive performance also using utility (cost) function
which is easier to interpret by the target audience (e.g. medical
doctor). In epidemiology these could be, e.g., classification accuracy
or area under curve (AUC). In the baseball example, when estimating the accuracy of the batting rate estimates, you could also report RMSE or MAE with the independent test data used as the ground truth. You could also consider betting scenarios such as
- guess who has the highest batting rate at the end of the season
- which three players (in any order) have the highest batting rates
and calculate which of the models would have given the best chance of
winning. (or you could add also loo, to show how you can estimate the
predictive performance even before you see the end of the season).
Aki
alp