Deep Learning in Breast Cancer Imaging: A Decade of Progress and Future Directions

Breast cancer has reached the highest incidence rate worldwide among all malignancies since 2020. Breast imaging plays a significant role in early diagnosis and intervention to improve the outcome of breast cancer patients. In the past decade, deep learning has shown remarkable progress in breast cancer imaging analysis, holding great promise in interpreting the rich information and complex context of breast imaging modalities. Considering the rapid improvement in the deep learning technology and the increasing severity of breast cancer, it is critical to summarize past progress and identify future challenges to be addressed. In this paper, we provide an extensive survey of deep learning-based breast cancer imaging research, covering studies on mammogram, ultrasound, magnetic resonance imaging, and digital pathology images over the past decade. The major deep learning methods, publicly available datasets, and applications on imaging-based screening, diagnosis, treatment response prediction, and prognosis are described in detail. Drawn from the findings of this survey, we present a comprehensive discussion of the challenges and potential avenues for future research in deep learning-based breast cancer imaging.Comment: Survey, 41 page

Advanced Computational Methods for Oncological Image Analysis

[Cancer is the second most common cause of death worldwide and encompasses highly variable clinical and biological scenarios. Some of the current clinical challenges are (i) early diagnosis of the disease and (ii) precision medicine, which allows for treatments targeted to specific clinical cases. The ultimate goal is to optimize the clinical workflow by combining accurate diagnosis with the most suitable therapies. Toward this, large-scale machine learning research can define associations among clinical, imaging, and multi-omics studies, making it possible to provide reliable diagnostic and prognostic biomarkers for precision oncology. Such reliable computer-assisted methods (i.e., artificial intelligence) together with clinicians’ unique knowledge can be used to properly handle typical issues in evaluation/quantification procedures (i.e., operator dependence and time-consuming tasks). These technical advances can significantly improve result repeatability in disease diagnosis and guide toward appropriate cancer care. Indeed, the need to apply machine learning and computational intelligence techniques has steadily increased to effectively perform image processing operations—such as segmentation, co-registration, classification, and dimensionality reduction—and multi-omics data integration.

Persistent Homology Tools for Image Analysis

Topological Data Analysis (TDA) is a new field of mathematics emerged rapidly since the first decade of the century from various works of algebraic topology and geometry. The goal of TDA and its main tool of persistent homology (PH) is to provide topological insight into complex and high dimensional datasets. We take this premise onboard to get more topological insight from digital image analysis and quantify tiny low-level distortion that are undetectable except possibly by highly trained persons. Such image distortion could be caused intentionally (e.g. by morphing and steganography) or naturally in abnormal human tissue/organ scan images as a result of onset of cancer or other diseases. The main objective of this thesis is to design new image analysis tools based on persistent homological invariants representing simplicial complexes on sets of pixel landmarks over a sequence of distance resolutions. We first start by proposing innovative automatic techniques to select image pixel landmarks to build a variety of simplicial topologies from a single image. Effectiveness of each image landmark selection demonstrated by testing on different image tampering problems such as morphed face detection, steganalysis and breast tumour detection. Vietoris-Rips simplicial complexes constructed based on the image landmarks at an increasing distance threshold and topological (homological) features computed at each threshold and summarized in a form known as persistent barcodes. We vectorise the space of persistent barcodes using a technique known as persistent binning where we demonstrated the strength of it for various image analysis purposes. Different machine learning approaches are adopted to develop automatic detection of tiny texture distortion in many image analysis applications. Homological invariants used in this thesis are the 0 and 1 dimensional Betti numbers. We developed an innovative approach to design persistent homology (PH) based algorithms for automatic detection of the above described types of image distortion. In particular, we developed the first PH-detector of morphing attacks on passport face biometric images. We shall demonstrate significant accuracy of 2 such morph detection algorithms with 4 types of automatically extracted image landmarks: Local Binary patterns (LBP), 8-neighbour super-pixels (8NSP), Radial-LBP (R-LBP) and centre-symmetric LBP (CS-LBP). Using any of these techniques yields several persistent barcodes that summarise persistent topological features that help gaining insights into complex hidden structures not amenable by other image analysis methods. We shall also demonstrate significant success of a similarly developed PH-based universal steganalysis tool capable for the detection of secret messages hidden inside digital images. We also argue through a pilot study that building PH records from digital images can differentiate breast malignant tumours from benign tumours using digital mammographic images. The research presented in this thesis creates new opportunities to build real applications based on TDA and demonstrate many research challenges in a variety of image processing/analysis tasks. For example, we describe a TDA-based exemplar image inpainting technique (TEBI), superior to existing exemplar algorithm, for the reconstruction of missing image regions

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

Multimodal representation learning with neural networks

Abstract: Representation learning methods have received a lot of attention by researchers and practitioners because of their successful application to complex problems in areas such as computer vision, speech recognition and text processing [1]. Many of these promising results are due to the development of methods to automatically learn the representation of complex objects directly from large amounts of sample data [2]. These efforts have concentrated on data involving one type of information (images, text, speech, etc.), despite data being naturally multimodal. Multimodality refers to the fact that the same real-world concept can be described by different views or data types. Addressing multimodal automatic analysis faces three main challenges: feature learning and extraction, modeling of relationships between data modalities and scalability to large multimodal collections [3, 4]. This research considers the problem of leveraging multiple sources of information or data modalities in neural networks. It defines a novel model called gated multimodal unit (GMU), designed as an internal unit in a neural network architecture whose purpose is to find an intermediate representation based on a combination of data from different modalities. The GMU learns to decide how modalities influence the activation of the unit using multiplicative gates. The GMU can be used as a building block for different kinds of neural networks and can be seen as a form of intermediate fusion. The model was evaluated on four supervised learning tasks in conjunction with fully-connected and convolutional neural networks. We compare the GMU with other early and late fusion methods, outperforming classification scores in the evaluated datasets. Strategies to understand how the model gives importance to each input were also explored. By measuring correlation between gate activations and predictions, we were able to associate modalities with classes. It was found that some classes were more correlated with some particular modality. Interesting findings in genre prediction show, for instance, that the model associates the visual information with animation movies while textual information is more associated with drama or romance movies. During the development of this project, three new benchmark datasets were built and publicly released. The BCDR-F03 dataset which contains 736 mammography images and serves as benchmark for mass lesion classification. The MM-IMDb dataset containing around 27000 movie plots, poster along with 50 metadata annotations and that motivates new research in multimodal analysis. And the Goodreads dataset, a collection of 1000 books that encourages the research on success prediction based on the book content. This research also facilitates reproducibility of the present work by releasing source code implementation of the proposed methods.Doctorad

Bioinformatics and Machine Learning for Cancer Biology

Cancer is a leading cause of death worldwide, claiming millions of lives each year. Cancer biology is an essential research field to understand how cancer develops, evolves, and responds to therapy. By taking advantage of a series of “omics” technologies (e.g., genomics, transcriptomics, and epigenomics), computational methods in bioinformatics and machine learning can help scientists and researchers to decipher the complexity of cancer heterogeneity, tumorigenesis, and anticancer drug discovery. Particularly, bioinformatics enables the systematic interrogation and analysis of cancer from various perspectives, including genetics, epigenetics, signaling networks, cellular behavior, clinical manifestation, and epidemiology. Moreover, thanks to the influx of next-generation sequencing (NGS) data in the postgenomic era and multiple landmark cancer-focused projects, such as The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CPTAC), machine learning has a uniquely advantageous role in boosting data-driven cancer research and unraveling novel methods for the prognosis, prediction, and treatment of cancer

Automated Characterisation and Classification of Liver Lesions From CT Scans

Cancer is a general term for a wide range of diseases that can affect any part of the body due to the rapid creation of abnormal cells that grow outside their normal boundaries. Liver cancer is one of the common diseases that cause the death of more than 600,000 each year. Early detection is important to diagnose and reduce the incidence of death. Examination of liver lesions is performed with various medical imaging modalities such as Ultrasound (US), Computer tomography (CT), and Magnetic resonance imaging (MRI). The improvements in medical imaging and image processing techniques have significantly enhanced the interpretation of medical images. Computer-Aided Diagnosis (CAD) systems based on these techniques play a vital role in the early detection of liver disease and hence reduce liver cancer death rate. Moreover, CAD systems can help physician, as a second opinion, in characterising lesions and making the diagnostic decision. Thus, CAD systems have become an important research area. Particularly, these systems can provide diagnostic assistance to doctors to improve overall diagnostic accuracy. The traditional methods to characterise liver lesions and differentiate normal liver tissues from abnormal ones are largely dependent on the radiologists experience. Thus, CAD systems based on the image processing and artificial intelligence techniques gained a lot of attention, since they could provide constructive diagnosis suggestions to clinicians for decision making. The liver lesions are characterised through two ways: (1) Using a content-based image retrieval (CBIR) approach to assist the radiologist in liver lesions characterisation. (2) Calculating the high-level features that describe/ characterise the liver lesion in a way that is interpreted by humans, particularly Radiologists/Clinicians, based on the hand-crafted/engineered computational features (low-level features) and learning process. However, the research gap is related to the high-level understanding and interpretation of the medical image contents from the low-level pixel analysis, based on mathematical processing and artificial intelligence methods. In our work, the research gap is bridged if a relation of image contents to medical meaning in analogy to radiologist understanding is established. This thesis explores an automated system for the classification and characterisation of liver lesions in CT scans. Firstly, the liver is segmented automatically by using anatomic medical knowledge, histogram-based adaptive threshold and morphological operations. The lesions and vessels are then extracted from the segmented liver by applying AFCM and Gaussian mixture model through a region growing process respectively. Secondly, the proposed framework categorises the high-level features into two groups; the first group is the high-level features that are extracted from the image contents such as (Lesion location, Lesion focality, Calcified, Scar, ...); the second group is the high-level features that are inferred from the low-level features through machine learning process to characterise the lesion such as (Lesion density, Lesion rim, Lesion composition, Lesion shape,...). The novel Multiple ROIs selection approach is proposed, in which regions are derived from generating abnormality level map based on intensity difference and the proximity distance for each voxel with respect to the normal liver tissue. Then, the association between low-level, high-level features and the appropriate ROI are derived by assigning the ability of each ROI to represents a set of lesion characteristics. Finally, a novel feature vector is built, based on high-level features, and fed into SVM for lesion classification. In contrast with most existing research, which uses low-level features only, the use of high-level features and characterisation helps in interpreting and explaining the diagnostic decision. The methods are evaluated on a dataset containing 174 CT scans. The experimental results demonstrated that the efficacy of the proposed framework in the successful characterisation and classification of the liver lesions in CT scans. The achieved average accuracy was 95:56% for liver lesion characterisation. While the lesion’s classification accuracy was 97:1% for the entire dataset. The proposed framework is developed to provide a more robust and efficient lesion characterisation framework through comprehensions of the low-level features to generate semantic features. The use of high-level features (characterisation) helps in better interpretation of CT liver images. In addition, the difference-of-features using multiple ROIs were developed for robust capturing of lesion characteristics in a reliable way. This is in contrast to the current research trend of extracting the features from the lesion only and not paying much attention to the relation between lesion and surrounding area. The design of the liver lesion characterisation framework is based on the prior knowledge of the medical background to get a better and clear understanding of the liver lesion characteristics in medical CT images