Fully-Automated Analysis of Body Composition from CT in Cancer Patients Using Convolutional Neural Networks

The amounts of muscle and fat in a person's body, known as body composition, are correlated with cancer risks, cancer survival, and cardiovascular risk. The current gold standard for measuring body composition requires time-consuming manual segmentation of CT images by an expert reader. In this work, we describe a two-step process to fully automate the analysis of CT body composition using a DenseNet to select the CT slice and U-Net to perform segmentation. We train and test our methods on independent cohorts. Our results show Dice scores (0.95-0.98) and correlation coefficients (R=0.99) that are favorable compared to human readers. These results suggest that fully automated body composition analysis is feasible, which could enable both clinical use and large-scale population studies

Deep-Learning Assessed Muscular Hypodensity Independently Predicts Mortality in DLBCL Patients Younger Than 60 Years.

[en] BACKGROUND: Muscle depletion (MD) assessed by computed tomography (CT) has been shown to be a predictive marker in solid tumors, but has not been assessed in non-Hodgkin's lymphomas. Despite software improvements, MD measurement remains highly time-consuming and cannot be used in clinical practice. METHODS: This study reports the development of a Deep-Learning automatic segmentation algorithm (DLASA) to measure MD, and investigate its predictive value in a cohort of 656 diffuse large B cell lymphoma (DLBCL) patients included in the GAINED phase III prospective trial (NCT01659099). RESULTS: After training on a series of 190 patients, the DLASA achieved a Dice coefficient of 0.97 ± 0.03. In the cohort, the median skeletal muscle index was 50.2 cm2/m2 and median muscle attenuation (MA) was 36.1 Hounsfield units (HU). No impact of sarcopenia was found on either progression free survival (PFS) or overall survival (OS). Muscular hypodensity, defined as MA below the tenth percentile according to sex, was associated with a lower OS and PFS, respectively (HR = 2.80 (95% CI 1.58-4.95), p < 0.001, and HR = 2.22 (95% CI 1.43-3.45), p < 0.001). Muscular hypodensity appears to be an independent risk factor for mortality in DLBCL and because of DLASA can be estimated in routine practice

DEEP-AD: The deep learning model for diagnostic classification and prognostic prediction of alzheimer's disease

In terms of context, the aim of this dissertation is to aid neuroradiologists in their clinical judgment regarding the early detection of AD by using DL. To that aim, the system design research methodology is suggested in this dissertation for achieving three goals. The first goal is to investigate the DL models that have performed well at identifying patterns associated with AD, as well as the accuracy so far attained, limitations, and gaps. A systematic review of the literature (SLR) revealed a shortage of empirical studies on the early identification of AD through DL. In this regard, thirteen empirical studies were identified and examined. We concluded that three-dimensional (3D) DL models have been generated far less often and that their performance is also inadequate to qualify them for clinical trials. The second goal is to provide the neuroradiologist with the computer-interpretable information they need to analyze neuroimaging biomarkers. Given this context, the next step in this dissertation is to find the optimum DL model to analyze neuroimaging biomarkers. It has been achieved in two steps. In the first step, eight state-of-the-art DL models have been implemented by training from scratch using end-to-end learning (E2EL) for two binary classification tasks (AD vs. CN and AD vs. stable MCI) and compared by utilizing MRI scans from the publicly accessible datasets of neuroimaging biomarkers. Comparative analysis is carried out by utilizing efficiency-effects graphs, comprehensive indicators, and ranking mechanisms. For the training of the AD vs. sMCI task, the EfficientNet-B0 model gets the highest value for the comprehensive indicator and has the fewest parameters. DenseNet264 performed better than the others in terms of evaluation matrices, but since it has the most parameters, it costs more to train. For the AD vs. CN task by DenseNet264, we achieved 100% accuracy for training and 99.56% accuracy for testing. However, the classification accuracy was still only 82.5% for the AD vs. sMCI task. In the second step, fusion of transfer learning (TL) with E2EL is applied to train the EfficientNet-B0 for the AD vs. sMCI task, which achieved 95.29% accuracy for training and 93.10% accuracy for testing. Additionally, we have also implemented EfficientNet-B0 for the multiclass AD vs. CN vs. sMCI classification task with E2EL to be used in ensemble of models and achieved 85.66% training accuracy and 87.38% testing accuracy. To evaluate the model&#8217;s robustness, neuroradiologists must validate the implemented model. As a result, the third goal of this dissertation is to create a tool that neuroradiologists may use at their convenience. To achieve this objective, this dissertation proposes a web-based application (DEEP-AD) that has been created by making an ensemble of Efficient-Net B0 and DenseNet 264 (based on the contribution of goal 2). The accuracy of a DEEP-AD prototype has undergone repeated evaluation and improvement. First, we validated 41 subjects of Spanish MRI datasets (acquired from HT Medica, Madrid, Spain), achieving an accuracy of 82.90%, which was later verified by neuroradiologists. The results of these evaluation studies showed the accomplishment of such goals and relevant directions for future research in applied DL for the early detection of AD in clinical settings.En términos de contexto, el objetivo de esta tesis es ayudar a los neurorradiólogos en su juicio clínico sobre la detección precoz de la AD mediante el uso de DL. Para ello, en esta tesis se propone la metodología de investigación de diseño de sistemas para lograr tres objetivos. El segundo objetivo es proporcionar al neurorradiólogo la información interpretable por ordenador que necesita para analizar los biomarcadores de neuroimagen. Dado este contexto, el siguiente paso en esta tesis es encontrar el modelo DL óptimo para analizar biomarcadores de neuroimagen. Esto se ha logrado en dos pasos. En el primer paso, se han implementado ocho modelos DL de última generación mediante entrenamiento desde cero utilizando aprendizaje de extremo a extremo (E2EL) para dos tareas de clasificación binarias (AD vs. CN y AD vs. MCI estable) y se han comparado utilizando escaneos MRI de los conjuntos de datos de biomarcadores de neuroimagen de acceso público. El análisis comparativo se lleva a cabo utilizando gráficos de efecto-eficacia, indicadores exhaustivos y mecanismos de clasificación. Para el entrenamiento de la tarea AD vs. sMCI, el modelo EfficientNet-B0 obtiene el valor más alto para el indicador exhaustivo y tiene el menor número de parámetros. DenseNet264 obtuvo mejores resultados que los demás en términos de matrices de evaluación, pero al ser el que tiene más parámetros, su entrenamiento es más costoso. Para la tarea AD vs. CN de DenseNet264, conseguimos una accuracy del 100% en el entrenamiento y del 99,56% en las pruebas. Sin embargo, la accuracy de la clasificación fue sólo del 82,5% para la tarea AD vs. sMCI. En el segundo paso, se aplica la fusión del aprendizaje por transferencia (TL) con E2EL para entrenar la EfficientNet-B0 para la tarea AD vs. sMCI, que alcanzó una accuracy del 95,29% en el entrenamiento y del 93,10% en las pruebas. Además, también hemos implementado EfficientNet-B0 para la tarea de clasificación multiclase AD vs. CN vs. sMCI con E2EL para su uso en conjuntos de modelos y hemos obtenido una accuracy de entrenamiento del 85,66% y una precisión de prueba del 87,38%. Para evaluar la solidez del modelo, los neurorradiólogos deben validar el modelo implementado. Como resultado, el tercer objetivo de esta disertación es crear una herramienta que los neurorradiólogos puedan utilizar a su conveniencia. Para lograr este objetivo, esta disertación propone una aplicación basada en web (DEEP-AD) que ha sido creada haciendo un ensemble de Efficient-Net B0 y DenseNet 264 (basado en la contribución del objetivo 2). La accuracy del prototipo DEEP-AD ha sido sometida a repetidas evaluaciones y mejoras. En primer lugar, validamos 41 sujetos de conjuntos de datos de MRI españoles (adquiridos de HT Medica, Madrid, España), logrando una accuracy del 82,90%, que posteriormente fue verificada por neurorradiólogos. Los resultados de estos estudios de evaluación mostraron el cumplimiento de dichos objetivos y las direcciones relevantes para futuras investigaciones en DL, aplicada en la detección precoz de la AD en entornos clínicos.Escuela de DoctoradoDoctorado en Tecnologías de la Información y las Telecomunicacione

Lung disease classification using GLCM and deep features from different deep learning architectures with principal component analysis

Lung disease classification is an important stage in implementing a Computer Aided Diagnosis (CADx) system. CADx systems can aid doctors as a second rater to increase diagnostic accuracy for medical applications. It has also potential to reduce waiting time and increasing patient throughput when hospitals high workload. Conventional lung classification systems utilize textural features. However textural features may not be enough to describe properties of an image. Deep features are an emerging source of features that can combat the weaknesses of textural features. The goal of this study is to propose a lung disease classification framework using deep features from five different deep networks and comparing its results with the conventional Gray-level Co-occurrence Matrix (GLCM). This study used a dataset of 81 diseased and 15 normal patients with five levels of High Resolution Computed Tomography (HRCT) slices. A comparison of five different deep learning networks namely, Alexnet, VGG16, VGG19, Res50 and Res101, with textural features from Gray-level Co-occurrence Matrix (GLCM) was performed. This study used a K-fold validation protocol with K = 2, 3, 5 and 10. This study also compared using five classifiers; Decision Tree, Support Vector Machine, Linear Discriminant Analysis, Regression and k-nearest neighbor (k-NN) classifiers. The usage of PCA increased the classification accuracy from 92.01% to 97.40% when using k-NN classifier. This was achieved with only using 14 features instead of the initial 1000 features. Using SVM classifier, a maximum accuracy of 100% was achieved when using all five of the deep learning features. Thus deep features show a promising application for classifying diseased and normal lungs

Automatic analysis of transperineal ultrasound images

This thesis focuses on the automatic image analysis of transperineal ultrasound (TPUS) data, which is used to investigate female pelvic floor problems. These problems have a high prevalence, but the understanding of pelvic floor (dys-)function is limited. TPUS analysis of the pelvic floor is done manually, which is time-consuming and observer dependent. This hinders both the research into interpretation of TPUS data and its clinical use. To overcome these problems we use automatic image analysis. Currently, one of the main methods used, to analyse the TPUS is manually selecting and segmenting the slice of minimal hiatal dimensions (SMHD). In the first chapter of this thesis we show that reliable automatic segmentation of the urogenital hiatus and the puborectalis muscle in the SMHD can be successfully implemented, using deep learning. Furthermore, we show that this can also be used to successfully automate the process of selecting and segmenting the SMHD. 4D TPUS is available in the clinical practice but by the aforementioned method only provides 1D and 2D parameters. Therefore, information stored within TPUS about the volume appearance of the pelvic floor muscles and muscle functionality is not analyzed. In the third chapter of this thesis we propose a reproducible manual 3D segmentation protocol of the puborectalis muscle. The resulting manual segmentations can be used to train active appearance models and convolutional neural networks, these algorithms can be used for reliable automatic 3D segmentation. In the fifth chapter of we show that on this data it is possible to identify all subdivisions of the main pelvic floor muscle group, the levator ani muscles, on new TPUS data. In the last chapter we apply unsupervised deep learning to our data and show that this can be used for classification of the TPUS data. The segmentation results presented in this thesis are an important step to reduce the TPUS analysis time and will therefore ease the study of large populations and clinical TPUS analysis. The 3D identification and segmentation of the levator ani muscle subdivisions helps to identify if they are still intact. This is an important step to better informed clinical decision-making