HiGP: A high-performance Python package for Gaussian Process

Abstract

Gaussian Processes (GPs) are flexible, nonparametric Bayesian models widely used for regression and classification because of their ability to capture complex data patterns and quantify predictive uncertainty. However, the O(n^3) computational cost of kernel matrix operations poses a major obstacle to applying GPs at scale. HiGP is a high-performance Python package designed to overcome these scalability limitations through advanced numerical linear algebra and hierarchical kernel representations. It integrates H^2 matrices to achieve near-linear complexity in both storage and computation for spatial datasets, supports on-the-fly kernel evaluation to avoid explicit storage in large-scale problems, and incorporates a robust Adaptive Factorized Nyström (AFN) preconditioner that accelerates convergence of iterative solvers across a broad range of kernel spectra. These computational kernels are implemented in C++ for maximum performance and exposed through Python interfaces, enabling seamless integration with modern machine learning workflows. HiGP also includes analytically derived gradient computations for efficient hyperparameter optimization, avoiding the inefficiencies of automatic differentiation in iterative solvers. By serving as a reusable numerical engine, HiGP complements existing GP frameworks such as GPJax, KeOps, and GaussianProcesses.jl, providing a reliable and scalable computational backbone for large-scale Gaussian Process regression and classification.