2,695 research outputs found

    UMSL Bulletin 2023-2024

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    The 2023-2024 Bulletin and Course Catalog for the University of Missouri St. Louis.https://irl.umsl.edu/bulletin/1088/thumbnail.jp

    UMSL Bulletin 2022-2023

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    The 2022-2023 Bulletin and Course Catalog for the University of Missouri St. Louis.https://irl.umsl.edu/bulletin/1087/thumbnail.jp

    Towards Saner Deep Image Registration

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    With recent advances in computing hardware and surges of deep-learning architectures, learning-based deep image registration methods have surpassed their traditional counterparts, in terms of metric performance and inference time. However, these methods focus on improving performance measurements such as Dice, resulting in less attention given to model behaviors that are equally desirable for registrations, especially for medical imaging. This paper investigates these behaviors for popular learning-based deep registrations under a sanity-checking microscope. We find that most existing registrations suffer from low inverse consistency and nondiscrimination of identical pairs due to overly optimized image similarities. To rectify these behaviors, we propose a novel regularization-based sanity-enforcer method that imposes two sanity checks on the deep model to reduce its inverse consistency errors and increase its discriminative power simultaneously. Moreover, we derive a set of theoretical guarantees for our sanity-checked image registration method, with experimental results supporting our theoretical findings and their effectiveness in increasing the sanity of models without sacrificing any performance. Our code and models are available at https://github.com/tuffr5/Saner-deep-registration.Comment: ICCV 202

    Deep Learning Approaches for Data Augmentation in Medical Imaging: A Review

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    Deep learning has become a popular tool for medical image analysis, but the limited availability of training data remains a major challenge, particularly in the medical field where data acquisition can be costly and subject to privacy regulations. Data augmentation techniques offer a solution by artificially increasing the number of training samples, but these techniques often produce limited and unconvincing results. To address this issue, a growing number of studies have proposed the use of deep generative models to generate more realistic and diverse data that conform to the true distribution of the data. In this review, we focus on three types of deep generative models for medical image augmentation: variational autoencoders, generative adversarial networks, and diffusion models. We provide an overview of the current state of the art in each of these models and discuss their potential for use in different downstream tasks in medical imaging, including classification, segmentation, and cross-modal translation. We also evaluate the strengths and limitations of each model and suggest directions for future research in this field. Our goal is to provide a comprehensive review about the use of deep generative models for medical image augmentation and to highlight the potential of these models for improving the performance of deep learning algorithms in medical image analysis

    Leveraging elasticity theory to calculate cell forces: From analytical insights to machine learning

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    Living cells possess capabilities to detect and respond to mechanical features of their surroundings. In traction force microscopy, the traction of cells on an elastic substrate is made visible by observing substrate deformation as measured by the movement of embedded marker beads. Describing the substrates by means of elasticity theory, we can calculate the adhesive forces, improving our understanding of cellular function and behavior. In this dissertation, I combine analytical solutions with numerical methods and machine learning techniques to improve traction prediction in a range of experimental applications. I describe how to include the normal traction component in regularization-based Fourier approaches, which I apply to experimental data. I compare the dominant strategies for traction reconstruction, the direct method and inverse, regularization-based approaches and find, that the latter are more precise while the former is more stress resilient to noise. I find that a point-force based reconstruction can be used to study the force balance evolution in response to microneedle pulling showing a transition from a dipolar into a monopolar force arrangement. Finally, I show how a conditional invertible neural network not only reconstructs adhesive areas more localized, but also reveals spatial correlations and variations in reliability of traction reconstructions

    Synthesising 3D solid models of natural heterogeneous materials from single sample image, using encoding deep convolutional generative adversarial networks

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    Three-dimensional solid computational representations of natural heterogeneous materials are challenging to generate due to their high degree of randomness and varying scales of patterns, such as veins and cracks, in different sizes and directions. In this regard, this paper introduces a new architecture to synthesise 3D solid material models by using encoding deep convolutional generative adversarial networks (EDCGANs). DCGANs have been useful in generative tasks in relation to image processing by successfully recreating similar results based on adequate training. While concentrating on natural heterogeneous materials, this paper uses an encoding and a decoding DCGAN combined in a similar way to auto-encoders to convert a given image into marble, based on patches. Additionally, the method creates an input dataset from a single 2D high-resolution exemplar. Further, it translates of 2D data, used as a seed, into 3D data to create material blocks. While the results on the Z-axis do not have size restrictions, the X- and Y-axis are constrained by the given image. Using the method, the paper explores possible ways to present 3D solid textures. The modelling potentials of the developed approach as a design tool is explored to synthesise a 3D solid texture of leaf-like material from an exemplar of a leaf image

    Modular lifelong machine learning

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    Deep learning has drastically improved the state-of-the-art in many important fields, including computer vision and natural language processing (LeCun et al., 2015). However, it is expensive to train a deep neural network on a machine learning problem. The overall training cost further increases when one wants to solve additional problems. Lifelong machine learning (LML) develops algorithms that aim to efficiently learn to solve a sequence of problems, which become available one at a time. New problems are solved with less resources by transferring previously learned knowledge. At the same time, an LML algorithm needs to retain good performance on all encountered problems, thus avoiding catastrophic forgetting. Current approaches do not possess all the desired properties of an LML algorithm. First, they primarily focus on preventing catastrophic forgetting (Diaz-Rodriguez et al., 2018; Delange et al., 2021). As a result, they neglect some knowledge transfer properties. Furthermore, they assume that all problems in a sequence share the same input space. Finally, scaling these methods to a large sequence of problems remains a challenge. Modular approaches to deep learning decompose a deep neural network into sub-networks, referred to as modules. Each module can then be trained to perform an atomic transformation, specialised in processing a distinct subset of inputs. This modular approach to storing knowledge makes it easy to only reuse the subset of modules which are useful for the task at hand. This thesis introduces a line of research which demonstrates the merits of a modular approach to lifelong machine learning, and its ability to address the aforementioned shortcomings of other methods. Compared to previous work, we show that a modular approach can be used to achieve more LML properties than previously demonstrated. Furthermore, we develop tools which allow modular LML algorithms to scale in order to retain said properties on longer sequences of problems. First, we introduce HOUDINI, a neurosymbolic framework for modular LML. HOUDINI represents modular deep neural networks as functional programs and accumulates a library of pre-trained modules over a sequence of problems. Given a new problem, we use program synthesis to select a suitable neural architecture, as well as a high-performing combination of pre-trained and new modules. We show that our approach has most of the properties desired from an LML algorithm. Notably, it can perform forward transfer, avoid negative transfer and prevent catastrophic forgetting, even across problems with disparate input domains and problems which require different neural architectures. Second, we produce a modular LML algorithm which retains the properties of HOUDINI but can also scale to longer sequences of problems. To this end, we fix the choice of a neural architecture and introduce a probabilistic search framework, PICLE, for searching through different module combinations. To apply PICLE, we introduce two probabilistic models over neural modules which allows us to efficiently identify promising module combinations. Third, we phrase the search over module combinations in modular LML as black-box optimisation, which allows one to make use of methods from the setting of hyperparameter optimisation (HPO). We then develop a new HPO method which marries a multi-fidelity approach with model-based optimisation. We demonstrate that this leads to improvement in anytime performance in the HPO setting and discuss how this can in turn be used to augment modular LML methods. Overall, this thesis identifies a number of important LML properties, which have not all been attained in past methods, and presents an LML algorithm which can achieve all of them, apart from backward transfer

    Learning Weakly Convex Regularizers for Convergent Image-Reconstruction Algorithms

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    We propose to learn non-convex regularizers with a prescribed upper bound on their weak-convexity modulus. Such regularizers give rise to variational denoisers that minimize a convex energy. They rely on few parameters (less than 15,000) and offer a signal-processing interpretation as they mimic handcrafted sparsity-promoting regularizers. Through numerical experiments, we show that such denoisers outperform convex-regularization methods as well as the popular BM3D denoiser. Additionally, the learned regularizer can be deployed to solve inverse problems with iterative schemes that provably converge. For both CT and MRI reconstruction, the regularizer generalizes well and offers an excellent tradeoff between performance, number of parameters, guarantees, and interpretability when compared to other data-driven approaches

    BlindHarmony: "Blind" Harmonization for MR Images via Flow model

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    In MRI, images of the same contrast (e.g., T1_1) from the same subject can exhibit noticeable differences when acquired using different hardware, sequences, or scan parameters. These differences in images create a domain gap that needs to be bridged by a step called image harmonization, to process the images successfully using conventional or deep learning-based image analysis (e.g., segmentation). Several methods, including deep learning-based approaches, have been proposed to achieve image harmonization. However, they often require datasets from multiple domains for deep learning training and may still be unsuccessful when applied to images from unseen domains. To address this limitation, we propose a novel concept called `Blind Harmonization', which utilizes only target domain data for training but still has the capability to harmonize images from unseen domains. For the implementation of blind harmonization, we developed BlindHarmony using an unconditional flow model trained on target domain data. The harmonized image is optimized to have a correlation with the input source domain image while ensuring that the latent vector of the flow model is close to the center of the Gaussian distribution. BlindHarmony was evaluated on both simulated and real datasets and compared to conventional methods. BlindHarmony demonstrated noticeable performance on both datasets, highlighting its potential for future use in clinical settings. The source code is available at: https://github.com/SNU-LIST/BlindHarmonyComment: ICCV 2023 accepted. 9 pages and 5 Figures for manuscipt, supplementary include
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