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.

Prompt-Tuning is an efficient method for adapting pre-trained language models to new tasks with minimal computational overhead by modifying prompt embeddings. In this work, we investigate how crucial the phenomenon of embedding collapse, frequently observed in Prompt-Tuning, is for the final performance of the model. To address this question, we designed embedding priors and compared them with posteriors of the converged Soft and Deep Prompt-Tuning methods. Our findings suggest that priors strongly affect the position of the tuned embeddings, and models can effectively work with embeddings from different parts of activation spaces, including completely new regions. As the final Prompt-Tuning capabilities are limited, we hypothesize that controllable Prompt-Tuning posteriors may serve as a good starting point for tasks such as chain-of-thought (COT) distillation. Our experiments also show that generated trajectories are not localized in the activation space of the models. However, there are distinct clusters of activations for distant tasks (e.g., NLP and arithmetic), while activations between NLP tasks (e.g., Question-Answering and MLM) lie in the same cluster. These observations raise questions about the importance of a single activation cluster for the generalization abilities of large language models.

Generative methods (Gen-AI) are reviewed with a particular goal to solving tasks in Machine Learning and Bayesian inference. Generative models require one to simulate a large training dataset and to use deep neural networks to solve a supervised learning problem. To do this, we require high dimensional regression methods and tools for dimensionality reduction (a.k.a feature selection). The main advantage of Gen-AI methods is their ability to be model-free and to use deep neural networks to estimate conditional densities or posterior quantiles of interest. To illustrate generative methods, we analyze the well-known Ebola data-set. Finally, we conclude with directions for future research.

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.

Tensor Robust Principal Component Analysis (TRPCA) holds a crucial position in machine learning and computer vision. It aims to recover underlying low-rank structures and characterizing the sparse structures of noise. Current approaches often encounter difficulties in accurately capturing the low-rank properties of tensors and balancing the trade-off between low-rank and sparse components, especially in a mixed-noise scenario. To address these challenges, we introduce a Bayesian framework for TRPCA, which integrates a low-rank tensor nuclear norm prior and a generalized sparsity-inducing prior. By embedding the proposed priors within the Bayesian framework, our method can automatically determine the optimal tensor nuclear norm and achieve a balance between the nuclear norm and sparse components. Furthermore, our method can be efficiently extended to the weighted tensor nuclear norm model. Experiments conducted on synthetic and real-world datasets demonstrate the effectiveness and superiority of our method compared to state-of-the-art approaches.

Systems thinking provides us with a way to model the algorithmic fairness problem by allowing us to encode prior knowledge and assumptions about where we believe bias might exist in the data generating process. We can then model this using a series of causal graphs, enabling us to link AI/ML systems to politics and the law. By treating the fairness problem as a complex system, we can combine techniques from machine learning, causal inference, and system dynamics. Each of these analytical techniques is designed to capture different emergent aspects of fairness, allowing us to develop a deeper and more holistic view of the problem. This can help policymakers on both sides of the political aisle to understand the complex trade-offs that exist from different types of fairness policies, providing a blueprint for designing AI policy that is aligned to their political agendas.

Advanced Aerial Mobility encompasses many outstanding applications that promise to revolutionize modern logistics and pave the way for various public services and industry uses. However, throughout its history, the development of such systems has been impeded by the complexity of legal restrictions and physical constraints. While airspaces are often tightly shaped by various legal requirements, Unmanned Aerial Vehicles (UAV) must simultaneously consider, among others, energy demands, signal quality, and noise pollution. In this work, we address this challenge by presenting a novel architecture that integrates methods of Probabilistic Mission Design (ProMis) and Many-Objective Optimization for UAV routing. Hereby, our framework is able to comply with legal requirements under uncertainty while producing effective paths that minimize various physical costs a UAV needs to consider when traversing human-inhabited spaces. To this end, we combine hybrid probabilistic first-order logic for spatial reasoning with mixed deterministic-stochastic route optimization, incorporating physical objectives such as energy consumption and radio interference with a logical, probabilistic model of legal requirements. We demonstrate the versatility and advantages of our system in a large-scale empirical evaluation over real-world, crowd-sourced data from a map extract from the city of Paris, France, showing how a network of effective and compliant paths can be formed.

Predictions in environments where a mix of legal policies, physical limitations, and operational preferences impacts an agent's motion are inherently difficult. Since Neuro-Symbolic systems allow for differentiable information flow between deep learning and symbolic building blocks, they present a promising avenue for expressing such high-level constraints. While prior work has demonstrated how to establish novel planning setups, e.g., in advanced aerial mobility tasks, their application in prediction tasks has been underdeveloped. We present the Constitutional Filter (CoFi), a novel filter architecture leveraging a Neuro-Symbolic representation of an agent's rules, i.e., its constitution, to (i) improve filter accuracy, (ii) leverage expert knowledge, (iii) incorporate deep learning architectures, and (iv) account for uncertainties in the environments through probabilistic spatial relations. CoFi follows a general, recursive Bayesian estimation setting, making it compatible with a vast landscape of estimation techniques such as Particle Filters. To underpin the advantages of CoFi, we validate its performance on real-world marine data from the Automatic Identification System and official Electronic Navigational Charts.

Given the ease of creating synthetic data from machine learning models, new models can be potentially trained on synthetic data generated by previous models. This recursive training process raises concerns about the long-term impact on model quality. As models are recursively trained on generated data from previous rounds, their ability to capture the nuances of the original human-generated data may degrade. This is often referred to as \emph{model collapse}. In this work, we ask how fast model collapse occurs for some well-studied distribution families under maximum likelihood (ML or near ML) estimation during recursive training. Surprisingly, even for fundamental distributions such as discrete and Gaussian distributions, the exact rate of model collapse is unknown. In this work, we theoretically characterize the rate of collapse in these fundamental settings and complement it with experimental evaluations. Our results show that for discrete distributions, the time to forget a word is approximately linearly dependent on the number of times it occurred in the original corpus, and for Gaussian models, the standard deviation reduces to zero roughly at $n$ iterations, where $n$ is the number of samples at each iteration. Both of these findings imply that model forgetting, at least in these simple distributions under near ML estimation with many samples, takes a long time.

Fine-grained emotion recognition (FER) plays a vital role in various fields, such as disease diagnosis, personalized recommendations, and multimedia mining. However, existing FER methods face three key challenges in real-world applications: (i) they rely on large amounts of continuously annotated data to ensure accuracy since emotions are complex and ambiguous in reality, which is costly and time-consuming; (ii) they cannot capture the temporal heterogeneity caused by changing emotion patterns, because they usually assume that the temporal correlation within sampling periods is the same; (iii) they do not consider the spatial heterogeneity of different FER scenarios, that is, the distribution of emotion information in different data may have bias or interference. To address these challenges, we propose a Spatio-Temporal Fuzzy-oriented Multi-modal Meta-learning framework (ST-F2M). Specifically, ST-F2M first divides the multi-modal videos into multiple views, and each view corresponds to one modality of one emotion. Multiple randomly selected views for the same emotion form a meta-training task. Next, ST-F2M uses an integrated module with spatial and temporal convolutions to encode the data of each task, reflecting the spatial and temporal heterogeneity. Then it adds fuzzy semantic information to each task based on generalized fuzzy rules, which helps handle the complexity and ambiguity of emotions. Finally, ST-F2M learns emotion-related general meta-knowledge through meta-recurrent neural networks to achieve fast and robust fine-grained emotion recognition. Extensive experiments show that ST-F2M outperforms various state-of-the-art methods in terms of accuracy and model efficiency. In addition, we construct ablation studies and further analysis to explore why ST-F2M performs well.