Endoscopic image analysis of aberrant crypt foci

Tese de Mestrado Integrado. Bioengenharia. Faculdade de Engenharia. Universidade do Porto. 201

REGION-COLOR BASED AUTOMATED BLEEDING DETECTION IN CAPSULE ENDOSCOPY VIDEOS

Capsule Endoscopy (CE) is a unique technique for facilitating non-invasive and practical visualization of the entire small intestine. It has attracted a critical mass of studies for improvements. Among numerous studies being performed in capsule endoscopy, tremendous efforts are being made in the development of software algorithms to identify clinically important frames in CE videos. This thesis presents a computer-assisted method which performs automated detection of CE video-frames that contain bleeding. Specifically, a methodology is proposed to classify the frames of CE videos into bleeding and non-bleeding frames. It is a Support Vector Machine (SVM) based supervised method which classifies the frames on the basis of color features derived from image-regions. Image-regions are characterized on the basis of statistical features. With 15 available candidate features, an exhaustive feature-selection is followed to obtain the best feature subset. The best feature-subset is the combination of features that has the highest bleeding discrimination ability as determined by the three performance-metrics: accuracy, sensitivity and specificity. Also, a ground truth label annotation method is proposed in order to partially automate delineation of bleeding regions for training of the classifier. The method produced promising results with sensitivity and specificity values up to 94%. All the experiments were performed separately for RGB and HSV color spaces. Experimental results show the combination of the mean planes in red and green planes to be the best feature-subset in RGB (Red-Green-Blue) color space and the combination of the mean values of all three planes of the color space to be the best feature-subset in HSV (Hue-Saturation-Value)

Frontiers of robotic endoscopic capsules: a review

Digestive diseases are a major burden for society and healthcare systems, and with an aging population, the importance of their effective management will become critical. Healthcare systems worldwide already struggle to insure quality and affordability of healthcare delivery and this will be a significant challenge in the midterm future. Wireless capsule endoscopy (WCE), introduced in 2000 by Given Imaging Ltd., is an example of disruptive technology and represents an attractive alternative to traditional diagnostic techniques. WCE overcomes conventional endoscopy enabling inspection of the digestive system without discomfort or the need for sedation. Thus, it has the advantage of encouraging patients to undergo gastrointestinal (GI) tract examinations and of facilitating mass screening programmes. With the integration of further capabilities based on microrobotics, e.g. active locomotion and embedded therapeutic modules, WCE could become the key-technology for GI diagnosis and treatment. This review presents a research update on WCE and describes the state-of-the-art of current endoscopic devices with a focus on research-oriented robotic capsule endoscopes enabled by microsystem technologies. The article also presents a visionary perspective on WCE potential for screening, diagnostic and therapeutic endoscopic procedures

Efficient Encoding of Wireless Capsule Endoscopy Images Using Direct Compression of Colour Filter Array Images

Since its invention in 2001, wireless capsule endoscopy (WCE) has played an important role in the endoscopic examination of the gastrointestinal tract. During this period, WCE has undergone tremendous advances in technology, making it the first-line modality for diseases from bleeding to cancer in the small-bowel. Current research efforts are focused on evolving WCE to include functionality such as drug delivery, biopsy, and active locomotion. For the integration of these functionalities into WCE, two critical prerequisites are the image quality enhancement and the power consumption reduction. An efficient image compression solution is required to retain the highest image quality while reducing the transmission power. The issue is more challenging due to the fact that image sensors in WCE capture images in Bayer Colour filter array (CFA) format. Therefore, standard compression engines provide inferior compression performance. The focus of this thesis is to design an optimized image compression pipeline to encode the capsule endoscopic (CE) image efficiently in CFA format. To this end, this thesis proposes two image compression schemes. First, a lossless image compression algorithm is proposed consisting of an optimum reversible colour transformation, a low complexity prediction model, a corner clipping mechanism and a single context adaptive Golomb-Rice entropy encoder. The derivation of colour transformation that provides the best performance for a given prediction model is considered as an optimization problem. The low complexity prediction model works in raster order fashion and requires no buffer memory. The application of colour transformation yields lower inter-colour correlation and allows the efficient independent encoding of the colour components. The second compression scheme in this thesis is a lossy compression algorithm with a integer discrete cosine transformation at its core. Using the statistics obtained from a large dataset of CE image, an optimum colour transformation is derived using the principal component analysis (PCA). The transformed coefficients are quantized using optimized quantization table, which was designed with a focus to discard medically irrelevant information. A fast demosaicking algorithm is developed to reconstruct the colour image from the lossy CFA image in the decoder. Extensive experiments and comparisons with state-of-the-art lossless image compression methods establish the superiority of the proposed compression methods as simple and efficient image compression algorithm. The lossless algorithm can transmit the image in a lossless manner within the available bandwidth. On the other hand, performance evaluation of lossy compression algorithm indicates that it can deliver high quality images at low transmission power and low computation costs

Uncertainty, interpretability and dataset limitations in Deep Learning

[eng] Deep Learning (DL) has gained traction in the last years thanks to the exponential increase in compute power. New techniques and methods are published at a daily basis, and records are being set across multiple disciplines. Undeniably, DL has brought a revolution to the machine learning field and to our lives. However, not everything has been resolved and some considerations must be taken into account. For instance, obtaining uncertainty measures and bounds is still an open problem. Models should be able to capture and express the confidence they have in their decisions, and Artificial Neural Networks (ANN) are known to lack in this regard. Be it through out of distribution samples, adversarial attacks, or simply unrelated or nonsensical inputs, ANN models demonstrate an unfounded and incorrect tendency to still output high probabilities. Likewise, interpretability remains an unresolved question. Some fields not only need but rely on being able to provide human interpretations of the thought process of models. ANNs, and specially deep models trained with DL, are hard to reason about. Last but not least, there is a tendency that indicates that models are getting deeper and more complex. At the same time, to cope with the increasing number of parameters, datasets are required to be of higher quality and, usually, larger. Not all research, and even less real world applications, can keep with the increasing demands. Therefore, taking into account the previous issues, the main aim of this thesis is to provide methods and frameworks to tackle each of them. These approaches should be applicable to any suitable field and dataset, and are employed with real world datasets as proof of concept. First, we propose a method that provides interpretability with respect to the results through uncertainty measures. The model in question is capable of reasoning about the uncertainty inherent in data and leverages that information to progressively refine its outputs. In particular, the method is applied to land cover segmentation, a classification task that aims to assign a type of land to each pixel in satellite images. The dataset and application serve to prove that the final uncertainty bound enables the end-user to reason about the possible errors in the segmentation result. Second, Recurrent Neural Networks are used as a method to create robust models towards lacking datasets, both in terms of size and class balance. We apply them to two different fields, road extraction in satellite images and Wireless Capsule Endoscopy (WCE). The former demonstrates that contextual information in the temporal axis of data can be used to create models that achieve comparable results to state-of-the-art while being less complex. The latter, in turn, proves that contextual information for polyp detection can be crucial to obtain models that generalize better and obtain higher performance. Last, we propose two methods to leverage unlabeled data in the model creation process. Often datasets are easier to obtain than to label, which results in many wasted opportunities with traditional classification approaches. Our approaches based on self-supervised learning result in a novel contrastive loss that is capable of extracting meaningful information out of pseudo-labeled data. Applying both methods to WCE data proves that the extracted inherent knowledge creates models that perform better in extremely unbalanced datasets and with lack of data. To summarize, this thesis demonstrates potential solutions to obtain uncertainty bounds, provide reasonable explanations of the outputs, and to combat lack of data or unbalanced datasets. Overall, the presented methods have a positive impact on the DL field and could have a real and tangible effect for the society.[cat] És innegable que el Deep Learning ha causat una revolució en molts aspectes no solament de l’aprenentatge automàtic però també de les nostres vides diàries. Tot i així, encara queden aspectes a millorar. Les xarxes neuronals tenen problemes per estimar la seva confiança en les prediccions, i sovint reporten probabilitats altes en casos que no tenen relació amb el model o que directament no tenen sentit. De la mateixa forma, interpretar els resultats d’un model profund i complex resulta una tasca extremadament complicada. Aquests mateixos models, cada cop amb més paràmetres i més potents, requereixen també de dades més ben etiquetades i més completes. Tenint en compte aquestes limitacions, l’objectiu principal és el de buscar mètodes i algoritmes per trobar-ne solució. Primerament, es proposa la creació d’un mètode capaç d’obtenir incertesa en imatges satèl·lit i d’utilitzar-la per crear models més robustos i resultats interpretables. En segon lloc, s’utilitzen Recurrent Neural Networks (RNN) per combatre la falta de dades mitjançant l’obtenció d’informació contextual de dades temporals. Aquestes s’apliquen per l’extracció de carreteres d’imatges satèl·lit i per la classificació de pòlips en imatges obtingudes amb Wireless Capsule Endoscopy (WCE). Finalment, es plantegen dos mètodes per tractar amb la falta de dades etiquetades i desbalancejos en les classes amb l’ús de Self-supervised Learning (SSL). Seqüències no etiquetades d’imatges d’intestins s’incorporen en el models en una fase prèvia a la classificació tradicional. Aquesta tesi demostra que les solucions proposades per obtenir mesures d’incertesa són efectives per donar explicacions raonables i interpretables sobre els resultats. Igualment, es prova que el context en dades de caràcter temporal, obtingut amb RNNs, serveix per obtenir models més simples que poden arribar a solucionar els problemes derivats de la falta de dades. Per últim, es mostra que SSL serveix per combatre de forma efectiva els problemes de generalització degut a dades no balancejades en diversos dominis de WCE. Concloem que aquesta tesi presenta mètodes amb un impacte real en diversos aspectes de DL a la vegada que demostra la capacitat de tenir un impacte positiu en la societat

Anatomical Classification of the Gastrointestinal Tract Using Ensemble Transfer Learning

Endoscopy is a procedure used to visualize disorders of the gastrointestinal (GI) lumen. GI disorders can occur without symptoms, which is why gastroenterologists often recommend routine examinations of the GI tract. It allows a doctor to directly visualize the inside of the GI tract and identify the cause of symptoms, reducing the need for exploratory surgery or other invasive procedures. It can also detect the early stages of GI disorders, such as cancer, enabling prompt treatment that can improve outcomes. Endoscopic examinations generate significant numbers of GI images. Because of this vast amount of endoscopic image data, relying solely on human interpretation can be problematic. Artificial intelligence is gaining popularity in clinical medicine. Assist in medical image analysis and early detection of diseases, help with personalized treatment planning by analyzing a patient’s medical history and genomic data, and be used by surgical robots to improve precision and reduce invasiveness. It enables automated diagnosis, provides physicians with assistance, and may improve performance. One of the significant challenges is defining the specific anatomic locations of GI tract abnormalities. Clinicians can then determine appropriate treatment options, reducing the need for repetitive endoscopy. Due to the difficulty of collecting annotated data, very limited research has been conducted on the localization of anatomical locations by classification of endoscopy images. In this study, we present a classification of GI tract anatomical localization based on transfer learning and ensemble learning. Our approach involves the use of an autoencoder and the Xception model. The autoencoder was initially trained on thousands of unlabeled images, and the encoder then separated and used as a feature extractor. The Xception model was also used as a second model to extract features from the input images. The extracted feature vectors were then concatenated and fed into a Convolutional Neural Network for classification. This combination of models provides a powerful and versatile solution for image classification. By using the encoder as a feature extractor that can transfer the learned knowledge, it is possible to improve learning by allowing the model to focus on more relevant and useful data, which is extremely valuable when there are not enough appropriately labelled data. On the other hand, the Xception model provides additional feature extraction capabilities. Sometimes, one classifier is not enough in machine learning, as it depends on the problem we are trying to solve and the quality and quantity of data available. With ensemble learning, multiple learning networks can work together to create a stronger classifier. The final classification results are obtained by combining the information from both models through the CNN model. This approach demonstrates the potential for combining multiple models to improve the accuracy of image classification tasks in the medical domain. The HyperKvasir dataset is the main dataset used in this study. It contains 4,104 labelled and 99,417 unlabeled images taken at six different locations in the GI tract, including the cecum, ileum, pylorus, rectum, stomach, and Z line. After dataset preprocessing, which includes noise deduction and similarity removal, 871 labelled images remained for the purpose of this study. Our method was more accurate than state-of-the-art studies and had a higher F1 score while categorizing the input images into six different anatomical locations with less than a thousand labelled images. According to the results, feature extraction and ensemble learning increase accuracy by 5%, and a comparison with existing methods using the same dataset indicate improved performance and reduced cross entropy loss. The proposed method can therefore be used in the classification of endoscopy images

Deep neural networks in the cloud: Review, applications, challenges and research directions

Deep neural networks (DNNs) are currently being deployed as machine learning technology in a wide range of important real-world applications. DNNs consist of a huge number of parameters that require millions of floating-point operations (FLOPs) to be executed both in learning and prediction modes. A more effective method is to implement DNNs in a cloud computing system equipped with centralized servers and data storage sub-systems with high-speed and high-performance computing capabilities. This paper presents an up-to-date survey on current state-of-the-art deployed DNNs for cloud computing. Various DNN complexities associated with different architectures are presented and discussed alongside the necessities of using cloud computing. We also present an extensive overview of different cloud computing platforms for the deployment of DNNs and discuss them in detail. Moreover, DNN applications already deployed in cloud computing systems are reviewed to demonstrate the advantages of using cloud computing for DNNs. The paper emphasizes the challenges of deploying DNNs in cloud computing systems and provides guidance on enhancing current and new deployments.The EGIA project (KK-2022/00119The Consolidated Research Group MATHMODE (IT1456-22

Advances in automated tongue diagnosis techniques

This paper reviews the recent advances in a significant constituent of traditional oriental medicinal technology, called tongue diagnosis. Tongue diagnosis can be an effective, noninvasive method to perform an auxiliary diagnosis any time anywhere, which can support the global need in the primary healthcare system. This work explores the literature to evaluate the works done on the various aspects of computerized tongue diagnosis, namely preprocessing, tongue detection, segmentation, feature extraction, tongue analysis, especially in traditional Chinese medicine (TCM). In spite of huge volume of work done on automatic tongue diagnosis (ATD), there is a lack of adequate survey, especially to combine it with the current diagnosis trends. This paper studies the merits, capabilities, and associated research gaps in current works on ATD systems. After exploring the algorithms used in tongue diagnosis, the current trend and global requirements in health domain motivates us to propose a conceptual framework for the automated tongue diagnostic system on mobile enabled platform. This framework will be able to connect tongue diagnosis with the future point-of-care health system

Deep Learning-based Solutions to Improve Diagnosis in Wireless Capsule Endoscopy

[eng] Deep Learning (DL) models have gained extensive attention due to their remarkable performance in a wide range of real-world applications, particularly in computer vision. This achievement, combined with the increase in available medical records, has made it possible to open up new opportunities for analyzing and interpreting healthcare data. This symbiotic relationship can enhance the diagnostic process by identifying abnormalities, patterns, and trends, resulting in more precise, personalized, and effective healthcare for patients. Wireless Capsule Endoscopy (WCE) is a non-invasive medical imaging technique used to visualize the entire Gastrointestinal (GI) tract. Up to this moment, physicians meticulously review the captured frames to identify pathologies and diagnose patients. This manual process is time- consuming and prone to errors due to the challenges of interpreting the complex nature of WCE procedures. Thus, it demands a high level of attention, expertise, and experience. To overcome these drawbacks, shorten the screening process, and improve the diagnosis, efficient and accurate DL methods are required. This thesis proposes DL solutions to the following problems encountered in the analysis of WCE studies: pathology detection, anatomical landmark identification, and Out-of-Distribution (OOD) sample handling. These solutions aim to achieve robust systems that minimize the duration of the video analysis and reduce the number of undetected lesions. Throughout their development, several DL drawbacks have appeared, including small and imbalanced datasets. These limitations have also been addressed, ensuring that they do not hinder the generalization of neural networks, leading to suboptimal performance and overfitting. To address the previous WCE problems and overcome the DL challenges, the proposed systems adopt various strategies that utilize the power advantage of Triplet Loss (TL) and Self-Supervised Learning (SSL) techniques. Mainly, TL has been used to improve the generalization of the models, while SSL methods have been employed to leverage the unlabeled data to obtain useful representations. The presented methods achieve State-of-the-art results in the aforementioned medical problems and contribute to the ongoing research to improve the diagnostic of WCE studies.[cat] Els models d’aprenentatge profund (AP) han acaparat molta atenció a causa del seu rendiment en una àmplia gamma d'aplicacions del món real, especialment en visió per ordinador. Aquest fet, combinat amb l'increment de registres mèdics disponibles, ha permès obrir noves oportunitats per analitzar i interpretar les dades sanitàries. Aquesta relació simbiòtica pot millorar el procés de diagnòstic identificant anomalies, patrons i tendències, amb la conseqüent obtenció de diagnòstics sanitaris més precisos, personalitzats i eficients per als pacients. La Capsula endoscòpica (WCE) és una tècnica d'imatge mèdica no invasiva utilitzada per visualitzar tot el tracte gastrointestinal (GI). Fins ara, els metges revisen minuciosament els fotogrames capturats per identificar patologies i diagnosticar pacients. Aquest procés manual requereix temps i és propens a errors. Per tant, exigeix un alt nivell d'atenció, experiència i especialització. Per superar aquests inconvenients, reduir la durada del procés de detecció i millorar el diagnòstic, es requereixen mètodes eficients i precisos d’AP. Aquesta tesi proposa solucions que utilitzen AP per als següents problemes trobats en l'anàlisi dels estudis de WCE: detecció de patologies, identificació de punts de referència anatòmics i gestió de mostres que pertanyen fora del domini. Aquestes solucions tenen com a objectiu aconseguir sistemes robustos que minimitzin la durada de l'anàlisi del vídeo i redueixin el nombre de lesions no detectades. Durant el seu desenvolupament, han sorgit diversos inconvenients relacionats amb l’AP, com ara conjunts de dades petits i desequilibrats. Aquestes limitacions també s'han abordat per assegurar que no obstaculitzin la generalització de les xarxes neuronals, evitant un rendiment subòptim. Per abordar els problemes anteriors de WCE i superar els reptes d’AP, els sistemes proposats adopten diverses estratègies que aprofiten l'avantatge de la Triplet Loss (TL) i les tècniques d’auto-aprenentatge. Principalment, s'ha utilitzat TL per millorar la generalització dels models, mentre que els mètodes d’autoaprenentatge s'han emprat per aprofitar les dades sense etiquetar i obtenir representacions útils. Els mètodes presentats aconsegueixen bons resultats en els problemes mèdics esmentats i contribueixen a la investigació en curs per millorar el diagnòstic dels estudis de WCE