Unveiling Secrets of Brain Function With Generative Modeling: Motion Perception in Primates & Cortical Network Organization in Mice

This Dissertation is comprised of two main projects, addressing questions in neuroscience through applications of generative modeling. Project #1 (Chapter 4) explores how neurons encode features of the external world. I combine Helmholtz's "Perception as Unconscious Inference" -- paralleled by modern generative models like variational autoencoders (VAE) -- with the hierarchical structure of the visual cortex. This combination leads to the development of a hierarchical VAE model, which I test for its ability to mimic neurons from the primate visual cortex in response to motion stimuli. Results show that the hierarchical VAE perceives motion similar to the primate brain. Additionally, the model identifies causal factors of retinal motion inputs, such as object- and self-motion, in a completely unsupervised manner. Collectively, these results suggest that hierarchical inference underlines the brain's understanding of the world, and hierarchical VAEs can effectively model this understanding. Project #2 (Chapter 5) investigates the spatiotemporal structure of spontaneous brain activity and its reflection of brain states like rest. Using simultaneous fMRI and wide-field Ca2+ imaging data, this project demonstrates that the mouse cortex can be decomposed into overlapping communities, with around half of the cortical regions belonging to multiple communities. Comparisons reveal similarities and differences between networks inferred from fMRI and Ca2+ signals. The introduction (Chapter 1) is divided similarly to this abstract: sections 1.1 to 1.8 provide background information about Project #1, and sections 1.9 to 1.13 are related to Project #2. Chapter 2 includes historical background, Chapter 3 provides the necessary mathematical background, and finally, Chapter 6 contains concluding remarks and future directions.