Challenges and Opportunities of End-to-End Learning in Medical Image Classification

Das Paradigma des End-to-End Lernens hat in den letzten Jahren die Bilderkennung revolutioniert, aber die klinische Anwendung hinkt hinterher. Bildbasierte computergestützte Diagnosesysteme basieren immer noch weitgehend auf hochtechnischen und domänen-spezifischen Pipelines, die aus unabhängigen regelbasierten Modellen bestehen, welche die Teilaufgaben der Bildklassifikation wiederspiegeln: Lokalisation von auffälligen Regionen, Merkmalsextraktion und Entscheidungsfindung. Das Versprechen einer überlegenen Entscheidungsfindung beim End-to-End Lernen ergibt sich daraus, dass domänenspezifische Zwangsbedingungen von begrenzter Komplexität entfernt werden und stattdessen alle Systemkomponenten gleichzeitig, direkt anhand der Rohdaten, und im Hinblick auf die letztendliche Aufgabe optimiert werden. Die Gründe dafür, dass diese Vorteile noch nicht den Weg in die Klinik gefunden haben, d.h. die Herausforderungen, die sich bei der Entwicklung Deep Learning-basierter Diagnosesysteme stellen, sind vielfältig: Die Tatsache, dass die Generalisierungsfähigkeit von Lernalgorithmen davon abhängt, wie gut die verfügbaren Trainingsdaten die tatsächliche zugrundeliegende Datenverteilung abbilden, erweist sich in medizinische Anwendungen als tiefgreifendes Problem. Annotierte Datensätze in diesem Bereich sind notorisch klein, da für die Annotation eine kostspielige Beurteilung durch Experten erforderlich ist und die Zusammenlegung kleinerer Datensätze oft durch Datenschutzauflagen und Patientenrechte erschwert wird. Darüber hinaus weisen medizinische Datensätze drastisch unterschiedliche Eigenschaften im Bezug auf Bildmodalitäten, Bildgebungsprotokolle oder Anisotropien auf, und die oft mehrdeutige Evidenz in medizinischen Bildern kann sich auf inkonsistente oder fehlerhafte Trainingsannotationen übertragen. Während die Verschiebung von Datenverteilungen zwischen Forschungsumgebung und Realität zu einer verminderten Modellrobustheit führt und deshalb gegenwärtig als das Haupthindernis für die klinische Anwendung von Lernalgorithmen angesehen wird, wird dieser Graben oft noch durch Störfaktoren wie Hardwarelimitationen oder Granularität von gegebenen Annotation erweitert, die zu Diskrepanzen zwischen der modellierten Aufgabe und der zugrunde liegenden klinischen Fragestellung führen. Diese Arbeit untersucht das Potenzial des End-to-End-Lernens in klinischen Diagnosesystemen und präsentiert Beiträge zu einigen der wichtigsten Herausforderungen, die derzeit eine breite klinische Anwendung verhindern. Zunächst wird der letzten Teil der Klassifikations-Pipeline untersucht, die Kategorisierung in klinische Pathologien. Wir demonstrieren, wie das Ersetzen des gegenwärtigen klinischen Standards regelbasierter Entscheidungen durch eine groß angelegte Merkmalsextraktion gefolgt von lernbasierten Klassifikatoren die Brustkrebsklassifikation im MRT signifikant verbessert und eine Leistung auf menschlichem Level erzielt. Dieser Ansatz wird weiter anhand von kardiologischer Diagnose gezeigt. Zweitens ersetzen wir, dem Paradigma des End-to-End Lernens folgend, das biophysikalische Modell, das für die Bildnormalisierung in der MRT angewandt wird, sowie die Extraktion handgefertigter Merkmale, durch eine designierte CNN-Architektur und liefern eine eingehende Analyse, die das verborgene Potenzial der gelernten Bildnormalisierung und einen Komplementärwert der gelernten Merkmale gegenüber den handgefertigten Merkmalen aufdeckt. Während dieser Ansatz auf markierten Regionen arbeitet und daher auf manuelle Annotation angewiesen ist, beziehen wir im dritten Teil die Aufgabe der Lokalisierung dieser Regionen in den Lernprozess ein, um eine echte End-to-End-Diagnose baserend auf den Rohbildern zu ermöglichen. Dabei identifizieren wir eine weitgehend vernachlässigte Zwangslage zwischen dem Streben nach der Auswertung von Modellen auf klinisch relevanten Skalen auf der einen Seite, und der Optimierung für effizientes Training unter Datenknappheit auf der anderen Seite. Wir präsentieren ein Deep Learning Modell, das zur Auflösung dieses Kompromisses beiträgt, liefern umfangreiche Experimente auf drei medizinischen Datensätzen sowie eine Serie von Toy-Experimenten, die das Verhalten bei begrenzten Trainingsdaten im Detail untersuchen, und publiziren ein umfassendes Framework, das unter anderem die ersten 3D-Implementierungen gängiger Objekterkennungsmodelle umfasst. Wir identifizieren weitere Hebelpunkte in bestehenden End-to-End-Lernsystemen, bei denen Domänenwissen als Zwangsbedingung dienen kann, um die Robustheit von Modellen in der medizinischen Bildanalyse zu erhöhen, die letztendlich dazu beitragen sollen, den Weg für die Anwendung in der klinischen Praxis zu ebnen. Zu diesem Zweck gehen wir die Herausforderung fehlerhafter Trainingsannotationen an, indem wir die Klassifizierungskompnente in der End-to-End-Objekterkennung durch Regression ersetzen, was es ermöglicht, Modelle direkt auf der kontinuierlichen Skala der zugrunde liegenden pathologischen Prozesse zu trainieren und so die Robustheit der Modelle gegenüber fehlerhaften Trainingsannotationen zu erhöhen. Weiter adressieren wir die Herausforderung der Input-Heterogenitäten, mit denen trainierte Modelle konfrontiert sind, wenn sie an verschiedenen klinischen Orten eingesetzt werden, indem wir eine modellbasierte Domänenanpassung vorschlagen, die es ermöglicht, die ursprüngliche Trainingsdomäne aus veränderten Inputs wiederherzustellen und damit eine robuste Generalisierung zu gewährleisten. Schließlich befassen wir uns mit dem höchst unsystematischen, aufwendigen und subjektiven Trial-and-Error-Prozess zum Finden von robusten Hyperparametern für einen gegebene Aufgabe, indem wir Domänenwissen in ein Set systematischer Regeln überführen, die eine automatisierte und robuste Konfiguration von Deep Learning Modellen auf einer Vielzahl von medizinischen Datensetzen ermöglichen. Zusammenfassend zeigt die hier vorgestellte Arbeit das enorme Potenzial von End-to-End Lernalgorithmen im Vergleich zum klinischen Standard mehrteiliger und hochtechnisierter Diagnose-Pipelines auf, und präsentiert Lösungsansätze zu einigen der wichtigsten Herausforderungen für eine breite Anwendung unter realen Bedienungen wie Datenknappheit, Diskrepanz zwischen der vom Modell behandelten Aufgabe und der zugrunde liegenden klinischen Fragestellung, Mehrdeutigkeiten in Trainingsannotationen, oder Verschiebung von Datendomänen zwischen klinischen Standorten. Diese Beiträge können als Teil des übergreifende Zieles der Automatisierung von medizinischer Bildklassifikation gesehen werden - ein integraler Bestandteil des Wandels, der erforderlich ist, um die Zukunft des Gesundheitswesens zu gestalten

Depth Segmentation Method for Cancer Detection in Mammography Images

Breast cancer detection remains a subject matter of intense and also a stream that will create a path for numerous debates. Mammography has long been the mainstay of breast cancer detection and is the only screening test proven to reduce mortality. Computer-aided diagnosis (CAD) systems have the potential to assist radiologists in the early detection of cancer. Many techniques were introduced based on SVM classifier, spatial and frequency domain, active contour method, k-NN clustering method but these methods have so many disadvantages on the SNR ratio, efficiency etc. The quality of detection of cancer cells is dependent with the segmentation of the mammography image. Here a new method is proposed for segmentation. This algorithm focuses to segment the image depth wise and also coloured based segmentation is implemented. Here the feature identification and detection of malignant and benign cells are done more easily and also to increase the efficiency to detect the early stages of breast cancer through mammography images. In which the relative signal enhancement technique is also done for high dynamic range images. Markovian random function can be used in the depth segmentation. Markov Random Field (MRF) is used in mammography images. It is because this method can model intensity in homogeneities occurring in these images. This will be helpful to find the featured tumor DOI: 10.17762/ijritcc2321-8169.15023

Medical Internet-of-Things Based Breast Cancer Diagnosis Using Hyperparameter-Optimized Neural Networks

In today’s healthcare setting, the accurate and timely diagnosis of breast cancer is critical for recovery and treatment in the early stages. In recent years, the Internet of Things (IoT) has experienced a transformation that allows the analysis of real-time and historical data using artificial intelligence (AI) and machine learning (ML) approaches. Medical IoT combines medical devices and AI applications with healthcare infrastructure to support medical diagnostics. The current state-of-the-art approach fails to diagnose breast cancer in its initial period, resulting in the death of most women. As a result, medical professionals and researchers are faced with a tremendous problem in early breast cancer detection. We propose a medical IoT-based diagnostic system that competently identifies malignant and benign people in an IoT environment to resolve the difficulty of identifying early-stage breast cancer. The artificial neural network (ANN) and convolutional neural network (CNN) with hyperparameter optimization are used for malignant vs. benign classification, while the Support Vector Machine (SVM) and Multilayer Perceptron (MLP) were utilized as baseline classifiers for comparison. Hyperparameters are important for machine learning algorithms since they directly control the behaviors of training algorithms and have a significant effect on the performance of machine learning models. We employ a particle swarm optimization (PSO) feature selection approach to select more satisfactory features from the breast cancer dataset to enhance the classification performance using MLP and SVM, while grid-based search was used to find the best combination of the hyperparameters of the CNN and ANN models. The Wisconsin Diagnostic Breast Cancer (WDBC) dataset was used to test the proposed approach. The proposed model got a classification accuracy of 98.5% using CNN, and 99.2% using ANN.publishedVersio

A Modified LeNet CNN for Breast Cancer Diagnosis in Ultrasound Images

Convolutional neural networks (CNNs) have been extensively utilized in medical image processing to automatically extract meaningful features and classify various medical conditions, enabling faster and more accurate diagnoses. In this paper, LeNet, a classic CNN architecture, has been successfully applied to breast cancer data analysis. It demonstrates its ability to extract discriminative features and classify malignant and benign tumors with high accuracy, thereby supporting early detection and diagnosis of breast cancer. LeNet with corrected Rectified Linear Unit (ReLU), a modification of the traditional ReLU activation function, has been found to improve the performance of LeNet in breast cancer data analysis tasks via addressing the “dying ReLU” problem and enhancing the discriminative power of the extracted features. This has led to more accurate, reliable breast cancer detection and diagnosis and improved patient outcomes. Batch normalization improves the performance and training stability of small and shallow CNN architecture like LeNet. It helps to mitigate the effects of internal covariate shift, which refers to the change in the distribution of network activations during training. This classifier will lessen the overfitting problem and reduce the running time. The designed classifier is evaluated against the benchmarking deep learning models, proving that this has produced a higher recognition rate. The accuracy of the breast image recognition rate is 89.91%. This model will achieve better performance in segmentation, feature extraction, classification, and breast cancer tumor detection

Genetic Algorithm to Optimize k-Nearest Neighbor Parameter for Benchmarked Medical Datasets Classification

Computer assisted medical diagnosis is a major machine learning problem being researched recently. General classifiers learn from the data itself through training process, due to the inexperience of an expert in determining parameters. This research proposes a methodology based on machine learning paradigm. Integrates the search heuristic that is inspired by natural evolution called genetic algorithm with the simplest and the most used learning algorithm, k-nearest Neighbor. The genetic algorithm were used for feature selection and parameter optimization while k-nearest Neighbor were used as a classifier. The proposed method is experimented on five benchmarked medical datasets from University California Irvine Machine Learning Repository and compared with original k-NN and other feature selection algorithm i.e., forward selection, backward elimination and greedy feature selection.  Experiment results show that the proposed method is able to achieve good performance with significant improvement with p value of t-Test is 0.0011

Pan-cancer classifications of tumor histological images using deep learning

Histopathological images are essential for the diagnosis of cancer type and selection of optimal treatment. However, the current clinical process of manual inspection of images is time consuming and prone to intra- and inter-observer variability. Here we show that key aspects of cancer image analysis can be performed by deep convolutional neural networks (CNNs) across a wide spectrum of cancer types. In particular, we implement CNN architectures based on Google Inception v3 transfer learning to analyze 27815 H&E slides from 23 cohorts in The Cancer Genome Atlas in studies of tumor/normal status, cancer subtype, and mutation status. For 19 solid cancer types we are able to classify tumor/normal status of whole slide images with extremely high AUCs (0.995±0.008). We are also able to classify cancer subtypes within 10 tissue types with AUC values well above random expectations (micro-average 0.87±0.1). We then perform a cross-classification analysis of tumor/normal status across tumor types. We find that classifiers trained on one type are often effective in distinguishing tumor from normal in other cancer types, with the relationships among classifiers matching known cancer tissue relationships. For the more challenging problem of mutational status, we are able to classify TP53 mutations in three cancer types with AUCs from 0.65-0.80 using a fully-trained CNN, and with similar cross-classification accuracy across tissues. These studies demonstrate the power of CNNs for not only classifying histopathological images in diverse cancer types, but also for revealing shared biology between tumors. We have made software available at: https://github.com/javadnoorb/HistCNNFirst author draf

Computer aided diagnosis system for breast cancer using deep learning.

The recent rise of big data technology surrounding the electronic systems and developed toolkits gave birth to new promises for Artificial Intelligence (AI). With the continuous use of data-centric systems and machines in our lives, such as social media, surveys, emails, reports, etc., there is no doubt that data has gained the center of attention by scientists and motivated them to provide more decision-making and operational support systems across multiple domains. With the recent breakthroughs in artificial intelligence, the use of machine learning and deep learning models have achieved remarkable advances in computer vision, ecommerce, cybersecurity, and healthcare. Particularly, numerous applications provided efficient solutions to assist radiologists and doctors for medical imaging analysis, which has remained the essence of the visual representation that is used to construct the final observation and diagnosis. Medical research in cancerology and oncology has been recently blended with the knowledge gained from computer engineering and data science experts. In this context, an automatic assistance or commonly known as Computer-aided Diagnosis (CAD) system has become a popular area of research and development in the last decades. As a result, the CAD systems have been developed using multidisciplinary knowledge and expertise and they have been used to analyze the patient information to assist clinicians and practitioners in their decision-making process. Treating and preventing cancer remains a crucial task that radiologists and oncologists face every day to detect and investigate abnormal tumors. Therefore, a CAD system could be developed to provide decision support for many applications in the cancer patient care processes, such as lesion detection, characterization, cancer staging, tumors assessment, recurrence, and prognosis prediction. Breast cancer has been considered one of the common types of cancers in females across the world. It was also considered the leading cause of mortality among women, and it has been increased drastically every year. Early detection and diagnosis of abnormalities in screened breasts has been acknowledged as the optimal solution to examine the risk of developing breast cancer and thus reduce the increasing mortality rate. Accordingly, this dissertation proposes a new state-of-the-art CAD system for breast cancer diagnosis that is based on deep learning technology and cutting-edge computer vision techniques. Mammography screening has been recognized as the most effective tool to early detect breast lesions for reducing the mortality rate. It helps reveal abnormalities in the breast such as Mass lesion, Architectural Distortion, Microcalcification. With the number of daily patients that were screened is continuously increasing, having a second reading tool or assistance system could leverage the process of breast cancer diagnosis. Mammograms could be obtained using different modalities such as X-ray scanner and Full-Field Digital mammography (FFDM) system. The quality of the mammograms, the characteristics of the breast (i.e., density, size) or/and the tumors (i.e., location, size, shape) could affect the final diagnosis. Therefore, radiologists could miss the lesions and consequently they could generate false detection and diagnosis. Therefore, this work was motivated to improve the reading of mammograms in order to increase the accuracy of the challenging tasks. The efforts presented in this work consists of new design and implementation of neural network models for a fully integrated CAD system dedicated to breast cancer diagnosis. The approach is designed to automatically detect and identify breast lesions from the entire mammograms at a first step using fusion models’ methodology. Then, the second step only focuses on the Mass lesions and thus the proposed system should segment the detected bounding boxes of the Mass lesions to mask their background. A new neural network architecture for mass segmentation was suggested that was integrated with a new data enhancement and augmentation technique. Finally, a third stage was conducted using a stacked ensemble of neural networks for classifying and diagnosing the pathology (i.e., malignant, or benign), the Breast Imaging Reporting and Data System (BI-RADS) assessment score (i.e., from 2 to 6), or/and the shape (i.e., round, oval, lobulated, irregular) of the segmented breast lesions. Another contribution was achieved by applying the first stage of the CAD system for a retrospective analysis and comparison of the model on Prior mammograms of a private dataset. The work was conducted by joining the learning of the detection and classification model with the image-to-image mapping between Prior and Current screening views. Each step presented in the CAD system was evaluated and tested on public and private datasets and consequently the results have been fairly compared with benchmark mammography datasets. The integrated framework for the CAD system was also tested for deployment and showcase. The performance of the CAD system for the detection and identification of breast masses reached an overall accuracy of 97%. The segmentation of breast masses was evaluated together with the previous stage and the approach achieved an overall performance of 92%. Finally, the classification and diagnosis step that defines the outcome of the CAD system reached an overall pathology classification accuracy of 96%, a BIRADS categorization accuracy of 93%, and a shape classification accuracy of 90%. Results given in this dissertation indicate that our suggested integrated framework might surpass the current deep learning approaches by using all the proposed automated steps. Limitations of the proposed work could occur on the long training time of the different methods which is due to the high computation of the developed neural networks that have a huge number of the trainable parameters. Future works can include new orientations of the methodologies by combining different mammography datasets and improving the long training of deep learning models. Moreover, motivations could upgrade the CAD system by using annotated datasets to integrate more breast cancer lesions such as Calcification and Architectural distortion. The proposed framework was first developed to help detect and identify suspicious breast lesions in X-ray mammograms. Next, the work focused only on Mass lesions and segment the detected ROIs to remove the tumor’s background and highlight the contours, the texture, and the shape of the lesions. Finally, the diagnostic decision was predicted to classify the pathology of the lesions and investigate other characteristics such as the tumors’ grading assessment and type of the shape. The dissertation presented a CAD system to assist doctors and experts to identify the risk of breast cancer presence. Overall, the proposed CAD method incorporates the advances of image processing, deep learning, and image-to-image translation for a biomedical application

Explorations of the semantic learning machine neuroevolution algorithm: dynamic training data use and ensemble construction methods

Dissertation presented as the partial requirement for obtaining a Master’s degree in Data Science and Advanced AnalyticsAs the world’s technology evolves, the power to implement new and more efficient algorithms increases but so does the complexity of the problems at hand. Neuroevolution algorithms fit in this context in the sense that they are able to evolve Artificial Neural Networks (ANNs). The recently proposed Neuroevolution algorithm called Semantic Learning Machine (SLM) has the advantage of searching over unimodal error landscapes in any Supervised Learning task where the error is measured as a distance to the known targets. The absence of local optima in the search space results in a more efficient learning when compared to other neuroevolution algorithms. This work studies how different approaches of dynamically using the training data affect the generalization of the SLM algorithm. Results show that these methods can be useful in offering different alternatives to achieve a superior generalization. These approaches are evaluated experimentally in fifteen real-world binary classification data sets. Across these fifteen data sets, results show that the SLM is able to outperform the Multilayer Perceptron (MLP) in 13 out of the 15 considered problems with statistical significance after parameter tuning was applied to both algorithms. Furthermore, this work also considers how different ensemble construction methods such as a simple averaging approach, Bagging and Boosting affect the resulting generalization of the SLM and MLP algorithms. Results suggest that the stochastic nature of the SLM offers enough diversity to the base learner in a way that a simple averaging method can be competitive when compared to more complex techniques like Bagging and Boosting.À medida que a tecnologia evolui, a possibilidade de implementar algoritmos novos e mais eficientes aumenta, no entanto, a complexidade dos problemas com que nos deparamos também se torna maior. Algoritmos de Neuroevolution encaixam-se neste contexto, na medida em que são capazes de evoluir Artificial Neural Networks (ANNs). O algoritmo de Neuroevolution recentemente proposto chamado Semantic Learning Machine (SLM) tem a vantagem de procurar sobre landscapes de erros unimodais em qualquer problema de Supervised Learning, onde o erro é medido como a distância aos alvos conhecidos. A não existência de local optima no espaço de procura resulta numa aprendizagem mais eficiente quando comparada com outros algoritmos de Neuroevolution. Este trabalho estuda como métodos diferentes de uso dinâmico de dados de treino afeta a generalização do algoritmo SLM. Os resultados mostram que estes métodos são úteis a oferecer uma alternativa que atinge uma generalização competitiva. Estes métodos são testados em quinze problemas reais de classificação binária. Nestes quinze problemas, o algoritmo SLM mostra superioridade ao Multilayer Perceptron (MLP) em treze deles com significância estatística depois de ser aplicado parameter tuning em ambos os algoritmos. Para além disso, este trabalho também considera como diferentes métodos de construção de ensembles, tal como um simples método de averaging, Bagging e Boosting afetam os valores de generalização dos algoritmos SLM e MLP. Os resultados sugerem que a natureza estocástica da SLM oferece diversidade suficiente aos base learners de maneira a que o método mais simples de construção de ensembles se torne competitivo quando comparado com técnicas mais complexas como Bagging e Boosting

Chasing a Better Decision Margin for Discriminative Histopathological Breast Cancer Image Classification

When considering a large dataset of histopathologic breast images captured at various magnification levels, the process of distinguishing between benign and malignant cancer from these images can be time-intensive. The automation of histopathological breast cancer image classification holds significant promise for expediting pathology diagnoses and reducing the analysis time. Convolutional neural networks (CNNs) have recently gained traction for their ability to more accurately classify histopathological breast cancer images. CNNs excel at extracting distinctive features that emphasize semantic information. However, traditional CNNs employing the softmax loss function often struggle to achieve the necessary discriminatory power for this task. To address this challenge, a set of angular margin-based softmax loss functions have emerged, including angular softmax (A-Softmax), large margin cosine loss (CosFace), and additive angular margin (ArcFace), each sharing a common objective: maximizing inter-class variation while minimizing intra-class variation. This study delves into these three loss functions and their potential to extract distinguishing features while expanding the decision boundary between classes. Rigorous experimentation on a well-established histopathological breast cancer image dataset, BreakHis, has been conducted. As per the results, it is evident that CosFace focuses on augmenting the differences between classes, while A-Softmax and ArcFace tend to emphasize augmenting within-class variations. These observations underscore the efficacy of margin penalties on angular softmax losses in enhancing feature discrimination within the embedding space. These loss functions consistently outperform softmax-based techniques, either by widening the gaps among classes or enhancing the compactness of individual classes

Chasing a Better Decision Margin for Discriminative Histopathological Breast Cancer Image Classification

When considering a large dataset of histopathologic breast images captured at various magnification levels, the process of distinguishing between benign and malignant cancer from these images can be time-intensive. The automation of histopathological breast cancer image classification holds significant promise for expediting pathology diagnoses and reducing the analysis time. Convolutional neural networks (CNNs) have recently gained traction for their ability to more accurately classify histopathological breast cancer images. CNNs excel at extracting distinctive features that emphasize semantic information. However, traditional CNNs employing the softmax loss function often struggle to achieve the necessary discriminatory power for this task. To address this challenge, a set of angular margin-based softmax loss functions have emerged, including angular softmax (A-Softmax), large margin cosine loss (CosFace), and additive angular margin (ArcFace), each sharing a common objective: maximizing inter-class variation while minimizing intra-class variation. This study delves into these three loss functions and their potential to extract distinguishing features while expanding the decision boundary between classes. Rigorous experimentation on a well-established histopathological breast cancer image dataset, BreakHis, has been conducted. As per the results, it is evident that CosFace focuses on augmenting the differences between classes, while A-Softmax and ArcFace tend to emphasize augmenting within-class variations. These observations underscore the efficacy of margin penalties on angular softmax losses in enhancing feature discrimination within the embedding space. These loss functions consistently outperform softmax-based techniques, either by widening the gaps among classes or enhancing the compactness of individual classes.This work is partially supported by the project GUI19/027 and by the grant PID2021-126701OB-I00 funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe”