Publications

Since numbers in the computer are represented with a fixed number of bits, loss of accuracy during calculation is unavoidable. At high precision where more bits (e.g. 64) are allocated to each number, round-off errors are typically small. On the other hand, calculating at lower precision, such as half (16 bits), has the advantage of being much faster. This research focuses on experimenting with arithmetic at different precision levels for large-scale inverse problems, which are represented by linear systems with ill-conditioned matrices. We modified the Conjugate Gradient Method for Least Squares (CGLS) and the Chebyshev Semi-Iterative Method (CS) with Tikhonov regularization to do arithmetic at lower precision using the MATLAB chop function, and we ran experiments on applications from image processing and compared their performance at different precision levels. We concluded that CGLS is a more stable algorithm, but overflows easily due to the computation of inner products, while CS is less likely to overflow but it has more erratic convergence behavior. When the noise level is high, CS outperforms CGLS by being able to run more iterations before overflow occurs; when the noise level is close to zero, CS appears to be more susceptible to accumulation of round-off errors.

We demonstrate that automatic differentiation, which has become commonly available in machine learning frameworks, is an efficient way to explore ideas that lead to algorithmic improvement in multi-scale affine image registration and affine super-resolution problems. In our first experiment on multi-scale registration, we implement an ODE predictor-corrector method involving a derivative with respect to the scale parameter and the Hessian of an image registration objective function, both of which would be difficult to compute without AD. Our findings indicate that exact Hessians are necessary for the method to provide any benefits over a traditional multi-scale method; a Gauss-Newton Hessian approximation fails to provide such benefits. In our second experiment, we implement a variable projected Gauss-Newton method for super-resolution and use AD to differentiate through the iteratively computed projection, a method previously unaddressed in the literature. We show that Jacobians obtained without differentiating through the projection are poor approximations to the true Jacobians of the variable projected forward map and explore the performance of some other approximations. By addressing these problems, this work contributes to the application of AD in image registration and sets a precedent for further use of machine learning tools in this field.

Recent efforts in applying implicit networks to solve inverse problems in imaging have achieved competitive or even superior results when compared to feedforward networks. These implicit networks only require constant memory during backpropagation, regardless of the number of layers. However, they are not necessarily easy to train. Gradient calculations are computationally expensive because they require backpropagating through a fixed point. In particular, this process requires solving a large linear system whose size is determined by the number of features in the fixed point iteration. This paper explores a recently proposed method, Jacobian-free Backpropagation (JFB), a backpropagation scheme that circumvents such calculation, in the context of image deblurring problems. Our results show that JFB is comparable against fine-tuned optimization schemes, state-of-the-art (SOTA) feedforward networks, and existing implicit networks at a reduced computational cost.

We propose Minority Class Rebalancing through Augmentation by Generative modeling (MCRAGE), a novel approach to augment imbalanced datasets using samples generated by a deep generative model. The MCRAGE process involves training a Conditional Denoising Diffusion Probabilistic Model (CDDPM) capable of generating high-quality synthetic EHR samples from underrepresented classes. We use this synthetic data to augment the existing imbalanced dataset, thereby achieving a more balanced distribution across all classes, which can be used to train an unbiased machine learning model.

Working with a two-stage ice sheet model, we explore how statistical data assimilation methods can be used to improve predictions of glacier melt and relatedly, sea level rise. We find that the EnKF improves model runs initialized using incorrect initial conditions or parameters, providing us with better models of future glacier melt. We explore the necessary number of observations needed to produce an accurate model run. Further, we determine that the deviations from the truth in output that stem from having few data points in the pre-satellite era can be corrected with modern observation data. Finally, using data derived from our improved model we calculate sea level rise and model storm surges to understand the affect caused by sea level rise.

It is well-established that graph neural networks (GNNs) can effectively model networked data in a variety of fields. However, whether GNNs can outperform traditional shallow graph classification models such as graph kernels for brain network analysis remains unclear. To this end, we analyze different approaches for modeling brain networks, including graph kernel based SVM, basic GNNs and kernelized GNNs. These models are designed to aid in the analysis of diseases and mental disorders such as bipolar disorder, human immunodeficiency virus (HIV), post-traumatic stress disorder (PTSD), and depression. In particular, we conduct experiments with three methods: kernelized support vector machines (SVM), message passing graph neural networks (MPGNNs), and kernel graph neural networks (KerGNN). We conclude that 1) deep models (GNNs) generally outperform shallow models (SVM) and 2) models considering specific graph motifs do not seem to significantly improve performance. We also identify other graph kernels and GNN frameworks that show promise in motivating further research in brain network analysis.

To analyze the abundance of multidimensional data, tensor-based frameworks have been developed. Traditionally, the matrix singular value decomposition (SVD) is used to extract the most dominant features from a matrix containing the vectorized data. While the SVD is highly useful for data that can be appropriately represented as a matrix, this step of vectorization causes us to lose the high-dimensional relationships intrinsic to the data. To facilitate efficient multidimensional feature extraction, we utilize a projection-based classification algorithm using the t-SVDM, a tensor analog of the matrix SVD. Our work extends the t-SVDM framework and the classification algorithm, both initially proposed for tensors of order 3, to any number of dimensions. We then apply this algorithm to a classification task using the StarPlus fMRI dataset. Our numerical experiments demonstrate that there exists a superior tensor-based approach to fMRI classification than the best possible equivalent matrix-based approach. Our results illustrate the advantages of our chosen tensor framework, provide insight into beneficial choices of parameters, and could be further developed for classification of more complex imaging data. We provide our Python implementation at this https URL.

Two segmentation methods, one atlas-based and one neural-network-based, were compared to see how well they can each automatically segment the brain stem and cerebellum in Displacement Encoding with Stimulated Echoes Magnetic Resonance Imaging (DENSE-MRI) data. The segmentation is a pre-requisite for estimating the average displacements in these regions, which have recently been proposed as biomarkers in the diagnosis of Chiari Malformation type I (CMI). In numerical experiments, the segmentations of both methods were similar to manual segmentations provided by trained experts. It was found that, overall, the neural-network-based method alone produced more accurate segmentations than the atlas-based method did alone, but that a combination of the two methods – in which the atlas-based method is used for the segmentation of the brain stem and the neural-network is used for the segmentation of the cerebellum – may be the most successful.

Due to the COVID-19 pandemic, there is an increasing demand for portable CT machines worldwide in order to diagnose patients in a variety of settings [16]. This has lead to a need for CT image reconstruction algorithms that can produce high-quality images in the case when multiple types of geometry parameters have been perturbed. In this paper, we present an alternating descent algorithm to address this issue, where one step minimizes a regularized linear least squares problem, and the other minimizes a bounded non-linear least-square problem. Additionally, we survey existing methods to accelerate the convergence algorithm and discuss implementation details through the use of MATLAB packages such as IRtools and imfil. Finally, numerical experiments are conducted to show the effectiveness of our algorithm.