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Register a new userBayesian deep neural networks for low-cost neurophysiological markers of Alzheimers disease severity
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As societies around the world are ageing, the number of Alzheimers disease (AD) patients is rapidly increasing. To date, no low-cost, non-invasive biomarkers have been established to advance the objectivization of AD diagnosis and progression assessment. Here, we utilize Bayesian neural networks to develop a multivariate predictor for AD severity using a wide range of quantitative EEG (QEEG) markers. The Bayesian treatment of neural networks both automatically controls model complexity and provides a predictive distribution over the target function, giving uncertainty bounds for our regression task. It is therefore well suited to clinical neuroscience, where data sets are typically sparse and practitioners require a precise assessment of the predictive uncertainty. We use data of one of the largest prospective AD EEG trials ever conducted to demonstrate the potential of Bayesian deep learning in this domain, while comparing two distinct Bayesian neural network approaches, i.e., Monte Carlo dropout and Hamiltonian Monte Carlo.
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For precision medicine and personalized treatment, we need to identify predictive markers of disease. We focus on Alzheimers disease (AD), where magnetic resonance imaging scans provide information about the disease status. By combining imaging with genome sequencing, we aim at identifying rare genetic markers associated with quantitative traits predicted from convolutional neural networks (CNNs), which traditionally have been derived manually by experts. Kernel-based tests are a powerful tool for associating sets of genetic variants, but how to optimally model rare genetic variants is still an open research question. We propose a generalized set of kernels that incorporate prior information from various annotations and multi-omics data. In the analysis of data from the Alzheimers Disease Neuroimaging Initiative (ADNI), we evaluate whether (i) CNNs yield precise and reliable brain traits, and (ii) the novel kernel-based tests can help to identify loci associated with AD. The results indicate that CNNs provide a fast, scalable and precise tool to derive quantitative AD traits and that new kernels integrating domain knowledge can yield higher power in association tests of very rare variants.
We propose a novel Bayesian neural network architecture that can learn invariances from data alone by inferring a posterior distribution over different weight-sharing schemes. We show that our model outperforms other non-invariant architectures, when trained on datasets that contain specific invariances. The same holds true when no data augmentation is performed.
We perform scalable approximate inference in a continuous-depth Bayesian neural network family. In this model class, uncertainty about separate weights in each layer gives hidden units that follow a stochastic differential equation. We demonstrate gradient-based stochastic variational inference in this infinite-parameter setting, producing arbitrarily-flexible approximate posteriors. We also derive a novel gradient estimator that approaches zero variance as the approximate posterior over weights approaches the true posterior. This approach brings continuous-depth Bayesian neural nets to a competitive comparison against discrete-depth alternatives, while inheriting the memory-efficient training and tunable precision of Neural ODEs.
Accurate diagnosis of Alzheimers Disease (AD) entails clinical evaluation of multiple cognition metrics and biomarkers. Metrics such as the Alzheimers Disease Assessment Scale - Cognitive test (ADAS-cog) comprise multiple subscores that quantify different aspects of a patients cognitive state such as learning, memory, and language production/comprehension. Although computer-aided diagnostic techniques for classification of a patients current disease state exist, they provide little insight into the relationship between changes in brain structure and different aspects of a patients cognitive state that occur over time in AD. We have developed a Convolutional Neural Network architecture that can concurrently predict the trajectories of the 13 subscores comprised by a subjects ADAS-cog examination results from a current minimally preprocessed structural MRI scan up to 36 months from image acquisition time without resorting to manual feature extraction. Mean performance metrics are within range of those of existing techniques that require manual feature selection and are limited to predicting aggregate scores.
We develop variational Laplace for Bayesian neural networks (BNNs) which exploits a local approximation of the curvature of the likelihood to estimate the ELBO without the need for stochastic sampling of the neural-network weights. The Variational Laplace objective is simple to evaluate, as it is (in essence) the log-likelihood, plus weight-decay, plus a squared-gradient regularizer. Variational Laplace gave better test performance and expected calibration errors than maximum a-posteriori inference and standard sampling-based variational inference, despite using the same variational approximate posterior. Finally, we emphasise care needed in benchmarking standard VI as there is a risk of stopping before the variance parameters have converged. We show that early-stopping can be avoided by increasing the learning rate for the variance parameters.
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