Browsing by Author "Dunson, David"
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Item Restricted Bayesian inference of the number of factors in gene-expression analysis: application to human virus challenge studies(BMC BIOINFORMATICS, 2010-11-09) Chen, Bo; Chen, Minhua; Paisley, John; Zaas, Aimee; Woods, Christopher; Ginsburg, Geoffrey S; Hero, Alfred; Lucas, Joseph; Dunson, David; Carin, LawrenceItem Open Access Graphical and Isoperimetric Perspectives on Sampling and Regularization(2024) Tam, EdricSeveral recurring themes in modern Bayesian statistics and probabilistic machine learning are sampling, regularization and embeddings/latent variables. This thesis examines particular aspects of these themes from the perspective of concentration of measure, isoperimetry and spectral graph theory. These mathematical topics are intricately connected, and we often leverage related tools, such as Laplacians and concentration inequalities, in the theory and methods developed in this thesis.
From the sampling methodology end, we develop a novel spanning tree sampler called the fast-forwarded cover algorithm that improves upon the celebrated Aldous-Broder algorithm. The Aldous-Broder algorithm, and other related random-walk based approaches for spanning tree sampling, can be stuck when the underlying graph exhibits bottleneck structures. We show that our fast-forwarded cover algorithm can break free of bottlenecks that are arbitrarily small, while maintaining exact sampling guarantees. We demonstrate how our novel sampler can be applied to posterior sampling from Bayesian models with tree components.
For sampling theory, we investigate the statistical capacity of broad classes of deep generative models. We use concentration of measure techniques to show that there is a limitation to what kinds of distributions deep generative models can learn to sample from. In particular, for generative adversarial networks and variational autoencoders, under standard priors on the latent variables, only light tailed distributions can be learned. This fact is generalized to the manifold setting using tools from concentration and geometry. We also provide extra quantification of these models' capacities based on functional inequalities. This debunks a popular belief about the learning capacity of deep generative models.
On the regularization side, we propose Fiedler regularization, a way to use a neural network's underlying graph structure to regularize itself. It can be used in the supervised learning setting, as well as more general settings such as for regularizing autoencoders. We give theoretial guarantees and empirical experimental results.
Last but not least, on the embeddings front, we propose a novel piece of methodology for graph comparison called embedded Laplacian distance. Typical methods for comparing graphs are computationally demanding, due to the discrete and combinatorial nature of graphs. We observe that for many applications where graph comparison is needed, an approximate comparison that captures the structures of the graphs suffice. We propose to compare graphs based on continuous representations that capture meaningful graph structure, namely spectral embeddings. Theoretical and empirical results are provided.
Item Open Access Rat intersubjective decisions are encoded by frequency-specific oscillatory contexts.(Brain Behav, 2017-06) Schaich Borg, Jana; Srivastava, Sanvesh; Lin, Lizhen; Heffner, Joseph; Dunson, David; Dzirasa, Kafui; de Lecea, LuisINTRODUCTION: It is unknown how the brain coordinates decisions to withstand personal costs in order to prevent other individuals' distress. Here we test whether local field potential (LFP) oscillations between brain regions create "neural contexts" that select specific brain functions and encode the outcomes of these types of intersubjective decisions. METHODS: Rats participated in an "Intersubjective Avoidance Test" (IAT) that tested rats' willingness to enter an innately aversive chamber to prevent another rat from getting shocked. c-Fos immunoreactivity was used to screen for brain regions involved in IAT performance. Multi-site local field potential (LFP) recordings were collected simultaneously and bilaterally from five brain regions implicated in the c-Fos studies while rats made decisions in the IAT. Local field potential recordings were analyzed using an elastic net penalized regression framework. RESULTS: Rats voluntarily entered an innately aversive chamber to prevent another rat from getting shocked, and c-Fos immunoreactivity in brain regions known to be involved in human empathy-including the anterior cingulate, insula, orbital frontal cortex, and amygdala-correlated with the magnitude of "intersubjective avoidance" each rat displayed. Local field potential recordings revealed that optimal accounts of rats' performance in the task require specific frequencies of LFP oscillations between brain regions in addition to specific frequencies of LFP oscillations within brain regions. Alpha and low gamma coherence between spatially distributed brain regions predicts more intersubjective avoidance, while theta and high gamma coherence between a separate subset of brain regions predicts less intersubjective avoidance. Phase relationship analyses indicated that choice-relevant coherence in the alpha range reflects information passed from the amygdala to cortical structures, while coherence in the theta range reflects information passed in the reverse direction. CONCLUSION: These results indicate that the frequency-specific "neural context" surrounding brain regions involved in social cognition encodes outcomes of decisions that affect others, above and beyond signals from any set of brain regions in isolation.Item Open Access Supervised Autoencoders Learn Robust Joint Factor Models of Neural Activity.(CoRR, 2020) Talbot, Austin; Dunson, David; Dzirasa, Kafui; Carlson, DavidFactor models are routinely used for dimensionality reduction in modeling of correlated, high-dimensional data. We are particularly motivated by neuroscience applications collecting high-dimensional `predictors' corresponding to brain activity in different regions along with behavioral outcomes. Joint factor models for the predictors and outcomes are natural, but maximum likelihood estimates of these models can struggle in practice when there is model misspecification. We propose an alternative inference strategy based on supervised autoencoders; rather than placing a probability distribution on the latent factors, we define them as an unknown function of the high-dimensional predictors. This mapping function, along with the loadings, can be optimized to explain variance in brain activity while simultaneously being predictive of behavior. In practice, the mapping function can range in complexity from linear to more complex forms, such as splines or neural networks, with the usual tradeoff between bias and variance. This approach yields distinct solutions from a maximum likelihood inference strategy, as we demonstrate by deriving analytic solutions for a linear Gaussian factor model. Using synthetic data, we show that this function-based approach is robust against multiple types of misspecification. We then apply this technique to a neuroscience application resulting in substantial gains in predicting behavioral tasks from electrophysiological measurements in multiple factor models.