87 research outputs found
Sparse feature learning for image analysis in segmentation, classification, and disease diagnosis.
The success of machine learning algorithms generally depends on intermediate data representation, called features that disentangle the hidden factors of variation in data. Moreover, machine learning models are required to be generalized, in order to reduce the specificity or bias toward the training dataset. Unsupervised feature learning is useful in taking advantage of large amount of unlabeled data, which is available to capture these variations. However, learned features are required to capture variational patterns in data space. In this dissertation, unsupervised feature learning with sparsity is investigated for sparse and local feature extraction with application to lung segmentation, interpretable deep models, and Alzheimer\u27s disease classification. Nonnegative Matrix Factorization, Autoencoder and 3D Convolutional Autoencoder are used as architectures or models for unsupervised feature learning. They are investigated along with nonnegativity, sparsity and part-based representation constraints for generalized and transferable feature extraction
Extracting Lungs from CT Images using Fully Convolutional Networks
Analysis of cancer and other pathological diseases, like the interstitial
lung diseases (ILDs), is usually possible through Computed Tomography (CT)
scans. To aid this, a preprocessing step of segmentation is performed to reduce
the area to be analyzed, segmenting the lungs and removing unimportant regions.
Generally, complex methods are developed to extract the lung region, also using
hand-made feature extractors to enhance segmentation. With the popularity of
deep learning techniques and its automated feature learning, we propose a lung
segmentation approach using fully convolutional networks (FCNs) combined with
fully connected conditional random fields (CRF), employed in many
state-of-the-art segmentation works. Aiming to develop a generalized approach,
the publicly available datasets from University Hospitals of Geneva (HUG) and
VESSEL12 challenge were studied, including many healthy and pathological CT
scans for evaluation. Experiments using the dataset individually, its trained
model on the other dataset and a combination of both datasets were employed.
Dice scores of for the HUG-ILD dataset and
for the VESSEL12 dataset were achieved, outperforming works
in the former and obtaining similar state-of-the-art results in the latter
dataset, showing the capability in using deep learning approaches.Comment: Accepted for presentation at the International Joint Conference on
Neural Networks (IJCNN) 201
A novel diffusion tensor imaging-based computer-aided diagnostic system for early diagnosis of autism.
Autism spectrum disorders (ASDs) denote a significant growing public health concern. Currently, one in 68 children has been diagnosed with ASDs in the United States, and most children are diagnosed after the age of four, despite the fact that ASDs can be identified as early as age two. The ultimate goal of this thesis is to develop a computer-aided diagnosis (CAD) system for the accurate and early diagnosis of ASDs using diffusion tensor imaging (DTI). This CAD system consists of three main steps. First, the brain tissues are segmented based on three image descriptors: a visual appearance model that has the ability to model a large dimensional feature space, a shape model that is adapted during the segmentation process using first- and second-order visual appearance features, and a spatially invariant second-order homogeneity descriptor. Secondly, discriminatory features are extracted from the segmented brains. Cortex shape variability is assessed using shape construction methods, and white matter integrity is further examined through connectivity analysis. Finally, the diagnostic capabilities of these extracted features are investigated. The accuracy of the presented CAD system has been tested on 25 infants with a high risk of developing ASDs. The preliminary diagnostic results are promising in identifying autistic from control patients
PadChest: A large chest x-ray image dataset with multi-label annotated reports
We present a labeled large-scale, high resolution chest x-ray dataset for the
automated exploration of medical images along with their associated reports.
This dataset includes more than 160,000 images obtained from 67,000 patients
that were interpreted and reported by radiologists at Hospital San Juan
Hospital (Spain) from 2009 to 2017, covering six different position views and
additional information on image acquisition and patient demography. The reports
were labeled with 174 different radiographic findings, 19 differential
diagnoses and 104 anatomic locations organized as a hierarchical taxonomy and
mapped onto standard Unified Medical Language System (UMLS) terminology. Of
these reports, 27% were manually annotated by trained physicians and the
remaining set was labeled using a supervised method based on a recurrent neural
network with attention mechanisms. The labels generated were then validated in
an independent test set achieving a 0.93 Micro-F1 score. To the best of our
knowledge, this is one of the largest public chest x-ray database suitable for
training supervised models concerning radiographs, and the first to contain
radiographic reports in Spanish. The PadChest dataset can be downloaded from
http://bimcv.cipf.es/bimcv-projects/padchest/
Algoritmos de procesado de señal basados en Non-negative Matrix Factorization aplicados a la separación, detección y clasificación de sibilancias en señales de audio respiratorias monocanal
La auscultación es el primer examen clínico que un médico lleva a cabo para evaluar el estado del sistema respiratorio, debido a que es un método no invasivo, de bajo coste, fácil de realizar y seguro para el paciente. Sin embargo, el diagnóstico que se deriva de la auscultación sigue siendo un diagnóstico subjetivo que se encuentra condicionado a la habilidad, experiencia y entrenamiento de cada médico en la escucha e interpretación de las señales de audio respiratorias. En consecuencia, se producen un alto porcentaje de diagnósticos erróneos que ponen en riesgo la salud de los pacientes e incrementan el coste asociado a los centros de salud. Esta Tesis propone nuevos métodos basados en Non-negative Matrix Factorization aplicados a la separación, detección y clasificación de sonidos sibilantes para proporcionar una vía de información complementaria al médico que ayude a mejorar la fiabilidad del diagnóstico emitido por el especialista. Auscultation is the first clinical examination that a physician performs to evaluate the condition of the respiratory system, because it is a non-invasive, low-cost, easy-to-perform and safe method for the patient. However, the diagnosis derived from auscultation remains a subjective diagnosis that is conditioned by the ability, experience and training of each physician in the listening and interpretation of respiratory audio signals. As a result, a high percentage of misdiagnoses are produced that endanger the health of patients and increase the cost associated with health centres. This Thesis proposes new methods based on Non-negative Matrix Factorization applied to separation, detection and classification of wheezing sounds in order to provide a complementary information pathway to the physician that helps to improve the reliability of the diagnosis made by the doctor.Tesis Univ. Jaén. Departamento INGENIERÍA DE TELECOMUNICACIÓ
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Synergizing human-machine intelligence: Visualizing, labeling, and mining the electronic health record
We live in a world where data surround us in every aspect of our lives. The key challenge for humans and machines is how we can make better use of such data. Imagine what would happen if you were to have intelligent machines that could give you insight into the data. Insight that will enable you to better 1) reason about, 2) learn, and 3) understand the underlying phenomena that produced the data. The possibilities of combined human-machine intelligence are endless and will impact our lives in ways we can not even imagine today.
Synergistic human-machine intelligence aims to facilitate the analytical reasoning and inference process of humans by creating machines that maximize a human's ability to 1) reason about, 2) learn, and 3) understand large, complex, and heterogeneous data. Combined human-machine intelligence is a powerful symbiosis of mutual benefit, in which we depend on the computational capabilities of the machine for the tasks we are not good at, and the machine requires human intervention for the tasks it performs poorly on.
This relationship provides a compelling alternative to either approach in isolation for solving today's and tomorrow's arising data challenges. In his regard, this dissertation proposes a diverse analytical framework that leverages synergistic human-machine intelligence to maximize a human's ability to better 1) reason about, 2) learn, and 3) understand different biomedical imaging and healthcare data present in the patient's electronic health record (EHR). Correspondingly, we approach the data analyses problem from the 1) visualization, 2) labeling, and 3) mining perspective and demonstrate the efficacy of our analytics on specific application scenarios and various data domains.
In the first part of this dissertation we explore the question how we can build intelligent imaging analytics that are commensurate with human capabilities and constraints, specifically for optimizing data visualization and automated labeling workflows. Our journey starts with heuristic rule-based analytical models that are derived from task-specific human knowledge. From this experience, we move on to data-driven analytics, where we adapt and combine the intelligence of the model based on prior information provided by the human and synthetic knowledge learned from partial data observations. Within this realm, we propose a novel Bayesian transductive Markov random field model that requires minimal human intervention and is able to cope with scarce label information to learn and infer object shapes in complex spatial, multimodal, spatio-temporal, and longitudinal data. We then study the question how machines can learn discriminative object representations from dense human provided label information by investigating learning and inference mechanisms that make use of deep learning architectures. The developed analytics can aid visualization and labeling tasks, which enables the interpretation and quantification of clinically relevant image information.
The second part explores the question how we can build data-driven analytics for exploratory analysis in longitudinal event data that are commensurate with human capabilities and constraints. We propose human-intuitive analytics that enable the representation and discovery of interpretable event patterns to ease knowledge absorption and comprehension of the employed analytics model and the underlying data. We propose a novel doubly-constrained convolutional sparse-coding framework that learns interpretable and shift-invariant latent temporal event patterns. We apply the model to mine complex event data in EHRs. By mapping the event space to heterogeneous patient encounters in the EHR we explore the linkage between healthcare resource utilization (HRU) in relation to disease severity. This linkage may help to better understand how disease specific co-morbidities and their clinical attributes incur different HRU patterns. Such insight helps to characterize the patient's care history, which then enables the comparison against clinical practice guidelines, the discovery of prevailing practices based on common HRU group patterns, and the identification of outliers that might indicate poor patient management
Biomedical Sensing and Imaging
This book mainly deals with recent advances in biomedical sensing and imaging. More recently, wearable/smart biosensors and devices, which facilitate diagnostics in a non-clinical setting, have become a hot topic. Combined with machine learning and artificial intelligence, they could revolutionize the biomedical diagnostic field. The aim of this book is to provide a research forum in biomedical sensing and imaging and extend the scientific frontier of this very important and significant biomedical endeavor
Contributions to Ensemble Classifiers with Image Analysis Applications
134 p.Ésta tesis tiene dos aspectos fundamentales, por un lado, la propuesta denuevas arquitecturas de clasificadores y, por otro, su aplicación a el análisis deimagen.Desde el punto de vista de proponer nuevas arquitecturas de clasificaciónla tesis tiene dos contribucciones principales. En primer lugar la propuestade un innovador ensemble de clasificadores basado en arquitecturas aleatorias,como pueden ser las Extreme Learning Machines (ELM), Random Forest (RF) yRotation Forest, llamado Hybrid Extreme Rotation Forest (HERF) y su mejoraAnticipative HERF (AHERF) que conlleva una selección del modelo basada enel rendimiento de predicción para cada conjunto de datos específico. Ademásde lo anterior, proveemos una prueba formal tanto del AHERF, como de laconvergencia de los ensembles de regresores ELMs que mejoran la usabilidad yreproducibilidad de los resultados.En la vertiente de aplicación hemos estado trabajando con dos tipos de imágenes:imágenes hiperespectrales de remote sensing, e imágenes médicas tanto depatologías específicas de venas de sangre como de imágenes para el diagnósticode Alzheimer. En todos los casos los ensembles de clasificadores han sido la herramientacomún además de estrategias especificas de aprendizaje activo basadasen dichos ensembles de clasificadores. En el caso concreto de la segmentaciónde vasos sanguíneos nos hemos enfrentado con problemas, uno relacionado conlos trombos del Aneurismas de Aorta Abdominal en imágenes 3D de tomografíacomputerizada y el otro la segmentación de venas sangineas en la retina. Losresultados en ambos casos en términos de rendimiento en clasificación y ahorrode tiempo en la segmentación humana nos permiten recomendar esos enfoquespara la práctica clínica.Chapter 1Background y contribuccionesDado el espacio limitado para realizar el resumen de la tesis hemos decididoincluir un resumen general con los puntos más importantes, una pequeña introducciónque pudiera servir como background para entender los conceptos básicosde cada uno de los temas que hemos tocado y un listado con las contribuccionesmás importantes.1.1 Ensembles de clasificadoresLa idea de los ensembles de clasificadores fue propuesta por Hansen y Salamon[4] en el contexto del aprendizaje de las redes neuronales artificiales. Sutrabajo mostró que un ensemble de redes neuronales con un esquema de consensogrupal podía mejorar el resultado obtenido con una única red neuronal.Los ensembles de clasificadores buscan obtener unos resultados de clasificaciónmejores combinando clasificadores débiles y diversos [8, 9]. La propuesta inicialde ensemble contenía una colección homogena de clasificadores individuales. ElRandom Forest es un claro ejemplo de ello, puesto que combina la salida de unacolección de árboles de decisión realizando una votación por mayoría [2, 3], yse construye utilizando una técnica de remuestreo sobre el conjunto de datos ycon selección aleatoria de variables.2CHAPTER 1. BACKGROUND Y CONTRIBUCCIONES 31.2 Aprendizaje activoLa construcción de un clasificador supervisado consiste en el aprendizaje de unaasignación de funciones de datos en un conjunto de clases dado un conjunto deentrenamiento etiquetado. En muchas situaciones de la vida real la obtenciónde las etiquetas del conjunto de entrenamiento es costosa, lenta y propensa aerrores. Esto hace que la construcción del conjunto de entrenamiento sea unatarea engorrosa y requiera un análisis manual exaustivo de la imagen. Esto se realizanormalmente mediante una inspección visual de las imágenes y realizandoun etiquetado píxel a píxel. En consecuencia el conjunto de entrenamiento esaltamente redundante y hace que la fase de entrenamiento del modelo sea muylenta. Además los píxeles ruidosos pueden interferir en las estadísticas de cadaclase lo que puede dar lugar a errores de clasificación y/o overfitting. Por tantoes deseable que un conjunto de entrenamiento sea construido de una manera inteligente,lo que significa que debe representar correctamente los límites de clasemediante el muestreo de píxeles discriminantes. La generalización es la habilidadde etiquetar correctamente datos que no se han visto previamente y quepor tanto son nuevos para el modelo. El aprendizaje activo intenta aprovecharla interacción con un usuario para proporcionar las etiquetas de las muestrasdel conjunto de entrenamiento con el objetivo de obtener la clasificación másprecisa utilizando el conjunto de entrenamiento más pequeño posible.1.3 AlzheimerLa enfermedad de Alzheimer es una de las causas más importantes de discapacidaden personas mayores. Dado el envejecimiento poblacional que es una realidaden muchos países, con el aumento de la esperanza de vida y con el aumentodel número de personas mayores, el número de pacientes con demencia aumentarátambién. Debido a la importancia socioeconómica de la enfermedad enlos países occidentales existe un fuerte esfuerzo internacional focalizado en laenfermedad del Alzheimer. En las etapas tempranas de la enfermedad la atrofiacerebral suele ser sutil y está espacialmente distribuida por diferentes regionescerebrales que incluyen la corteza entorrinal, el hipocampo, las estructuras temporaleslateral e inferior, así como el cíngulo anterior y posterior. Son muchoslos esfuerzos de diseño de algoritmos computacionales tratando de encontrarbiomarcadores de imagen que puedan ser utilizados para el diagnóstico no invasivodel Alzheimer y otras enfermedades neurodegenerativas.CHAPTER 1. BACKGROUND Y CONTRIBUCCIONES 41.4 Segmentación de vasos sanguíneosLa segmentación de los vasos sanguíneos [1, 7, 6] es una de las herramientas computacionalesesenciales para la evaluación clínica de las enfermedades vasculares.Consiste en particionar un angiograma en dos regiones que no se superponen:la región vasculares y el fondo. Basándonos en los resultados de dicha particiónse pueden extraer, modelar, manipular, medir y visualizar las superficies vasculares.Éstas estructuras son muy útiles y juegan un rol muy imporntate en lostratamientos endovasculares de las enfermedades vasculares. Las enfermedadesvasculares son una de las principales fuentes de morbilidad y mortalidad en todoel mundo.Aneurisma de Aorta Abdominal El Aneurisma de Aorta Abdominal (AAA)es una dilatación local de la Aorta que ocurre entre las arterias renal e ilíaca. Eldebilitamiento de la pared de la aorta conduce a su deformación y la generaciónde un trombo. Generalmente, un AAA se diagnostica cuando el diámetro anterioposteriormínimo de la aorta alcanza los 3 centímetros [5]. La mayoría delos aneurismas aórticos son asintomáticos y sin complicaciones. Los aneurismasque causan los síntomas tienen un mayor riesgo de ruptura. El dolor abdominalo el dolor de espalda son las dos principales características clínicas que sugiereno bien la reciente expansión o fugas. Las complicaciones son a menudo cuestiónde vida o muerte y pueden ocurrir en un corto espacio de tiempo. Por lo tanto,el reto consiste en diagnosticar lo antes posible la aparición de los síntomas.Imágenes de Retina La evaluación de imágenes del fondo del ojo es una herramientade diagnóstico de la patología vascular y no vascular. Dicha inspecciónpuede revelar hipertensión, diabetes, arteriosclerosis, enfermedades cardiovascularese ictus. Los principales retos para la segmentación de vasos retinianos son:(1) la presencia de lesiones que se pueden interpretar de forma errónea comovasos sanguíneos; (2) bajo contraste alrededor de los vasos más delgados, (3)múltiples escalas de tamaño de los vasos.1.5 ContribucionesÉsta tesis tiene dos tipos de contribuciones. Contribuciones computacionales ycontribuciones orientadas a una aplicación o prácticas.CHAPTER 1. BACKGROUND Y CONTRIBUCCIONES 5Desde un punto de vista computacional las contribuciones han sido las siguientes:¿ Un nuevo esquema de aprendizaje activo usando Random Forest y el cálculode la incertidumbre que permite una segmentación de imágenes rápida,precisa e interactiva.¿ Hybrid Extreme Rotation Forest.¿ Adaptative Hybrid Extreme Rotation Forest.¿ Métodos de aprendizaje semisupervisados espectrales-espaciales.¿ Unmixing no lineal y reconstrucción utilizando ensembles de regresoresELM.Desde un punto de vista práctico:¿ Imágenes médicas¿ Aprendizaje activo combinado con HERF para la segmentación deimágenes de tomografía computerizada.¿ Mejorar el aprendizaje activo para segmentación de imágenes de tomografíacomputerizada con información de dominio.¿ Aprendizaje activo con el clasificador bootstrapped dendritic aplicadoa segmentación de imágenes médicas.¿ Meta-ensembles de clasificadores para detección de Alzheimer conimágenes de resonancia magnética.¿ Random Forest combinado con aprendizaje activo para segmentaciónde imágenes de retina.¿ Segmentación automática de grasa subcutanea y visceral utilizandoresonancia magnética.¿ Imágenes hiperespectrales¿ Unmixing no lineal y reconstrucción utilizando ensembles de regresoresELM.¿ Métodos de aprendizaje semisupervisados espectrales-espaciales concorrección espacial usando AHERF.¿ Método semisupervisado de clasificación utilizando ensembles de ELMsy con regularización espacial
Machine learning approaches for lung cancer diagnosis.
The enormity of changes and development in the field of medical imaging technology is hard to fathom, as it does not just represent the technique and process of constructing visual representations of the body from inside for medical analysis and to reveal the internal structure of different organs under the skin, but also it provides a noninvasive way for diagnosis of various disease and suggest an efficient ways to treat them. While data surrounding all of our lives are stored and collected to be ready for analysis by data scientists, medical images are considered a rich source that could provide us with a huge amount of data, that could not be read easily by physicians and radiologists, with valuable information that could be used in smart ways to discover new knowledge from these vast quantities of data. Therefore, the design of computer-aided diagnostic (CAD) system, that can be approved for use in clinical practice that aid radiologists in diagnosis and detecting potential abnormalities, is of a great importance. This dissertation deals with the development of a CAD system for lung cancer diagnosis, which is the second most common cancer in men after prostate cancer and in women after breast cancer. Moreover, lung cancer is considered the leading cause of cancer death among both genders in USA. Recently, the number of lung cancer patients has increased dramatically worldwide and its early detection doubles a patient’s chance of survival. Histological examination through biopsies is considered the gold standard for final diagnosis of pulmonary nodules. Even though resection of pulmonary nodules is the ideal and most reliable way for diagnosis, there is still a lot of different methods often used just to eliminate the risks associated with the surgical procedure. Lung nodules are approximately spherical regions of primarily high density tissue that are visible in computed tomography (CT) images of the lung. A pulmonary nodule is the first indication to start diagnosing lung cancer. Lung nodules can be benign (normal subjects) or malignant (cancerous subjects). Large (generally defined as greater than 2 cm in diameter) malignant nodules can be easily detected with traditional CT scanning techniques. However, the diagnostic options for small indeterminate nodules are limited due to problems associated with accessing small tumors. Therefore, additional diagnostic and imaging techniques which depends on the nodules’ shape and appearance are needed. The ultimate goal of this dissertation is to develop a fast noninvasive diagnostic system that can enhance the accuracy measures of early lung cancer diagnosis based on the well-known hypotheses that malignant nodules have different shape and appearance than benign nodules, because of the high growth rate of the malignant nodules. The proposed methodologies introduces new shape and appearance features which can distinguish between benign and malignant nodules. To achieve this goal a CAD system is implemented and validated using different datasets. This CAD system uses two different types of features integrated together to be able to give a full description to the pulmonary nodule. These two types are appearance features and shape features. For the appearance features different texture appearance descriptors are developed, namely the 3D histogram of oriented gradient, 3D spherical sector isosurface histogram of oriented gradient, 3D adjusted local binary pattern, 3D resolved ambiguity local binary pattern, multi-view analytical local binary pattern, and Markov Gibbs random field. Each one of these descriptors gives a good description for the nodule texture and the level of its signal homogeneity which is a distinguishable feature between benign and malignant nodules. For the shape features multi-view peripheral sum curvature scale space, spherical harmonics expansions, and different group of fundamental geometric features are utilized to describe the nodule shape complexity. Finally, the fusion of different combinations of these features, which is based on two stages is introduced. The first stage generates a primary estimation for every descriptor. Followed by the second stage that consists of an autoencoder with a single layer augmented with a softmax classifier to provide us with the ultimate classification of the nodule. These different combinations of descriptors are combined into different frameworks that are evaluated using different datasets. The first dataset is the Lung Image Database Consortium which is a benchmark publicly available dataset for lung nodule detection and diagnosis. The second dataset is our local acquired computed tomography imaging data that has been collected from the University of Louisville hospital and the research protocol was approved by the Institutional Review Board at the University of Louisville (IRB number 10.0642). These frameworks accuracy was about 94%, which make the proposed frameworks demonstrate promise to be valuable tool for the detection of lung cancer
Quantitative PET and SPECT
Since the introduction of personalized medicine, the primary focus of imaging has moved from detection and diagnosis to tissue characterization, the determination of prognosis, prediction of treatment efficacy, and measurement of treatment response. Precision (personalized) imaging heavily relies on the use of hybrid technologies and quantitative imaging biomarkers. The growing number of promising theragnostics require accurate quantification for pre- and post-treatment dosimetry. Furthermore, quantification is required in the pharmacokinetic analysis of new tracers and drugs and in the assessment of drug resistance. Positron Emission Tomography (PET) is, by nature, a quantitative imaging tool, relating the time–activity concentration in tissues and the basic functional parameters governing the biological processes being studied. Recent innovations in single photon emission computed tomography (SPECT) reconstruction techniques have allowed for SPECT to move from relative/semi-quantitative measures to absolute quantification. The strength of PET and SPECT is that they permit whole-body molecular imaging in a noninvasive way, evaluating multiple disease sites. Furthermore, serial scanning can be performed, allowing for the measurement of functional changes over time during therapeutic interventions. This Special Issue highlights the hot topics on quantitative PET and SPECT
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