6,284 research outputs found

    Undergraduate Catalog of Studies, 2023-2024

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    Graduate Catalog of Studies, 2023-2024

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    Undergraduate Catalog of Studies, 2023-2024

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    Development and assessment of learning-based vessel biomarkers from CTA in ischemic stroke

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    Graduate Catalog of Studies, 2023-2024

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    Development and assessment of learning-based vessel biomarkers from CTA in ischemic stroke

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    Backpropagation Beyond the Gradient

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    Automatic differentiation is a key enabler of deep learning: previously, practitioners were limited to models for which they could manually compute derivatives. Now, they can create sophisticated models with almost no restrictions and train them using first-order, i. e. gradient, information. Popular libraries like PyTorch and TensorFlow compute this gradient efficiently, automatically, and conveniently with a single line of code. Under the hood, reverse-mode automatic differentiation, or gradient backpropagation, powers the gradient computation in these libraries. Their entire design centers around gradient backpropagation. These frameworks are specialized around one specific task—computing the average gradient in a mini-batch. This specialization often complicates the extraction of other information like higher-order statistical moments of the gradient, or higher-order derivatives like the Hessian. It limits practitioners and researchers to methods that rely on the gradient. Arguably, this hampers the field from exploring the potential of higher-order information and there is evidence that focusing solely on the gradient has not lead to significant recent advances in deep learning optimization. To advance algorithmic research and inspire novel ideas, information beyond the batch-averaged gradient must be made available at the same level of computational efficiency, automation, and convenience. This thesis presents approaches to simplify experimentation with rich information beyond the gradient by making it more readily accessible. We present an implementation of these ideas as an extension to the backpropagation procedure in PyTorch. Using this newly accessible information, we demonstrate possible use cases by (i) showing how it can inform our understanding of neural network training by building a diagnostic tool, and (ii) enabling novel methods to efficiently compute and approximate curvature information. First, we extend gradient backpropagation for sequential feedforward models to Hessian backpropagation which enables computing approximate per-layer curvature. This perspective unifies recently proposed block- diagonal curvature approximations. Like gradient backpropagation, the computation of these second-order derivatives is modular, and therefore simple to automate and extend to new operations. Based on the insight that rich information beyond the gradient can be computed efficiently and at the same time, we extend the backpropagation in PyTorch with the BackPACK library. It provides efficient and convenient access to statistical moments of the gradient and approximate curvature information, often at a small overhead compared to computing just the gradient. Next, we showcase the utility of such information to better understand neural network training. We build the Cockpit library that visualizes what is happening inside the model during training through various instruments that rely on BackPACK’s statistics. We show how Cockpit provides a meaningful statistical summary report to the deep learning engineer to identify bugs in their machine learning pipeline, guide hyperparameter tuning, and study deep learning phenomena. Finally, we use BackPACK’s extended automatic differentiation functionality to develop ViViT, an approach to efficiently compute curvature information, in particular curvature noise. It uses the low-rank structure of the generalized Gauss-Newton approximation to the Hessian and addresses shortcomings in existing curvature approximations. Through monitoring curvature noise, we demonstrate how ViViT’s information helps in understanding challenges to make second-order optimization methods work in practice. This work develops new tools to experiment more easily with higher-order information in complex deep learning models. These tools have impacted works on Bayesian applications with Laplace approximations, out-of-distribution generalization, differential privacy, and the design of automatic differentia- tion systems. They constitute one important step towards developing and establishing more efficient deep learning algorithms

    LIPIcs, Volume 251, ITCS 2023, Complete Volume

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    LIPIcs, Volume 251, ITCS 2023, Complete Volum

    Multimodal MRI analysis using deep learning methods

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    Magnetic resonance imaging (MRI) has been widely used in scientific and clinical research. It is a non-invasive medical imaging technique that reveals anatomical structures and provides useful information for investigators to explore aging and pathological processes. Different MR modalities offer different useful properties. Automatic MRI analysis algorithms have been developed to address problems in many applications such as classification, segmentation, and disease diagnosis. Segmentation and labeling algorithms applied to brain MRIs enable evaluations of the volumetric changes of specific structures in neurodegenerative diseases. Reconstruction of fiber orientations using diffusion MRI is beneficial to obtain better understanding of the underlying structures. In this thesis, we focused on development of deep learning methods for MRI analysis using different image modalities. Specifically, we applied deep learning techniques on different applications, including segmentation of brain structures and reconstruction of tongue muscle fiber orientations. For segmentation of brain structures, we developed an end-to-end deep learning algorithm for ventricle parcellation of brains with ventriculomegaly using T1-w MR images. The deep network provides robust and accurate segmentation results in subjects with high variability in ventricle shapes and sizes. We developed another deep learning method to automatically parcellate the thalamus into a set of thalamic nuclei using T1-w MRI and features from diffusion MRI. The algorithm incorporates a harmonization step to make the network adapt to input images with different contrasts. We also studied the strains associated with tongue muscles during speech production using multiple MRI modalities. To enable this study, we first developed a deep network to reconstruct crossing tongue muscle fiber orientations using diffusion MRI. The network was specifically designed for the human tongue and accounted for the orthogonality property of the tongue muscles. Next, we proposed a comprehensive pipeline to analyze the strains associated with tongue muscle fiber orientations during speech using diffusion MRI, and tagged and cine MRI. The proposed pipeline provides a solution to analyze the cooperation between muscle groups during speech production

    Medical Image Analysis using Deep Relational Learning

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    In the past ten years, with the help of deep learning, especially the rapid development of deep neural networks, medical image analysis has made remarkable progress. However, how to effectively use the relational information between various tissues or organs in medical images is still a very challenging problem, and it has not been fully studied. In this thesis, we propose two novel solutions to this problem based on deep relational learning. First, we propose a context-aware fully convolutional network that effectively models implicit relation information between features to perform medical image segmentation. The network achieves the state-of-the-art segmentation results on the Multi Modal Brain Tumor Segmentation 2017 (BraTS2017) and Multi Modal Brain Tumor Segmentation 2018 (BraTS2018) data sets. Subsequently, we propose a new hierarchical homography estimation network to achieve accurate medical image mosaicing by learning the explicit spatial relationship between adjacent frames. We use the UCL Fetoscopy Placenta dataset to conduct experiments and our hierarchical homography estimation network outperforms the other state-of-the-art mosaicing methods while generating robust and meaningful mosaicing result on unseen frames.Comment: arXiv admin note: substantial text overlap with arXiv:2007.0778
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