Machine Learning Based Diagnostic Paradigm in Viral and Non-Viral Hepatocellular Carcinoma

© 2024 The Author(s). This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY), https://creativecommons.org/licenses/by/4.0/Viral and non-viral hepatocellular carcinoma (HCC) is becoming predominant in developing countries. A major issue linked to HCC-related mortality rate is the late diagnosis of cancer development. Although traditional approaches to diagnosing HCC have become gold-standard, there remain several limitations due to which the confirmation of cancer progression takes a longer period. The recent emergence of artificial intelligence tools with the capacity to analyze biomedical datasets is assisting traditional diagnostic approaches for early diagnosis with certainty. Here we present a review of traditional HCC diagnostic approaches versus the use of artificial intelligence (Machine Learning and Deep Learning) for HCC diagnosis. The overview of the cancer-related databases along with the use of AI in histopathology, radiology, biomarker, and electronic health records (EHRs) based HCC diagnosis is given.Peer reviewe

Learning strategies for improving neural networks for image segmentation under class imbalance

This thesis aims to improve convolutional neural networks (CNNs) for image segmentation under class imbalance, which is referred to the problem of training dataset when the class distributions are unequal. We particularly focus on medical image segmentation because of its imbalanced nature and clinical importance. Based on our observations of model behaviour, we argue that CNNs cannot generalize well on imbalanced segmentation tasks, mainly because of two counterintuitive reasons. CNNs are prone to overfit the under-represented foreground classes as it would memorize the regions of interest (ROIs) in the training data because they are so rare. Besides, CNNs could underfit the heterogenous background classes as it is difficult to learn from the samples with diverse and complex characteristics. Those behaviours of CNNs are not limited to specific loss functions. To address those limitations, firstly we propose novel asymmetric variants of popular loss functions and regularization techniques, which are explicitly designed to increase the variance of foreground samples to counter overfitting under class imbalance. Secondly we propose context label learning (CoLab) to tackle background underfitting by automatically decomposing the background class into several subclasses. This is achieved by optimizing an auxiliary task generator to generate context labels such that the main network will produce good ROIs segmentation performance. Then we propose a meta-learning based automatic data augmentation framework which builds a balance of foreground and background samples to alleviate class imbalance. Specifically, we learn class-specific training-time data augmentation (TRA) and jointly optimize TRA and test-time data augmentation (TEA) effectively aligning training and test data distribution for better generalization. Finally, we explore how to estimate model performance under domain shifts when trained with imbalanced dataset. We propose class-specific variants of existing confidence-based model evaluation methods which adapts separate parameters per class, enabling class-wise calibration to reduce model bias towards the minority classes.Open Acces

Radiomics in [¹⁸F]FDG PET/CT:A leap in the dark?

Positron emission tomography (PET) imaging with the non-metabolisable glucose analogue 2-[18F]fluoro-2-deoxy-D-glucose ([18F]FDG), combined with low dose computed tomography (CT) for anatomical reference, is an important tool to detect and stage cancer or active inflammations. Visual interpretation of PET/CT images consists of (qualitative) assessment of radiotracer uptake in different tissues and their density. Furthermore, the location, size, shape, and relation with surrounding tissues of these lesions provide important clues on their nature. Yet, medical images contain much more information about tissue biology hidden in the myriad of voxels of both lesions and healthy tissue than can be assessed visually. Quantification of radiotracer uptake heterogeneity and other tissue characteristics is studied in the field of radiomics. Radiomics is a form of medical image processing that aims to find stable and clinically relevant image-derived biomarkers for lesion characterisation, prognostic stratification, and response prediction, thereby contributing to precision medicine. Radiomics consists of the conversion of (parts of) medical images into a high-dimensional set of quantitative features and the subsequent mining of this dataset for potential information useful for the quantification or monitoring of tumour or disease characteristics in clinical practice. This thesis contributed to a deeper understanding of the methodological aspects of handcrafted radiomics in [18F]FDG PET/CT, specifically in small datasets. However, most radiomic papers present proof-of-concept studies and clinical implementation is still far away. At some point in the future, radiomic biomarkers may be used in clinical practice, but at the moment we should acknowledge the limitations of the field and try to overcome these. Only then, we will be able to cross the translational gap towards clinical readiness. Future research should focus on standardisation of feature selection, model building, and ideally a tool that implements these aspects. In such a way, radiomics may redeem the promise of bringing forth imaging biomarkers that contribute to precision medicine.<br/

Computational Pathology: A Survey Review and The Way Forward

Computational Pathology CPath is an interdisciplinary science that augments developments of computational approaches to analyze and model medical histopathology images. The main objective for CPath is to develop infrastructure and workflows of digital diagnostics as an assistive CAD system for clinical pathology, facilitating transformational changes in the diagnosis and treatment of cancer that are mainly address by CPath tools. With evergrowing developments in deep learning and computer vision algorithms, and the ease of the data flow from digital pathology, currently CPath is witnessing a paradigm shift. Despite the sheer volume of engineering and scientific works being introduced for cancer image analysis, there is still a considerable gap of adopting and integrating these algorithms in clinical practice. This raises a significant question regarding the direction and trends that are undertaken in CPath. In this article we provide a comprehensive review of more than 800 papers to address the challenges faced in problem design all-the-way to the application and implementation viewpoints. We have catalogued each paper into a model-card by examining the key works and challenges faced to layout the current landscape in CPath. We hope this helps the community to locate relevant works and facilitate understanding of the field's future directions. In a nutshell, we oversee the CPath developments in cycle of stages which are required to be cohesively linked together to address the challenges associated with such multidisciplinary science. We overview this cycle from different perspectives of data-centric, model-centric, and application-centric problems. We finally sketch remaining challenges and provide directions for future technical developments and clinical integration of CPath (https://github.com/AtlasAnalyticsLab/CPath_Survey).Comment: Accepted in Elsevier Journal of Pathology Informatics (JPI) 202

The impact of pre- and post-image processing techniques on deep learning frameworks: A comprehensive review for digital pathology image analysis.

Recently, deep learning frameworks have rapidly become the main methodology for analyzing medical images. Due to their powerful learning ability and advantages in dealing with complex patterns, deep learning algorithms are ideal for image analysis challenges, particularly in the field of digital pathology. The variety of image analysis tasks in the context of deep learning includes classification (e.g., healthy vs. cancerous tissue), detection (e.g., lymphocytes and mitosis counting), and segmentation (e.g., nuclei and glands segmentation). The majority of recent machine learning methods in digital pathology have a pre- and/or post-processing stage which is integrated with a deep neural network. These stages, based on traditional image processing methods, are employed to make the subsequent classification, detection, or segmentation problem easier to solve. Several studies have shown how the integration of pre- and post-processing methods within a deep learning pipeline can further increase the model's performance when compared to the network by itself. The aim of this review is to provide an overview on the types of methods that are used within deep learning frameworks either to optimally prepare the input (pre-processing) or to improve the results of the network output (post-processing), focusing on digital pathology image analysis. Many of the techniques presented here, especially the post-processing methods, are not limited to digital pathology but can be extended to almost any image analysis field