2,051 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

    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

    Advances and Applications of DSmT for Information Fusion. Collected Works, Volume 5

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    This fifth volume on Advances and Applications of DSmT for Information Fusion collects theoretical and applied contributions of researchers working in different fields of applications and in mathematics, and is available in open-access. The collected contributions of this volume have either been published or presented after disseminating the fourth volume in 2015 in international conferences, seminars, workshops and journals, or they are new. The contributions of each part of this volume are chronologically ordered. First Part of this book presents some theoretical advances on DSmT, dealing mainly with modified Proportional Conflict Redistribution Rules (PCR) of combination with degree of intersection, coarsening techniques, interval calculus for PCR thanks to set inversion via interval analysis (SIVIA), rough set classifiers, canonical decomposition of dichotomous belief functions, fast PCR fusion, fast inter-criteria analysis with PCR, and improved PCR5 and PCR6 rules preserving the (quasi-)neutrality of (quasi-)vacuous belief assignment in the fusion of sources of evidence with their Matlab codes. Because more applications of DSmT have emerged in the past years since the apparition of the fourth book of DSmT in 2015, the second part of this volume is about selected applications of DSmT mainly in building change detection, object recognition, quality of data association in tracking, perception in robotics, risk assessment for torrent protection and multi-criteria decision-making, multi-modal image fusion, coarsening techniques, recommender system, levee characterization and assessment, human heading perception, trust assessment, robotics, biometrics, failure detection, GPS systems, inter-criteria analysis, group decision, human activity recognition, storm prediction, data association for autonomous vehicles, identification of maritime vessels, fusion of support vector machines (SVM), Silx-Furtif RUST code library for information fusion including PCR rules, and network for ship classification. Finally, the third part presents interesting contributions related to belief functions in general published or presented along the years since 2015. These contributions are related with decision-making under uncertainty, belief approximations, probability transformations, new distances between belief functions, non-classical multi-criteria decision-making problems with belief functions, generalization of Bayes theorem, image processing, data association, entropy and cross-entropy measures, fuzzy evidence numbers, negator of belief mass, human activity recognition, information fusion for breast cancer therapy, imbalanced data classification, and hybrid techniques mixing deep learning with belief functions as well

    Is attention all you need in medical image analysis? A review

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    Medical imaging is a key component in clinical diagnosis, treatment planning and clinical trial design, accounting for almost 90% of all healthcare data. CNNs achieved performance gains in medical image analysis (MIA) over the last years. CNNs can efficiently model local pixel interactions and be trained on small-scale MI data. The main disadvantage of typical CNN models is that they ignore global pixel relationships within images, which limits their generalisation ability to understand out-of-distribution data with different 'global' information. The recent progress of Artificial Intelligence gave rise to Transformers, which can learn global relationships from data. However, full Transformer models need to be trained on large-scale data and involve tremendous computational complexity. Attention and Transformer compartments (Transf/Attention) which can well maintain properties for modelling global relationships, have been proposed as lighter alternatives of full Transformers. Recently, there is an increasing trend to co-pollinate complementary local-global properties from CNN and Transf/Attention architectures, which led to a new era of hybrid models. The past years have witnessed substantial growth in hybrid CNN-Transf/Attention models across diverse MIA problems. In this systematic review, we survey existing hybrid CNN-Transf/Attention models, review and unravel key architectural designs, analyse breakthroughs, and evaluate current and future opportunities as well as challenges. We also introduced a comprehensive analysis framework on generalisation opportunities of scientific and clinical impact, based on which new data-driven domain generalisation and adaptation methods can be stimulated

    Systemic Circular Economy Solutions for Fiber Reinforced Composites

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    This open access book provides an overview of the work undertaken within the FiberEUse project, which developed solutions enhancing the profitability of composite recycling and reuse in value-added products, with a cross-sectorial approach. Glass and carbon fiber reinforced polymers, or composites, are increasingly used as structural materials in many manufacturing sectors like transport, constructions and energy due to their better lightweight and corrosion resistance compared to metals. However, composite recycling is still a challenge since no significant added value in the recycling and reprocessing of composites is demonstrated. FiberEUse developed innovative solutions and business models towards sustainable Circular Economy solutions for post-use composite-made products. Three strategies are presented, namely mechanical recycling of short fibers, thermal recycling of long fibers and modular car parts design for sustainable disassembly and remanufacturing. The validation of the FiberEUse approach within eight industrial demonstrators shows the potentials towards new Circular Economy value-chains for composite materials

    Cerebrovascular dysfunction in cerebral small vessel disease

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    INTRODUCTION: Cerebral small vessel disease (SVD) is the cause of a quarter of all ischaemic strokes and is postulated to have a role in up to half of all dementias. SVD pathophysiology remains unclear but cerebrovascular dysfunction may be important. If confirmed many licensed medications have mechanisms of action targeting vascular function, potentially enabling new treatments via drug repurposing. Knowledge is limited however, as most studies assessing cerebrovascular dysfunction are small, single centre, single imaging modality studies due to the complexities in measuring cerebrovascular dysfunctions in humans. This thesis describes the development and application of imaging techniques measuring several cerebrovascular dysfunctions to investigate SVD pathophysiology and trial medications that may improve small blood vessel function in SVD. METHODS: Participants with minor ischaemic strokes were recruited to a series of studies utilising advanced MRI techniques to measure cerebrovascular dysfunction. Specifically MRI scans measured the ability of different tissues in the brain to change blood flow in response to breathing carbon dioxide (cerebrovascular reactivity; CVR) and the flow and pulsatility through the cerebral arteries, venous sinuses and CSF spaces. A single centre observational study optimised and established feasibility of the techniques and tested associations of cerebrovascular dysfunctions with clinical and imaging phenotypes. Then a randomised pilot clinical trial tested two medications’ (cilostazol and isosorbide mononitrate) ability to improve CVR and pulsatility over a period of eight weeks. The techniques were then expanded to include imaging of blood brain barrier permeability and utilised in multi-centre studies investigating cerebrovascular dysfunction in both sporadic and monogenetic SVDs. RESULTS: Imaging protocols were feasible, consistently being completed with usable data in over 85% of participants. After correcting for the effects of age, sex and systolic blood pressure, lower CVR was associated with higher white matter hyperintensity volume, Fazekas score and perivascular space counts. Lower CVR was associated with higher pulsatility of blood flow in the superior sagittal sinus and lower CSF flow stroke volume at the foramen magnum. Cilostazol and isosorbide mononitrate increased CVR in white matter. The CVR, intra-cranial flow and pulsatility techniques, alongside blood brain barrier permeability and microstructural integrity imaging were successfully employed in a multi-centre observational study. A clinical trial assessing the effects of drugs targeting blood pressure variability is nearing completion. DISCUSSION: Cerebrovascular dysfunction in SVD has been confirmed and may play a more direct role in disease pathogenesis than previously established risk factors. Advanced imaging measures assessing cerebrovascular dysfunction are feasible in multi-centre studies and trials. Identifying drugs that improve cerebrovascular dysfunction using these techniques may be useful in selecting candidates for definitive clinical trials which require large sample sizes and long follow up periods to show improvement against outcomes of stroke and dementia incidence and cognitive function

    Machine Learning Approaches for Semantic Segmentation on Partly-Annotated Medical Images

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    Semantic segmentation of medical images plays a crucial role in assisting medical practitioners in providing accurate and swift diagnoses; nevertheless, deep neural networks require extensive labelled data to learn and generalise appropriately. This is a major issue in medical imagery because most of the datasets are not fully annotated. Training models with partly-annotated datasets generate plenty of predictions that belong to correct unannotated areas that are categorised as false positives; as a result, standard segmentation metrics and objective functions do not work correctly, affecting the overall performance of the models. In this thesis, the semantic segmentation of partly-annotated medical datasets is extensively and thoroughly studied. The general objective is to improve the segmentation results of medical images via innovative supervised and semi-supervised approaches. The main contributions of this work are the following. Firstly, a new metric, specifically designed for this kind of dataset, can provide a reliable score to partly-annotated datasets with positive expert feedback in their generated predictions by exploiting all the confusion matrix values except the false positives. Secondly, an innovative approach to generating better pseudo-labels when applying co-training with the disagreement selection strategy. This method expands the pixels in disagreement utilising the combined predictions as a guide. Thirdly, original attention mechanisms based on disagreement are designed for two cases: intra-model and inter-model. These attention modules leverage the disagreement between layers (from the same or different model instances) to enhance the overall learning process and generalisation of the models. Lastly, innovative deep supervision methods improve the segmentation results by training neural networks one subnetwork at a time following the order of the supervision branches. The methods are thoroughly evaluated on several histopathological datasets showing significant improvements

    Towards contrast-agnostic soft segmentation of the spinal cord

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    Spinal cord segmentation is clinically relevant and is notably used to compute spinal cord cross-sectional area (CSA) for the diagnosis and monitoring of cord compression or neurodegenerative diseases such as multiple sclerosis. While several semi and automatic methods exist, one key limitation remains: the segmentation depends on the MRI contrast, resulting in different CSA across contrasts. This is partly due to the varying appearance of the boundary between the spinal cord and the cerebrospinal fluid that depends on the sequence and acquisition parameters. This contrast-sensitive CSA adds variability in multi-center studies where protocols can vary, reducing the sensitivity to detect subtle atrophies. Moreover, existing methods enhance the CSA variability by training one model per contrast, while also producing binary masks that do not account for partial volume effects. In this work, we present a deep learning-based method that produces soft segmentations of the spinal cord. Using the Spine Generic Public Database of healthy participants (n=267\text{n}=267; contrasts=6\text{contrasts}=6), we first generated participant-wise soft ground truth (GT) by averaging the binary segmentations across all 6 contrasts. These soft GT, along with a regression-based loss function, were then used to train a UNet model for spinal cord segmentation. We evaluated our model against state-of-the-art methods and performed ablation studies involving different GT mask types, loss functions, and contrast-specific models. Our results show that using the soft average segmentations along with a regression loss function reduces CSA variability (p<0.05p < 0.05, Wilcoxon signed-rank test). The proposed spinal cord segmentation model generalizes better than the state-of-the-art contrast-specific methods amongst unseen datasets, vendors, contrasts, and pathologies (compression, lesions), while accounting for partial volume effects.Comment: Submitted to Medical Image Analysi
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