Precision-medicine-toolbox: An open-source python package for facilitation of quantitative medical imaging and radiomics analysis

Medical image analysis plays a key role in precision medicine as it allows the clinicians to identify anatomical abnormalities and it is routinely used in clinical assessment. Data curation and pre-processing of medical images are critical steps in the quantitative medical image analysis that can have a significant impact on the resulting model performance. In this paper, we introduce a precision-medicine-toolbox that allows researchers to perform data curation, image pre-processing and handcrafted radiomics extraction (via Pyradiomics) and feature exploration tasks with Python. With this open-source solution, we aim to address the data preparation and exploration problem, bridge the gap between the currently existing packages, and improve the reproducibility of quantitative medical imaging research.

Transparency of Deep Neural Networks for Medical Image Analysis: A Review of Interpretability Methods

Artificial Intelligence has emerged as a useful aid in numerous clinical applications for diagnosis and treatment decisions. Deep neural networks have shown same or better performance than clinicians in many tasks owing to the rapid increase in the available data and computational power. In order to conform to the principles of trustworthy AI, it is essential that the AI system be transparent, robust, fair and ensure accountability. Current deep neural solutions are referred to as black-boxes due to a lack of understanding of the specifics concerning the decision making process. Therefore, there is a need to ensure interpretability of deep neural networks before they can be incorporated in the routine clinical workflow. In this narrative review, we utilized systematic keyword searches and domain expertise to identify nine different types of interpretability methods that have been used for understanding deep learning models for medical image analysis applications based on the type of generated explanations and technical similarities. Furthermore, we report the progress made towards evaluating the explanations produced by various interpretability methods. Finally we discuss limitations, provide guidelines for using interpretability methods and future directions concerning the interpretability of deep neural networks for medical imaging analysis.

FUTURE-AI: Guiding Principles and Consensus Recommendations for Trustworthy Artificial Intelligence in Medical Imaging

The recent advancements in artificial intelligence (AI) combined with the extensive amount of data generated by today's clinical systems, has led to the development of imaging AI solutions across the whole value chain of medical imaging, including image reconstruction, medical image segmentation, image-based diagnosis and treatment planning. Notwithstanding the successes and future potential of AI in medical imaging, many stakeholders are concerned of the potential risks and ethical implications of imaging AI solutions, which are perceived as complex, opaque, and difficult to comprehend, utilise, and trust in critical clinical applications. Despite these concerns and risks, there are currently no concrete guidelines and best practices for guiding future AI developments in medical imaging towards increased trust, safety and adoption. To bridge this gap, this paper introduces a careful selection of guiding principles drawn from the accumulated experiences, consensus, and best practices from five large European projects on AI in Health Imaging. These guiding principles are named FUTURE-AI and its building blocks consist of (i) Fairness, (ii) Universality, (iii) Traceability, (iv) Usability, (v) Robustness and (vi) Explainability. In a step-by-step approach, these guidelines are further translated into a framework of concrete recommendations for specifying, developing, evaluating, and deploying technically, clinically and ethically trustworthy AI solutions into clinical practice.

Leveraging SLIC Superpixel Segmentation and Cascaded Ensemble SVM for Fully Automated Mass Detection In Mammograms

Identification and segmentation of breast masses in mammograms face complex challenges, owing to the highly variable nature of malignant densities with regards to their shape, contours, texture and orientation. Additionally, classifiers typically suffer from high class imbalance in region candidates, where normal tissue regions vastly outnumber malignant masses. This paper proposes a rigorous segmentation method, supported by morphological enhancement using grayscale linear filters. A novel cascaded ensemble of support vector machines (SVM) is used to effectively tackle the class imbalance and provide significant predictions. For True Positive Rate (TPR) of 0.35, 0.69 and 0.82, the system generates only 0.1, 0.5 and 1.0 False Positives/Image (FPI), respectively.

Multi-Resolution 3D Convolutional Neural Networks for Automatic Coronary Centerline Extraction in Cardiac CT Angiography Scans

We propose a deep learning-based automatic coronary artery tree centerline tracker (AuCoTrack) extending the vessel tracker by Wolterink (arXiv:1810.03143). A dual pathway Convolutional Neural Network (CNN) operating on multi-scale 3D inputs predicts the direction of the coronary arteries as well as the presence of a bifurcation. A similar multi-scale dual pathway 3D CNN is trained to identify coronary artery endpoints for terminating the tracking process. Two or more continuation directions are derived based on the bifurcation detection. The iterative tracker detects the entire left and right coronary artery trees based on only two ostium landmarks derived from a model-based segmentation of the heart. The 3D CNNs were trained on a proprietary dataset consisting of 43 CCTA scans. An average sensitivity of 87.1% and clinically relevant overlap of 89.1% was obtained relative to a refined manual segmentation. In addition, the MICCAI 2008 Coronary Artery Tracking Challenge (CAT08) training and test datasets were used to benchmark the algorithm and to assess its generalization. An average overlap of 93.6% and a clinically relevant overlap of 96.4% were obtained. The proposed method achieved better overlap scores than the current state-of-the-art automatic centerline extraction techniques on the CAT08 dataset with a vessel detection rate of 95%.