MarginalLogDensities.jl

This package implements tools for integrating out (marginalizing) parameters from log-probability functions, such as likelihoods and posteriors of statistical models. This approach is useful for fitting models that incorporate random effects or latent variables that are important for structuring the model, but whose exact values may not be of interest in and of themselves. In the language of regression, these are known as "random effects," and in other contexts, they may be called "nuisance parameters." Whatever they are called, we hope that our log-density function can be optimized faster and/or more reliably if we focus on the parameters we are actually interested in, averaging the log-density over all possible values of the ones we are not.

A basic example is shown below. We start out by writing a function for our target log- density. This function must have the signature f(u, data), where u is a numeric vector of parameters and data contains any data, or fixed parameters, needed by the function. The data argument can be anything you'd like, such as a Vector, NamedTuple, DataFrame, or some other struct. (If your function does not depend on any external data, just ignore that argument in the function body)

⚠️ Note that the convention for this package is to write the function as a positive log-density.

using MarginalLogDensities, Distributions, LinearAlgebra

N = 3
σ = 1.5
dist = MvNormal(σ^2 * I(3))
data = (N=N, dist=dist)

function logdensity(u, data)
   return logpdf(data.dist, u) 
end

We then set up a marginalized version of this function. First, we set an initial value for our parameter vector u, as well as a set of indices iw indicating the subset of u that we want to integrate out.

u = [1.1, -0.3, 0.1] # arbitrary initial values
iw = [1, 3]

We create the marginalized version of the function by calling the MarginalLogDensity constructor with the original function logdensity, the full parameter vector u, the indices of the marginalized values iw, and the data. (If your function does not depend on the data argument, it can be omitted here.)

marginal_logdensity = MarginalLogDensity(logdensity, u, iw, data)

Here, we are saying that we want to calculate logdensity as a function of u[2] only, while integrating over all possible values of u[1] and u[3]. In the laguage of mathematics, if we write u -> logdensity(u, data) as $f(u)$, then the marginalized function v -> marginal_logdensity(v, data) is calculating

$$ f_m(u_2) = \int \int f(u) ; du_1 du_2. $$

By default, this package uses Laplace's method to approximate this integral. The Laplace approximation is fast in high dimensions, and works well for log-densities that are approximately Gaussian. The marginalization can also be done via numerical integration, a.k.a. cubature, which may be more accurate but will not scale well for higher dimensional problems. You can choose which marginalizer to use by passing the appropriate AbstractMarginalizer to MarginalLogDensity:

MarginalLogDensity(logdensity, u, iw, data, Cubature())
MarginalLogDensity(logdensity, u, iw, data, LaplaceApprox())

Both Cubature() and LaplaceApprox() can be specified with various options; refer to their docstrings for details.

After defining marginal_logdensity, you can call it just like the original function, with the difference that you only need to supply v, the subset of parameters you're interested in, rather than the entire set u. You also can re-run the same MarginalLogDensity with different data if you want (though if you're depending on the sparsity of your changing the data causes the sparsity).

initial_v = [1.0] # another arbitrary starting value
length(initial_v) == N - length(iw) # true
marginal_logdensity(initial_v, data)
# -1.5466258635350596

Compare this value to the analytic marginal density, i.e. the log-probability of $N(0, 1.5)$ at 1.0:

logpdf(Normal(0, 1.5), 1.0)
# -1.5466258635350594

The point of doing all this was to find an optimal set of parameters v for your data. This package defines a method for Optim.optimize that works directly with a MarginalLogDensity object, making optimization easy. Just pass it your marginalized function, a vector of starting values for v, and your data (which can be omitted if your function doesn't use it).

using Optim
fit = optimize(marginal_logdensity, initial_v, data)

Options for optimize can be passed as subsequent arguments; refer to the Optim.jl docs for details. One of particular interest is the choice of optimizer: the default is Nelder-Mead, but you can also use gradient-based and second-order methods:

optimize(marginal_logdensity, initial_v, data, LBFGS())
optimize(marginal_logdensity, initial_v, data, Newton())

(Note that these outer optimizations only work with autodiff=:finite for now.)

A more realistic application to a mixed-effects regression can be found in this example script.

ElOceanografo/MarginalLogDensities.jl

MarginalLogDensities.jl