Addressing Batch Allocation
I am at least tangentially familiar with batch Bayesian optimisation, so I will try to offer an intuitive explanation. If this explanation doesn't help, you can consider posting it as part of another (!) question with an explanation of what is unclear and I'm sure someone will be able to help.
When performing batch Bayesian optimisation, we aim to select a series of $B$ points, $x_1, \dots, x_B$, which jointly maximise some measure of expected utility (the "acquisition function"), with $B$ being the batch size.
In order to pose this problem properly, the desired measure of utility needs some notion of "repulsion" between sample points. This tends to be accomplished in one of two ways:
- By explicitly including some kind of "virtual" observation in the GP predictive distribution. Since the acquisition function is a function of the GP predictive distribution, this naturally encodes some notion of repulsion.
- By imposing some kind of penalty function designed to imitate the effect of the above. Examples include the local penalisation method in the paper you linked (Gonzalez et. al.), and rather more complex methods such as repulsion simulated using determinantal point processes (Kathuria et. al.).
Now, let's say we were going to use a sequential strategy to choose a batch of points using method 1 (that is, introducing virtual observations to induce repulsion between our batch points). Assuming we have a GP model, the procedure looks something like this:
- Maximise the acquisition function to find the point of highest utility. Let's call this $x'$.
- Add $x'$ to our batch of points.
- Update our GP model with a virtual observation for $y' = f(x')$, using the predictive distribution at $x'$.
- (Temporarily) augment the GP with new data: $x'$ and $y'$. By temporarily I mean that this is not "real" data and can be forgotten after the batch points are selected.
- Repeat 1 - 4 until $B$ points have been selected.
Now, item 3 presents a problem: $y'$, given our model, is uncertain, and subsequent steps clearly depend on the value we choose. One strategy is to repeat all subsequent steps a number of times to "marginalise" the uncertainty in $y'$. This is where I believe your questions regarding marginalisation come from.
This is unfortunately very expensive (due to repeat optimisation of the acquisition function with different virtual observations), which is why methods which model repulsion (rather than the posterior itself) are more common (at least as far as my understanding goes).
In fact, for even moderately large batch sizes, this method is intractably expensive -- even when exploiting quadrature to perform the marginalisation -- since the number of required optimisations grows exponentially with the batch size. A way of getting around this is to approach the problem in a rather more dynamic than sequential way, which is explored by Lam et. al. and Gonzalez et. al..