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

Time-based self-supervised learning for Wireless Capsule Endoscopy

State-of-the-art machine learning models, and especially deep learning ones, are significantly data-hungry; they require vast amounts of manually labeled samples to function correctly. However, in most medical imaging fields, obtaining said data can be challenging. Not only the volume of data is a problem, but also the imbalances within its classes; it is common to have many more images of healthy patients than of those with pathology. Computer-aided diagnostic systems suffer from these issues, usually over-designing their models to perform accurately. This work proposes using self-supervised learning for wireless endoscopy videos by introducing a custom-tailored method that does not initially need labels or appropriate balance. We prove that using the inferred inherent structure learned by our method, extracted from the temporal axis, improves the detection rate on several domain-specific applications even under severe imbalance. State-of-the-art results are achieved in polyp detection, with 95.00 ± 2.09% Area Under the Curve, and 92.77 ± 1.20% accuracy in the CAD-CAP dataset

Transfer Learning Based Deep Neural Network for Detecting Artefacts in Endoscopic Images

Endoscopy is typically used to visualize various parts of the digestive tract. The technique is well suited to detect abnormalities like cancer/polyp, taking sample tissue called a biopsy, or cauterizing a bleeding vessel. During the procedure, video/ images are generated. It is affected by eight different artefacts: saturation, specularity, blood, blur, bubbles, contrast, instrument and miscellaneous artefacts like floating debris, chromatic aberration etc. The frames affected by artefacts are mostly discarded as the clinician could extract no valuable information from them. It affects post-processing steps. Based on the transfer learning approach, three state-of-the-art deep learning models, namely YOLOv3, YOLOv4 and Faster R-CNN, were trained with images from EAD public datasets and a custom dataset of endoscopic images of Indian patients annotated for artefacts mentioned above. The training set of images are data augmented and used to train all the three-artefact detectors. The predictions of the artefact detectors are combined to form an ensemble model whose results outperformed well compared to existing literature works by obtaining a mAP score of 0.561 and an IoU score of 0.682. The inference time of 80.4ms was recorded, which stands out best in the literature

Explainable Information Retrieval using Deep Learning for Medical images

Image segmentation is useful to extract valuable information for an efficient analysis on the region of interest. Mostly, the number of images generated from a real life situation such as streaming video, is large and not ideal for traditional segmentation with machine learning algorithms. This is due to the following factors (a) numerous image features (b) complex distribution of shapes, colors and textures (c) imbalance data ratio of underlying classes (d) movements of the camera, objects and (e) variations in luminance for site capture. So, we have proposed an efficient deep learning model for image classification and the proof-of-concept has been the case studied on gastrointestinal images for bleeding detection. The Explainable Artificial Intelligence (XAI) module has been utilised to reverse engineer the test results for the impact of features on a given test dataset. The architecture is generally applicable in other areas of image classification. The proposed method has been compared with state-of-the-art including Logistic Regression, Support Vector Machine, Artificial Neural Network and Random Forest. It has reported F1 score of 0.76 on the real world streaming dataset which is comparatively better than traditional methods

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

SCALING ARTIFICIAL INTELLIGENCE IN ENDOSCOPY: FROM MODEL DEVELOPMENT TO MACHINE LEARNING OPERATIONS FRAMEWORKS

Questa tesi esplora l'integrazione dell'intelligenza artificiale (IA) in Otorinolaringoiatria – Chirurgia di Testa e Collo, concentrandosi sui progressi della computer vision per l’endoscopia e le procedure chirurgiche. La ricerca inizia con una revisione completa dello stato dell’arte dell'IA e della computer vision in questo campo, identificando aree per ulteriori sviluppi. L'obiettivo principale è stato quello di sviluppare un sistema di computer vision per l'analisi di immagini e video endoscopici. La ricerca ha coinvolto la progettazione di strumenti per la rilevazione e segmentazione di neoplasie nelle vie aerodigestive superiori (VADS) e la valutazione della motilità delle corde vocali, cruciale nella stadiazione del carcinoma laringeo. Inoltre, lo studio si è focalizzato sul potenziale dei foundation vision models, vision transformers basati su self-supervised learning, per ridurre la necessità di annotazione da parte di esperti, approccio particolarmente vantaggioso in campi con dati limitati. Inoltre, la ricerca ha incluso lo sviluppo di un'applicazione web per migliorare e velocizzare il processo di annotazione in endoscopia delle VADS, nell’ambito generale delle tecniche di MLOps. La tesi copre varie fasi della ricerca, a partire dalla definizione del quadro concettuale e della metodologia, denominata "Videomics". Include una revisione della letteratura sull'IA in endoscopia clinica, focalizzata sulla Narrow Band Imaging (NBI) e sulle reti neurali convoluzionali (CNN). Lo studio progredisce attraverso diverse fasi, dalla valutazione della qualità delle immagini endoscopiche alla caratterizzazione approfondita delle lesioni neoplastiche. Si affronta anche la necessità di standard nel reporting degli studi di computer vision in ambito medico e si valuta l'applicazione dell'IA in setting dinamici come la motilità delle corde vocali. Una parte significativa della ricerca indaga l'uso di algoritmi di computer vision generalizzati (“foundation models”) e la “commoditization” degli algoritmi di machine learning, utilizzando polipi nasali e il carcinoma orofaringeo come casi studio. Infine, la tesi discute lo sviluppo di ENDO-CLOUD, un sistema basato su cloud per l’analisi della videolaringoscopia, evidenziando le sfide e le soluzioni nella gestione dei dati e l’utilizzo su larga scala di modelli di IA nell'imaging medico.This thesis explores the integration of artificial intelligence (AI) in Otolaryngology – Head and Neck Surgery, focusing on advancements in computer vision for endoscopy and surgical procedures. It begins with a comprehensive review of AI and computer vision advancements in this field, identifying areas for further exploration. The primary aim was to develop a computer vision system for endoscopy analysis. The research involved designing tools for detecting and segmenting neoplasms in the upper aerodigestive tract (UADT) and assessing vocal fold motility, crucial in laryngeal cancer staging. Further, the study delves into the potential of vision foundation models, like vision transformers trained via self-supervision, to reduce the need for expert annotations, particularly beneficial in fields with limited cases. Additionally, the research includes the development of a web application for enhancing and speeding up the annotation process in UADT endoscopy, under the umbrella of Machine Learning Operations (MLOps). The thesis covers various phases of research, starting with defining the conceptual framework and methodology, termed "Videomics". It includes a literature review on AI in clinical endoscopy, focusing on Narrow Band Imaging (NBI) and convolutional neural networks (CNNs). The research progresses through different stages, from quality assessment of endoscopic images to in-depth characterization of neoplastic lesions. It also addresses the need for standards in medical computer vision study reporting and evaluates the application of AI in dynamic vision scenarios like vocal fold motility. A significant part of the research investigates the use of "general purpose" vision algorithms and the commoditization of machine learning algorithms, using nasal polyps and oropharyngeal cancer as case studies. Finally, the thesis discusses the development of ENDO-CLOUD, a cloud-based system for videolaryngoscopy, highlighting the challenges and solutions in data management and the large-scale deployment of AI models in medical imaging