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Collaborating Authors

 Navott, Jhonathan


DeepRV: pre-trained spatial priors for accelerated disease mapping

arXiv.org Machine Learning

Recently introduced prior-encoding deep generative models (e.g., PriorVAE, $\pi$VAE, and PriorCVAE) have emerged as powerful tools for scalable Bayesian inference by emulating complex stochastic processes like Gaussian processes (GPs). However, these methods remain largely a proof-of-concept and inaccessible to practitioners. We propose DeepRV, a lightweight, decoder-only approach that accelerates training, and enhances real-world applicability in comparison to current VAE-based prior encoding approaches. Leveraging probabilistic programming frameworks (e.g., NumPyro) for inference, DeepRV achieves significant speedups while also improving the quality of parameter inference, closely matching full MCMC sampling. We showcase its effectiveness in process emulation and spatial analysis of the UK using simulated data, gender-wise cancer mortality rates for individuals under 50, and HIV prevalence in Zimbabwe. To bridge the gap between theory and practice, we provide a user-friendly API, enabling scalable and efficient Bayesian inference.


Transformer Neural Processes -- Kernel Regression

arXiv.org Machine Learning

Stochastic processes model various natural phenomena from disease transmission to stock prices, but simulating and quantifying their uncertainty can be computationally challenging. For example, modeling a Gaussian Process with standard statistical methods incurs an $\mathcal{O}(n^3)$ penalty, and even using state-of-the-art Neural Processes (NPs) incurs an $\mathcal{O}(n^2)$ penalty due to the attention mechanism. We introduce the Transformer Neural Process - Kernel Regression (TNP-KR), a new architecture that incorporates a novel transformer block we call a Kernel Regression Block (KRBlock), which reduces the computational complexity of attention in transformer-based Neural Processes (TNPs) from $\mathcal{O}((n_C+n_T)^2)$ to $O(n_C^2+n_Cn_T)$ by eliminating masked computations, where $n_C$ is the number of context, and $n_T$ is the number of test points, respectively, and a fast attention variant that further reduces all attention calculations to $\mathcal{O}(n_C)$ in space and time complexity. In benchmarks spanning such tasks as meta-regression, Bayesian optimization, and image completion, we demonstrate that the full variant matches the performance of state-of-the-art methods while training faster and scaling two orders of magnitude higher in number of test points, and the fast variant nearly matches that performance while scaling to millions of both test and context points on consumer hardware.