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DeepRV: Accelerating Spatiotemporal Inference with Pre-trained Neural Priors

arXiv stat.MLby Jhonathan Navott, Daniel Jenson, Seth Flaxman, Elizaveta SemenovaApril 1, 20261 min read0 views
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arXiv:2503.21473v3 Announce Type: replace Abstract: Gaussian Processes (GPs) provide a flexible and statistically principled foundation for modelling spatiotemporal phenomena, but their $O(N^3)$ scaling makes them intractable for large datasets. Approximate methods such as variational inference (VI), inducing-point (sparse) GPs, low-rank kernel approximations (e.g., Nystrom methods and random Fourier features), and approximations such as INLA improve scalability but typically trade off accuracy, calibration, or modelling flexibility. We introduce DeepRV, a neural-network surrogate that replaces GP prior sampling, while closely matching full GP accuracy at inference including hyperparameter estimates, and reducing computational complexity to $O(N^2)$, increasing scalability and inference sp

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Abstract:Gaussian Processes (GPs) provide a flexible and statistically principled foundation for modelling spatiotemporal phenomena, but their $O(N^3)$ scaling makes them intractable for large datasets. Approximate methods such as variational inference (VI), inducing-point (sparse) GPs, low-rank kernel approximations (e.g., Nystrom methods and random Fourier features), and approximations such as INLA improve scalability but typically trade off accuracy, calibration, or modelling flexibility. We introduce DeepRV, a neural-network surrogate that replaces GP prior sampling, while closely matching full GP accuracy at inference including hyperparameter estimates, and reducing computational complexity to $O(N^2)$, increasing scalability and inference speed. DeepRV serves as a drop-in replacement for GP prior realisations in e.g. MCMC-based probabilistic programming pipelines, preserving full model flexibility. Across simulated benchmarks, non-separable spatiotemporal GPs, and a real-world application to education deprivation in London (n = 4,994 locations), DeepRV achieves the highest fidelity to exact GPs while substantially accelerating inference. Code is provided in the dl4bi Python package, with all experiments run on a single consumer-grade GPU to ensure accessibility for practitioners.

Comments: Code to reproduce all experiments is available in the dl4bi codebase: this https URL

Subjects:

Machine Learning (stat.ML); Machine Learning (cs.LG)

Cite as: arXiv:2503.21473 [stat.ML]

(or arXiv:2503.21473v3 [stat.ML] for this version)

https://doi.org/10.48550/arXiv.2503.21473

arXiv-issued DOI via DataCite

Submission history

From: Jhonathan Navott [view email] [v1] Thu, 27 Mar 2025 13:04:41 UTC (47,469 KB) [v2] Fri, 17 Oct 2025 16:20:58 UTC (11,913 KB) [v3] Tue, 31 Mar 2026 11:47:10 UTC (4,466 KB)

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