Tutorial: VAE as an inference paradigm for neuroimaging

In this tutorial, we explore Variational Autoencoders (VAEs), an essential framework for unsupervised learning, particularly suited for high-dimensional datasets such as neuroimaging. By integrating deep learning with Bayesian inference, VAEs enable the generation of interpretable latent representations. This tutorial outlines the theoretical foundations of VAEs, addresses practical challenges such as convergence issues and over-fitting, and discusses strategies like the reparameterization trick and hyperparameter optimization. We also highlight key applications of VAEs in neuroimaging, demonstrating their potential to uncover meaningful patterns, including those associated with neurodegenerative processes, and their broader implications for analyzing complex brain data.

A Review of Latent Representation Models in Neuroimaging

Neuroimaging data, particularly from techniques like MRI or PET, offer rich but complex information about brain structure and activity. To manage this complexity, latent representation models - such as Autoencoders, Generative Adversarial Networks (GANs), and Latent Diffusion Models (LDMs) - are increasingly applied. These models are designed to reduce high-dimensional neuroimaging data to lower-dimensional latent spaces, where key patterns and variations related to brain function can be identified. By modeling these latent spaces, researchers hope to gain insights into the biology and function of the brain, including how its structure changes with age or disease, or how it encodes sensory information, predicts and adapts to new inputs. This review discusses how these models are used for clinical applications, like disease diagnosis and progression monitoring, but also for exploring fundamental brain mechanisms such as active inference and predictive coding. These approaches provide a powerful tool for both understanding and simulating the brain's complex computational tasks, potentially advancing our knowledge of cognition, perception, and neural disorders.