Sparsity by Default: The Theory and Practice of ARD in Gaussian Process Regression for Variable Selection

Automatic relevance determination (ARD), the default tool for variable selection in Gaussian-process (GP) regression, ranks inputs by inverse lengthscales -- which measure how fast a function varies, not how much an input contributes to prediction -- and offers no calibrated rule for deciding which inputs to keep. The prediction-centred alternative, the derivative sensitivity $ν_j = \mathbb{E}[(\partial f/\partial x_j)^2]$, is available in closed form from a fitted GP, but turning it into a selection rule is harder than it looks: at a null input the estimator is a degenerate quadratic form, so Wald and Bernstein-von Mises cutoffs are anti-conservative, and the natural residual bootstrap is mis-scaled. We show that a studentized multiplier bootstrap of the GP derivative process repairs both, prove its validity through an invariance principle for quadratic forms, and obtain asymptotic family-wise and false-discovery-rate control across inputs. Over 100 replications the rule controls FDR wherever inputs are truly null, while uncalibrated derivative rankings breach the target by up to 2x and a Bernstein-von Mises cutoff by 2.2x; at matched FDR it loses no power; it holds under a Matérn kernel and input correlation up to 0.99; on real data with planted and authentic null inputs it admits 5-12x fewer spurious inputs; it costs 5-18% of the GP fit; and a block-averaged variant retains validity at cost linear in $n$.

Sparse Gaussian processes achieve $O(N)$ inference by replacing the kernel with an appropriate expansion in a fixed basis $\{φ_j\}$ on the input space. Given a compute budget $M \ll N$, practitioners conventionally truncate the basis to its first $M$ entries. Nothing in the formalism, however, prevents one from selecting only those $M$ basis functions that matter for the data at hand. This would avoid spending budget on basis functions where there is no signal, but it requires a criterion for ranking the candidates. We propose three such criteria derived from an information-theoretic view of the basis-function selection problem. Each criterion matches a different state of knowledge at selection time: a no-data state, a no-prior state, and an in-between state. We then study the performance of truncation versus selection strategies on six UCI regression benchmarks across three basis families: Hilbert-space Gaussian processes (HSGP), variational Fourier features (VFF), and variational inducing spherical harmonics (VISH). We observe that the no-data criterion is a safe default, matching or improving on truncation for HSGP, VFF and VISH, with substantial gains for VISH and improvements over a recently developed selection heuristic for that basis family. The data-aware no-prior and in-between criteria provide substantial gains over truncation specifically for HSGP, which is the most broadly used of the three families in practice.

High-dimensional Bayesian optimization (BO) often fits Gaussian process (GP) surrogates from far fewer observations than input dimensions. Modern Vanilla BO can perform well in this regime with dimension-aware priors, initialization, and acquisition optimization, but it typically retains automatic relevance determination (ARD), fitting one lengthscale per input coordinate. We study this modeling choice and propose Iso-BO, a controlled modification that replaces the ARD GP with an isotropic GP using one shared lengthscale while keeping the surrounding BO pipeline matched. For radial kernels, we show that the marginal log likelihood (MLL) depends on the inverse-squared ARD lengthscales only through weighted pairwise distances among the observed inputs. The current design can therefore leave some ARD directions exactly invisible or only weakly constrained by the MLL. Iso-BO removes coordinatewise reweighting and fits a single shared scale instead. Lengthscale-fitting and predictive-density diagnostics show that this finite-data effect appears in practice, including when the data-generating process is anisotropic. Across GP-prior, synthetic, and real-world benchmarks, Iso-BO often improves over matched modern Vanilla BO and remains competitive with the included high-dimensional BO baselines under the tested budgets. Stress tests also show the expected boundary wherein sufficiently strong, learnable anisotropy can favor the more flexible ARD model.