Técnicas de análise de imagens para detecção de retinopatia diabética

Orientadores: Anderson de Rezende Rocha. Jacques WainerTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Retinopatia Diabética (RD) é uma complicação a longo prazo do diabetes e a principal causa de cegueira da população ativa. Consultas regulares são necessárias para diagnosticar a retinopatia em um estágio inicial, permitindo um tratamento com o melhor prognóstico capaz de retardar ou até mesmo impedir a cegueira. Alavancados pela evolução da prevalência do diabetes e pelo maior risco que os diabéticos têm de desenvolver doenças nos olhos, diversos trabalhos com abordagens bem estabelecidas e promissoras vêm sendo desenvolvidos para triagem automática de retinopatia. Entretanto, a maior parte dos trabalhos está focada na detecção de lesões utilizando características visuais particulares de cada tipo de lesão. Além do mais, soluções artesanais para avaliação de necessidade de consulta e de identificação de estágios da retinopatia ainda dependem bastante das lesões, cujo repetitivo procedimento de detecção é complexo e inconveniente, mesmo se um esquema unificado for adotado. O estado da arte para avaliação automatizada de necessidade de consulta é composto por abordagens que propõem uma representação altamente abstrata obtida inteiramente por meio dos dados. Usualmente, estas abordagens recebem uma imagem e produzem uma resposta ¿ que pode ser resultante de um único modelo ou de uma combinação ¿ e não são facilmente explicáveis. Este trabalho objetivou melhorar a detecção de lesões e reforçar decisões relacionadas à necessidade de consulta, fazendo uso de avançadas representações de imagens em duas etapas. Nós também almejamos compor um modelo sofisticado e direcionado pelos dados para triagem de retinopatia, bem como incorporar aprendizado supervisionado de características com representação orientada por mapa de calor, resultando em uma abordagem robusta e ainda responsável para triagem automatizada. Finalmente, tivemos como objetivo a integração das soluções em dispositivos portáteis de captura de imagens de retina. Para detecção de lesões, propusemos abordagens de caracterização de imagens que possibilitem uma detecção eficaz de diferentes tipos de lesões. Nossos principais avanços estão centrados na modelagem de uma nova técnica de codificação para imagens de retina, bem como na preservação de informações no processo de pooling ou agregação das características obtidas. Decidir automaticamente pela necessidade de encaminhamento do paciente a um especialista é uma investigação ainda mais difícil e muito debatida. Nós criamos um método mais simples e robusto para decisões de necessidade de consulta, e que não depende da detecção de lesões. Também propusemos um modelo direcionado pelos dados que melhora significativamente o desempenho na tarefa de triagem da RD. O modelo produz uma resposta confiável com base em respostas (locais e globais), bem como um mapa de ativação que permite uma compreensão de importância de cada pixel para a decisão. Exploramos a metodologia de explicabilidade para criar um descritor local codificado em uma rica representação em nível médio. Os modelos direcionados pelos dados são o estado da arte para triagem de retinopatia diabética. Entretanto, mapas de ativação são essenciais para interpretar o aprendizado em termos de importância de cada pixel e para reforçar pequenas características discriminativas que têm potencial de melhorar o diagnósticoAbstract: Diabetic Retinopathy (DR) is a long-term complication of diabetes and the leading cause of blindness among working-age adults. A regular eye examination is necessary to diagnose DR at an early stage, when it can be treated with the best prognosis and the visual loss delayed or deferred. Leveraged by the continuous expansion of diabetics and by the increased risk that those people have to develop eye diseases, several works with well-established and promising approaches have been proposed for automatic screening. Therefore, most existing art focuses on lesion detection using visual characteristics specific to each type of lesion. Additionally, handcrafted solutions for referable diabetic retinopathy detection and DR stages identification still depend too much on the lesions, whose repetitive detection is complex and cumbersome to implement, even when adopting a unified detection scheme. Current art for automated referral assessment resides on highly abstract data-driven approaches. Usually, those approaches receive an image and spit the response out ¿ that might be resulting from only one model or ensembles ¿ and are not easily explainable. Hence, this work aims at enhancing lesion detection and reinforcing referral decisions with advanced handcrafted two-tiered image representations. We also intended to compose sophisticated data-driven models for referable DR detection and incorporate supervised learning of features with saliency-oriented mid-level image representations to come up with a robust yet accountable automated screening approach. Ultimately, we aimed at integrating our software solutions with simple retinal imaging devices. In the lesion detection task, we proposed advanced handcrafted image characterization approaches to detecting effectively different lesions. Our leading advances are centered on designing a novel coding technique for retinal images and preserving information in the pooling process. Automatically deciding on whether or not the patient should be referred to the ophthalmic specialist is a more difficult, and still hotly debated research aim. We designed a simple and robust method for referral decisions that does not rely upon lesion detection stages. We also proposed a novel and effective data-driven model that significantly improves the performance for DR screening. Our accountable data-driven model produces a reliable (local- and global-) response along with a heatmap/saliency map that enables pixel-based importance comprehension. We explored this methodology to create a local descriptor that is encoded into a rich mid-level representation. Data-driven methods are the state of the art for diabetic retinopathy screening. However, saliency maps are essential not only to interpret the learning in terms of pixel importance but also to reinforce small discriminative characteristics that have the potential to enhance the diagnosticDoutoradoCiência da ComputaçãoDoutor em Ciência da ComputaçãoCAPE

Automatic Classification of Bright Retinal Lesions via Deep Network Features

The diabetic retinopathy is timely diagonalized through color eye fundus images by experienced ophthalmologists, in order to recognize potential retinal features and identify early-blindness cases. In this paper, it is proposed to extract deep features from the last fully-connected layer of, four different, pre-trained convolutional neural networks. These features are then feeded into a non-linear classifier to discriminate three-class diabetic cases, i.e., normal, exudates, and drusen. Averaged across 1113 color retinal images collected from six publicly available annotated datasets, the deep features approach perform better than the classical bag-of-words approach. The proposed approaches have an average accuracy between 91.23% and 92.00% with more than 13% improvement over the traditional state of art methods.Comment: Preprint submitted to Journal of Medical Imaging | SPIE (Tue, Jul 28, 2017

Triagem robusta de melanoma : em defesa dos descritores aprimorados de nível médio

Orientadores: Eduardo Alves do Valle Junior, Sandra Eliza Fontes de AvilaDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Elétrica e de ComputaçãoResumo: Melanoma é o tipo de câncer de pele que mais leva à morte, mesmo sendo o mais curável, se detectado precocemente. Considerando que a presença de um dermatologista em tempo integral não é economicamente viável para muitas cidades e especialmente em comunidades carentes, ferramentas de auxílio ao diagnóstico para a triagem do melanoma têm sido um tópico de pesquisa ativo. Muitos trabalhos existentes são baseados no modelo Bag-of-Visual-Words (BoVW), combinando descritores de cor e textura. No entanto, o modelo BoVW vem se aprimorando e hoje existem várias extensões que levam a melhores taxas de acerto em tarefas gerais de classificação de imagens. Estes modelos avançados ainda não foram explorados para rastreio de melanoma, motivando assim este trabalho. Aqui nós apresentamos uma nova abordagem para rastreio de melanoma baseado nos descritores BossaNova, que são estado-da-arte, mostrando resultados muito promissores, com uma AUC de 93,7%. Este trabalho também propõe uma nova estratégia de pooling espacial especialmente desenhada para rastreio de melanoma. Outra contribuição dessa pesquisa é o uso inédito do BossaNova na classificação de melanoma. Isso abre oportunidades de exploração deste descritor em outros contextos médicosAbstract: Melanoma is the type of skin cancer that most leads to death, even being the most curable, if detected early. Since the presence of a full time dermatologist is not economical feasible for many small cities and specially in underserved communities, computer-aided diagnosis for melanoma screening has been a topic of active research. Much of the existing art is based on the Bag-of-Visual-Words (BoVW) model, combining color and texture descriptors. However, the BoVW model has been improving and nowadays there are several extensions that perform better classification rates in general image classification tasks. These enhanced models were not explored yet for melanoma screening, thus motivating our work. Here we present a new approach for melanoma screening, based upon the state-of-the-art BossaNova descriptors, showing very promising results for screening, reaching an AUC of up to 93.7%. This work also proposes a new spatial pooling strategy specially designed for melanoma screening. Other contribution of this research is the unprecedented use of BossaNova in melanoma classification. This opens the opportunity to explore this enhanced mid-level descriptors in other medical contextsMestradoEngenharia de ComputaçãoMestre em Engenharia Elétric

Mid-level Image Representation for Fruit Fly Identification (Diptera: Tephritidae)

Fruit flies are of huge biological and economic importance for the farming of different countries in the World, especially for Brazil. Brazil is the third largest fruit producer in the world with 44 million tons in 2016. The direct and indirect losses caused by fruit flies can exceed USD 2 billion, putting these pests as one of the biggest problems of the world agriculture. In Brazil, it is estimated that the economic losses directly related to production, the cost of pest control and in the loss of export markets, are between USD 120 and 200 million/year. The species of the genus Anastrepha are among the fruit flies economically important in the America tropics and subtropics with approximately 300 known species, of which 120 are recorded in Brazil. However, few species are economically important in Brazil and are considered pests of quarantine significance by regulatory agencies. In this sense, the development of automatic and semi-automatic tools for fruit fly species identification of the genus Anastrepha can assist the few existing specialists to reduce the insect analysis time and the economic losses related to these agricultural pests. We propose to apply mid-level image representations based on local descriptors for fruit fly identification tasks of three species of the genus Anastrepha. In our experiments, several local image descriptors based on keypoints and machine learning techniques have been studied for the target task. Furthermore, the proposed approaches have achieved excellent effectiveness results when compared with a state-of-art technique.CNPq Universal ProjectFAPESPCNPqCAPESUniv Fed Sao Paulo, Inst Sci & Technol, GIBIS Lab, Sao Jose Dos Campos, BrazilUniv Estadual Campinas, Inst Comp, RECOD Lab, Campinas, SP, BrazilUniv Sao Paulo, Luiz de Queiroz Coll Agr, Piracicaba, BrazilUniv Fed Sao Paulo, Inst Sci & Technol, GIBIS Lab, Sao Jose Dos Campos, BrazilCNPq Universal Project: 408919/2016-7Web of Scienc

Système d'apprentissage multitâche dédié à la segmentation des lésions sombres et claires de la rétine dans les images de fond d'oeil

Le travail de recherche mené dans le cadre de cette maîtrise porte sur l’exploitation de l’imagerie de la rétine à des fins de diagnostic automatique. Il se concentre sur l’image de fond d’oeil, qui donne accès à une représentation en deux dimensions et en couleur de la surface de la rétine. Ces images peuvent présenter des symptômes de maladie, sous forme de lésions ou de déformations des structures anatomiques de la rétine. L’objet de cette maîtrise est de proposer une méthodologie de segmentation simultanée de ces lésions dans l’image de fond d’oeil, regroupées en deux catégories : claires ou sombres. Réaliser cette double segmentation de façon simultanée est inédit : la vaste majorité des travaux précédents se concentrant sur un seul type de lésions. Or, du fait des contraintes de temps et de la difficulté que cela représente dans un environnement clinique, il est impossible pour un clinicien de tester la multitude d’algorithmes existants. D’autant plus que lorsqu’un patient se présente pour un examen, le clinicien n’a aucune connaissance a priori sur le type de pathologie et par conséquent sur le type d’algorithme à utiliser. Pour envisager une utilisation clinique, il est donc important de réfléchir à une solution polyvalente, rapide et aisément déployable. Parallèlement, l’apprentissage profond a démontré sa capacité à s’adapter à de nombreux problèmes de visions par ordinateur et à généraliser ses performances sur des données variées malgré des ensembles d’entraînement parfois restreints. Pour cela, de nouvelles stratégies sont régulièrement proposées, ambitionnant d’extraire toujours mieux les informations issues de la base d’entraînement. En conséquence, nous nous sommes fixés pour objectif de développer une architecture de réseaux de neurones capable de rechercher toutes les lésions dans une image de fond d’oeil. Pour répondre à cet objectif, notre méthodologie s’appuie sur une nouvelle architecture de réseaux de neurones convolutifs reposant sur une structure multitâche entraînée selon une approche hybride faisant appel à de l’apprentissage supervisé et faiblement supervisé. L’architecture se compose d’un encodeur partagé par deux décodeurs spécialisés chacun dans un type de lésions. Ainsi, les mêmes caractéristiques sont extraites par l’encodeur pour les deux décodeurs. Dans un premier temps, le réseau est entraîné avec des régions d’images et la vérité terrain correspondante indiquant les lésions (apprentissage supervisé). Dans un second temps, seul l’encodeur est ré-entraîné avec des images complètes avec une vérité terrain composé d’un simple scalaire indiquant si l’image présente des pathologies ou non, sans préciser leur position et leur type (apprentissage faiblement supervisé).----------ABSTRACT: This work focuses on automatic diagnosis on fundus images, which are a bidimensional representation of the inner structure of the eye. The aim of this master’s thesis is to discuss a solution for an automatic segmentation of the lesions that can be observed in the retina. The proposed methodology regroups those lesions in two categories: red and bright. Obtaining a simultaneous double segmentation is a novel approach; most of the previous works focus on the detection of a single type of lesions. However, due to time constraints and the tedeous nature of this work, clinicians usually can not test all the existing methods. Moreover, from a screening perspective, the clinician has no clue a priori on the nature of the pathology he deals with and thus on which algorithm to start with. Therefore, the proposed algorithm requires to be versatile, fast and easily deployable. Conforted by the recent progresses obtained with machine learning methods (and especially deep learning), we decide to develop a novel convolutional neural network able to segment both types of lesions on fundus images. To reach this goal, our methodology relies on a new multitask architecture, trained on a hybrid method combining weak and normal supervised training. The architecture relies on hard parameter sharing: two decoders (one per type of lesion) share a single encoder. Therefore, the encoder is trained on deriving an abstrast representation of the input image. Those extracted features permit a discrimination between both bright and red lesions. In other words, the encoder is trained on detecting pathological tissues from normal ones. The training is done in two steps. During the first one, the whole architecture is trained with patches, with a groundtruth at a pixel level, which is the typical way of training a segmentation network. The second step consists in weak supervision. Only the encoder is trained with full images and its task is to predict the status of the given image (pathological or healthy), without specifying anything concerning the potential lesions in it (neither location nor type). In this case, the groundtruth is a simple boolean number. This second step allows the network to see a larger number of images: indeed, this type of groundtruth is considerably easier to acquire and already available in large public databases. This step relies on the hypothesis that it is possible to use an annotation at an image level (globally) to enhance the performance at a pixel level (locally). This is an intuitive idea, as the pathological status is directly correlated with the presence of lesions

Automatic Diabetic Retinopathy detection using BossaNova representation

The biomedical community has shown a continued interest in automated detection of Diabetic Retinopathy (DR), with new imaging techniques, evolving diagnostic criteria, and advancing computing methods. Existing state of the art for detecting DR-related lesions tends to emphasize different, specific approaches for each type of lesion. However, recent research has aimed at general frameworks adaptable for large classes of lesions. In this paper, we follow this latter trend by exploring a very flexible framework, based upon two-tiered feature extraction (low-level and mid-level) from images and Support Vector Machines. The main contribution of this work is the evaluation of BossaNova, a recent and powerful mid-level image characterization technique, which we contrast with previous art based upon classical Bag of Visual Words (BoVW). The new technique using BossaNova achieves a detection performance (measured by area under the curve - AUC) of 96.4% for hard exudates, and 93.5% for red lesions using a cross-dataset training/testing protocol.4 page(s

Jornadas Nacionales de Investigación en Ciberseguridad: actas de las VIII Jornadas Nacionales de Investigación en ciberseguridad: Vigo, 21 a 23 de junio de 2023

Jornadas Nacionales de Investigación en Ciberseguridad (8ª. 2023. Vigo)atlanTTicAMTEGA: Axencia para a modernización tecnolóxica de GaliciaINCIBE: Instituto Nacional de Cibersegurida