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

Automatic Detection of Out-of-body Frames in Surgical Videos for Privacy Protection Using Self-supervised Learning and Minimal Labels

Endoscopic video recordings are widely used in minimally invasive robot-assisted surgery, but when the endoscope is outside the patient's body, it can capture irrelevant segments that may contain sensitive information. To address this, we propose a framework that accurately detects out-of-body frames in surgical videos by leveraging self-supervision with minimal data labels. We use a massive amount of unlabeled endoscopic images to learn meaningful representations in a self-supervised manner. Our approach, which involves pre-training on an auxiliary task and fine-tuning with limited supervision, outperforms previous methods for detecting out-of-body frames in surgical videos captured from da Vinci X and Xi surgical systems. The average F1 scores range from 96.00 to 98.02. Remarkably, using only 5% of the training labels, our approach still maintains an average F1 score performance above 97, outperforming fully-supervised methods with 95% fewer labels. These results demonstrate the potential of our framework to facilitate the safe handling of surgical video recordings and enhance data privacy protection in minimally invasive surgery.Comment: A 15-page journal article submitted to Journal of Medical Robotics Research (JMRR

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

Predictive Models for Bariatric Surgery Risks with Imbalanced Medical Datasets

Bariatric surgery (BAR) has become a popular treatment for type 2 diabetes mellitus (T2DM) which is among the most critical obesity-related comorbidities. Patients who have bariatric surgery, are exposed to complications after surgery. Furthermore, the mid- to long-term complications after bariatric surgery can be deadly and increase the complexity of managing safety of these operations and healthcare costs. Current studies on BAR complications have mainly used risk scoring for identifying patients who are more likely to have complications after surgery. Though, these studies do not take into considera-tion the imbalanced nature of the data where the size of the class of interest (patients who have complications after surgery) is relatively small. We propose the use of imbalanced classification techniques to tackle the imbalanced bariatric surgery data: synthetic minority oversampling technique (SMOTE), random undersampling, and en-semble learning classification methods including Random Forest, Bagging, and AdaBoost. Moreover, we improve classification performance through using Chi-Squared, Information Gain, and Correlation-based feature selection (CFS) techniques. We study the Premier Healthcare Database with focus on the most-frequent complications includ-ing Diabetes, Angina, Heart Failure, and Stroke. Our results show that the ensemble learning-based classification techniques using any feature selection method mentioned above are the best approach for handling the imbalanced nature of the bariatric surgical outcome data. In our evaluation, we find a slight preference toward using SMOTE method compared to the random undersampling method. These results demonstrate the potential of machine-learning tools as clinical decision support in identifying risks/outcomes associated with bariatric surgery and their effectiveness in reducing the surgery complications as well as improving patient care

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

Color Image Enhancement Techniques for Endoscopic images

Modern endoscopes play an important role in diagnosing various gastrointestinal (GI) tract related diseases. Although clinical findings of modern endoscopic imaging techniques are encouraging, there still remains much room for improvement of image quality. Of greatest concern, endoscopic images suffer from various degradations, such as specular highlights, non-uniform brightness and poor contrast. As a result, gastroenterologists often face difficulty in successfully identifying the subtle features, such as mucosal surface and structures, pit patterns, size and pattern of micro-vessels, tissue and vascular characteristics, superficial layer of mucosal and abnormal growths in endoscopic images. The improved visual quality of images can provide better diagnosis. This paper presents two proposed post-processing techniques for enhancing the subtle features of endoscopic images. The first proposed technique is named as endoscopic image enhancement based on adaptive sigmoid function and space-variant color reproduction (ASSVCR). It is achieved in two stages: image enhancement at gray level followed by color reproduction with the help of space variant chrominance mapping. Image enhancement is achieved by performing adaptive sigmoid function and uniform distribution of sigmoid pixels. Then color reproduction is used to generate new chrominance components. The second proposed technique is named as tri-scan. It is achieved in three stages: (1) Tissue and surface enhancement: a modified linear unsharp masking is used to sharpen the surface and edges of tissue and vascular characteristics, (2) Mucosa layer enhancement: an adaptive sigmoid function similar to the ASSVCR technique is employed on the R plane of the image to highlight the superficial layers of mucosa, (3) Color tone enhancement: the pixels are uniformly distributed to create a different color effect to highlight mucosa structures, superficial layers of mucosa and tissue characteristics. Both techniques are compared with other related works. Several performance metrics like focus value, statistic of visual representation, measurement of uniform distribution, color similarity test, color enhancement factor (CEF) and time complexity are used to assess the performance. The results showed improved performance compared to similar existing methods. In the post-processed images, we have observed that the ASSVCR can enhance and highlight pit patterns, tissue and vascular characteristics, mucosa structures and abnormal growths. It cannot highlight size and pattern of micro-vessels, and superficial layer of mucosa. In contrast, tri-scan can enhance and highlight all above mentioned features of endoscopic images

A clinical study of upper gastrointestinal endoscopy findings in patients presenting with dyspepsia

INTRODUCTION: Dyspepsia is affecting about 25% of general population in developed nations and it is a major cause for medical visits. New patients comprise about 10% of population every year. Dyspepsia majorly affects quality of life and it is a major burden in view of social costs. Directly the expenses are for laboratory tests, medical consultation and drugs and indirectly by absence from work. Dyspepsia refers to spectrum of diseases and heterogeneous group of symptoms confined to upper abdomen. Dyspepsia is a vague term used to explain upper abdominal collection of symptoms like indigestion, fullness, early satiety (not able to complete the meals), bloating, belching, nausea, epigastric discomfort or pain and anorexia. Indigestion is very common in general population; almost all have had indigestion at some time in their lifetime. Sometimes patients will include constipation and undigested food particles in the stool. Rome II working team defined dyspepsia as discomfort or pain in upper abdomen. Central abdominal pain is considered to be a vital symptom. Pain which is present in other regions or associated to defecation is not considered. Non ulcer dyspepsia, this description comprises a group of symptom complex simulating peptic ulcer in patients who have no provable or objective evidence of an ulcer. Based on analysis of problems individuals with non ulcer dyspepsia categorized into two types. Pseudo ulcer syndrome—with classic symptoms of ulcer disease Functional dyspepsia—with post prandial fullness, belching and bloating, occasionally associated with pyloroduodenal irritability and prolonged gastric emptying. Usually this functional component is attributed to uncoordinated motor activity and afferent hyper reactivity. Gastro-oesophageal reflux disease is a condition, defined as abnormal entering of gastric juice into oesophagus and causes symptoms due to tissue damage. The principal pathophysiological problem is the presence of unusual amount of gastric juice in the lumen of oesophagus. Symptoms thought to suggest of gastro-oesophageal disease , such as heart burn or regurgitation are very much prevalent in general population and many individuals do not seek medical advice. The presence of symptoms doesn’t correlate well with the tissue damage. For instance the significant problem like Barrett’s oesophgus, even in early adenocarcinoma, can occur without symptoms. Gastro-oesophageal reflux disease is most commonly treated by physicians, this is substantiated by amount of revenue recorded by many pharmacteutical company. The symptoms are due to failure of protective antireflux mechanisms. A clear understanding of the normal anatomy and physiology of esophagus is mandatory to decide the surgical and medical management. OBJECTIVES: 1. To study the endoscopic presentation of dyspepsia. 2. Early detection of esophagogastroduodenal carcinoma. 3. To study the age and sex prevalence in patients presenting with dyspepsia. 4. To study the common site of lesion in patients presenting with dyspepsia. METHODOLOGY: A prospective clinical study was undertaken at Tirunelveli Medical College Hospital, Tirunelveli to know the various upper gastro-intestinal endoscopic findings in patients presenting with dyspepsia. The study was conducted from march 2011 to October 2012. The patient selection was by convenience sampling. Dyspeptic patients were included in this study with their informed consent. A detailed clinically history was elucidated, followed by careful clinical examination, which were recorded as per the proforma. All the patients included in the study underwent upper gastrointestinal endoscopy and the findings were noted. The inclusion and exclusion criterias were as follows: Inclusion criteria: 1. Patients above 13 years of age. 2. Patients showing symptoms of dyspepsia for 4 or more than 4 weeks. 3. Patients with uncomplicated and uninvestigated dyspepsia. Exclusion criteria: 1. Patients below 10 years of age. 2. Pregnant and lactating women. 3. Patients on proto-pump inhibitors. 4. Patients who are known cases of chronic pancreatitis and liver disease. 5. Patients on NSAID’s for more than one month duration. 6. Unwilling or unfit patients for endoscopy. SUMMARY A prospective clinico-pathological study was undertaken in Tirunelveli Medical College Hospital to know the various endoscopic findings in patients presenting with dyspepsia and early detection of oesophagogastroduodenal malignancy in these patients. 140 patients presenting with dyspepsia were evaluated. The following were the observations: 1. Highest prevalence of dyspepsia in the age group of 30-39years. 2. Most common presenting complaint was epigastric pain and discomfort. 3. Dyspepsia was more common in males (58%) when compared to Females (42%) 4. Most common endoscopic finding was normal study followed by gastritis. 5. Malignancy was diagnosed in 5.7% patients with dyspepsia. 6. Stomach is the common site of lesion in patients presenting with dyspepsia 7. Gastritis, duodenitis and gastric ulcer is common in males while malignancy/growth is more common in females presenting with dyspepsia. 8. Incidence of malignancy increases as the age advances. CONCLUSION: From the present study of “A clinical study of various findings in upper gastro-intestinal endoscopy in patients presenting with dyspepsia”. On endoscopic examination gastritis accounted for the majority of the cases. Incidence of malignancy in the present study was observed to be 5.7% (gastric malignancies). Clinically significant endoscopic findings were observed in 52.14% of patients with uninvestigated dyspepsia. Most patients presented with a complex of three or more dyspeptic symptoms and the symptom profile was not predictive of the endoscopic findings. Prevalence of large number of inflammatory lesions as a result of increased acid production and low incidence of malignancy in the study group suggests that the uninvestigated patients with dyspepsia may be initially managed medically with acid suppressive therapy

From Fully-Supervised Single-Task to Semi-Supervised Multi-Task Deep Learning Architectures for Segmentation in Medical Imaging Applications

Medical imaging is routinely performed in clinics worldwide for the diagnosis and treatment of numerous medical conditions in children and adults. With the advent of these medical imaging modalities, radiologists can visualize both the structure of the body as well as the tissues within the body. However, analyzing these high-dimensional (2D/3D/4D) images demands a significant amount of time and effort from radiologists. Hence, there is an ever-growing need for medical image computing tools to extract relevant information from the image data to help radiologists perform efficiently. Image analysis based on machine learning has pivotal potential to improve the entire medical imaging pipeline, providing support for clinical decision-making and computer-aided diagnosis. To be effective in addressing challenging image analysis tasks such as classification, detection, registration, and segmentation, specifically for medical imaging applications, deep learning approaches have shown significant improvement in performance. While deep learning has shown its potential in a variety of medical image analysis problems including segmentation, motion estimation, etc., generalizability is still an unsolved problem and many of these successes are achieved at the cost of a large pool of datasets. For most practical applications, getting access to a copious dataset can be very difficult, often impossible. Annotation is tedious and time-consuming. This cost is further amplified when annotation must be done by a clinical expert in medical imaging applications. Additionally, the applications of deep learning in the real-world clinical setting are still limited due to the lack of reliability caused by the limited prediction capabilities of some deep learning models. Moreover, while using a CNN in an automated image analysis pipeline, it’s critical to understand which segmentation results are problematic and require further manual examination. To this extent, the estimation of uncertainty calibration in a semi-supervised setting for medical image segmentation is still rarely reported. This thesis focuses on developing and evaluating optimized machine learning models for a variety of medical imaging applications, ranging from fully-supervised, single-task learning to semi-supervised, multi-task learning that makes efficient use of annotated training data. The contributions of this dissertation are as follows: (1) developing a fully-supervised, single-task transfer learning for the surgical instrument segmentation from laparoscopic images; and (2) utilizing supervised, single-task, transfer learning for segmenting and digitally removing the surgical instruments from endoscopic/laparoscopic videos to allow the visualization of the anatomy being obscured by the tool. The tool removal algorithms use a tool segmentation mask and either instrument-free reference frames or previous instrument-containing frames to fill in (inpaint) the instrument segmentation mask; (3) developing fully-supervised, single-task learning via efficient weight pruning and learned group convolution for accurate left ventricle (LV), right ventricle (RV) blood pool and myocardium localization and segmentation from 4D cine cardiac MR images; (4) demonstrating the use of our fully-supervised memory-efficient model to generate dynamic patient-specific right ventricle (RV) models from cine cardiac MRI dataset via an unsupervised learning-based deformable registration field; and (5) integrating a Monte Carlo dropout into our fully-supervised memory-efficient model with inherent uncertainty estimation, with the overall goal to estimate the uncertainty associated with the obtained segmentation and error, as a means to flag regions that feature less than optimal segmentation results; (6) developing semi-supervised, single-task learning via self-training (through meta pseudo-labeling) in concert with a Teacher network that instructs the Student network by generating pseudo-labels given unlabeled input data; (7) proposing largely-unsupervised, multi-task learning to demonstrate the power of a simple combination of a disentanglement block, variational autoencoder (VAE), generative adversarial network (GAN), and a conditioning layer-based reconstructor for performing two of the foremost critical tasks in medical imaging — segmentation of cardiac structures and reconstruction of the cine cardiac MR images; (8) demonstrating the use of 3D semi-supervised, multi-task learning for jointly learning multiple tasks in a single backbone module – uncertainty estimation, geometric shape generation, and cardiac anatomical structure segmentation of the left atrial cavity from 3D Gadolinium-enhanced magnetic resonance (GE-MR) images. This dissertation summarizes the impact of the contributions of our work in terms of demonstrating the adaptation and use of deep learning architectures featuring different levels of supervision to build a variety of image segmentation tools and techniques that can be used across a wide spectrum of medical image computing applications centered on facilitating and promoting the wide-spread computer-integrated diagnosis and therapy data science