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

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

A survey of deep learning models in medical therapeutic areas.

pre-print1407 K

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

Models and analysis of vocal emissions for biomedical applications: 5th International Workshop: December 13-15, 2007, Firenze, Italy

The MAVEBA Workshop proceedings, held on a biannual basis, collect the scientific papers presented both as oral and poster contributions, during the conference. The main subjects are: development of theoretical and mechanical models as an aid to the study of main phonatory dysfunctions, as well as the biomedical engineering methods for the analysis of voice signals and images, as a support to clinical diagnosis and classification of vocal pathologies. The Workshop has the sponsorship of: Ente Cassa Risparmio di Firenze, COST Action 2103, Biomedical Signal Processing and Control Journal (Elsevier Eds.), IEEE Biomedical Engineering Soc. Special Issues of International Journals have been, and will be, published, collecting selected papers from the conference

Deep learning in medical imaging and radiation therapy

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146980/1/mp13264_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146980/2/mp13264.pd

Image Quality Assessment for Population Cardiac MRI: From Detection to Synthesis

Cardiac magnetic resonance (CMR) images play a growing role in diagnostic imaging of cardiovascular diseases. Left Ventricular (LV) cardiac anatomy and function are widely used for diagnosis and monitoring disease progression in cardiology and to assess the patient's response to cardiac surgery and interventional procedures. For population imaging studies, CMR is arguably the most comprehensive imaging modality for non-invasive and non-ionising imaging of the heart and great vessels and, hence, most suited for population imaging cohorts. Due to insufficient radiographer's experience in planning a scan, natural cardiac muscle contraction, breathing motion, and imperfect triggering, CMR can display incomplete LV coverage, which hampers quantitative LV characterization and diagnostic accuracy. To tackle this limitation and enhance the accuracy and robustness of the automated cardiac volume and functional assessment, this thesis focuses on the development and application of state-of-the-art deep learning (DL) techniques in cardiac imaging. Specifically, we propose new image feature representation types that are learnt with DL models and aimed at highlighting the CMR image quality cross-dataset. These representations are also intended to estimate the CMR image quality for better interpretation and analysis. Moreover, we investigate how quantitative analysis can benefit when these learnt image representations are used in image synthesis. Specifically, a 3D fisher discriminative representation is introduced to identify CMR image quality in the UK Biobank cardiac data. Additionally, a novel adversarial learning (AL) framework is introduced for the cross-dataset CMR image quality assessment and we show that the common representations learnt by AL can be useful and informative for cross-dataset CMR image analysis. Moreover, we utilize the dataset invariance (DI) representations for CMR volumes interpolation by introducing a novel generative adversarial nets (GANs) based image synthesis framework, which enhance the CMR image quality cross-dataset

Deep Learning in Medical Image Analysis

The accelerating power of deep learning in diagnosing diseases will empower physicians and speed up decision making in clinical environments. Applications of modern medical instruments and digitalization of medical care have generated enormous amounts of medical images in recent years. In this big data arena, new deep learning methods and computational models for efficient data processing, analysis, and modeling of the generated data are crucially important for clinical applications and understanding the underlying biological process. This book presents and highlights novel algorithms, architectures, techniques, and applications of deep learning for medical image analysis

Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries

This two-volume set LNCS 12962 and 12963 constitutes the thoroughly refereed proceedings of the 7th International MICCAI Brainlesion Workshop, BrainLes 2021, as well as the RSNA-ASNR-MICCAI Brain Tumor Segmentation (BraTS) Challenge, the Federated Tumor Segmentation (FeTS) Challenge, the Cross-Modality Domain Adaptation (CrossMoDA) Challenge, and the challenge on Quantification of Uncertainties in Biomedical Image Quantification (QUBIQ). These were held jointly at the 23rd Medical Image Computing for Computer Assisted Intervention Conference, MICCAI 2020, in September 2021. The 91 revised papers presented in these volumes were selected form 151 submissions. Due to COVID-19 pandemic the conference was held virtually. This is an open access book