Multi-modal and multi-dimensional biomedical image data analysis using deep learning

There is a growing need for the development of computational methods and tools for automated, objective, and quantitative analysis of biomedical signal and image data to facilitate disease and treatment monitoring, early diagnosis, and scientific discovery. Recent advances in artificial intelligence and machine learning, particularly in deep learning, have revolutionized computer vision and image analysis for many application areas. While processing of non-biomedical signal, image, and video data using deep learning methods has been very successful, high-stakes biomedical applications present unique challenges such as different image modalities, limited training data, need for explainability and interpretability etc. that need to be addressed. In this dissertation, we developed novel, explainable, and attention-based deep learning frameworks for objective, automated, and quantitative analysis of biomedical signal, image, and video data. The proposed solutions involve multi-scale signal analysis for oraldiadochokinesis studies; ensemble of deep learning cascades using global soft attention mechanisms for segmentation of meningeal vascular networks in confocal microscopy; spatial attention and spatio-temporal data fusion for detection of rare and short-term video events in laryngeal endoscopy videos; and a novel discrete Fourier transform driven class activation map for explainable-AI and weakly-supervised object localization and segmentation for detailed vocal fold motion analysis using laryngeal endoscopy videos. Experiments conducted on the proposed methods showed robust and promising results towards automated, objective, and quantitative analysis of biomedical data, that is of great value for potential early diagnosis and effective disease progress or treatment monitoring.Includes bibliographical references

Using deep learning to identify the recurrent laryngeal nerve during thyroidectomy

Surgeons must visually distinguish soft-tissues, such as nerves, from surrounding anatomy to prevent complications and optimize patient outcomes. An accurate nerve segmentation and analysis tool could provide useful insight for surgical decision-making. Here, we present an end-to-end, automatic deep learning computer vision algorithm to segment and measure nerves. Unlike traditional medical imaging, our unconstrained setup with accessible handheld digital cameras, along with the unstructured open surgery scene, makes this task uniquely challenging. We investigate one common procedure, thyroidectomy, during which surgeons must avoid damaging the recurrent laryngeal nerve (RLN), which is responsible for human speech. We evaluate our segmentation algorithm on a diverse dataset across varied and challenging settings of operating room image capture, and show strong segmentation performance in the optimal image capture condition. This work lays the foundation for future research in real-time tissue discrimination and integration of accessible, intelligent tools into open surgery to provide actionable insights.ope

Instance segmentation of upper aerodigestive tract cancer: site-specific outcomes

Objective. To achieve instance segmentation of upper aerodigestive tract (UADT) neoplasms using a deep learning (DL) algorithm, and to identify differences in its diagnostic performance in three different sites: larynx/hypopharynx, oral cavity and oropharynx.Methods. A total of 1034 endoscopic images from 323 patients were examined under narrow band imaging (NBI). The Mask R-CNN algorithm was used for the analysis. The dataset split was: 935 training, 48 validation and 51 testing images. Dice Similarity Coefficient (Dsc) was the main outcome measure.Results. Instance segmentation was effective in 76.5% of images. The mean Dsc was 0.90 & PLUSMN; 0.05. The algorithm correctly predicted 77.8%, 86.7% and 55.5% of lesions in the larynx/hypopharynx, oral cavity, and oropharynx, respectively. The mean Dsc was 0.90 & PLUSMN; 0.05 for the larynx/hypopharynx, 0.60 & PLUSMN; 0.26 for the oral cavity, and 0.81 & PLUSMN; 0.30 for the oropharynx. The analysis showed inferior diagnostic results in the oral cavity compared with the larynx/hypopharynx (p < 0.001). Conclusions. The study confirms the feasibility of instance segmentation of UADT using DL algorithms and shows inferior diagnostic results in the oral cavity compared with other anatomic areas

Invariant Scattering Transform for Medical Imaging

Invariant scattering transform introduces new area of research that merges the signal processing with deep learning for computer vision. Nowadays, Deep Learning algorithms are able to solve a variety of problems in medical sector. Medical images are used to detect diseases brain cancer or tumor, Alzheimer's disease, breast cancer, Parkinson's disease and many others. During pandemic back in 2020, machine learning and deep learning has played a critical role to detect COVID-19 which included mutation analysis, prediction, diagnosis and decision making. Medical images like X-ray, MRI known as magnetic resonance imaging, CT scans are used for detecting diseases. There is another method in deep learning for medical imaging which is scattering transform. It builds useful signal representation for image classification. It is a wavelet technique; which is impactful for medical image classification problems. This research article discusses scattering transform as the efficient system for medical image analysis where it's figured by scattering the signal information implemented in a deep convolutional network. A step by step case study is manifested at this research work.Comment: 11 pages, 8 figures and 1 tabl

Noninvasive Dynamic Characterization of Swallowing Kinematics and Impairments in High Resolution Cervical Auscultation via Deep Learning

Swallowing is a complex sensorimotor activity by which food and liquids are transferred from the oral cavity to the stomach. Swallowing requires the coordination between multiple subsystems which makes it subject to impairment secondary to a variety of medical or surgically related conditions. Dysphagia refers to any swallowing disorder and is common in patients with head and neck cancer and neurological conditions such as stroke. Dysphagia affects nearly 9 million adults and causes death for more than 60,000 yearly in the US. In this research, we utilize advanced signal processing techniques with sensor technology and deep learning methods to develop a noninvasive and widely available tool for the evaluation and diagnosis of swallowing problems. We investigate the use of modern spectral estimation methods in addition to convolutional recurrent neural networks to demarcate and localize the important swallowing physiological events that contribute to airway protection solely based on signals collected from non-invasive sensors attached to the anterior neck. These events include the full swallowing activity, upper esophageal sphincter opening duration and maximal opening diameter, and aspiration. We believe that combining sensor technology and state of the art deep learning architectures specialized in time series analysis, will help achieve great advances for dysphagia detection and management in terms of non-invasiveness, portability, and availability. Like never before, such advances will enable patients to get continuous feedback about their swallowing out of standard clinical care setting which will extremely facilitate their daily activities and enhance the quality of their lives

Advances in Management of Voice and Swallowing Disorders

Special Issue “Advances in Management of Voice and Swallowing Disorders” is dedicated to innovations in screening and assessment and the effectiveness of interventions in both dysphonia and dysphagia. In contemporary practice, novel techniques have been introduced in diagnostics and rehabilitative interventions (e.g., machine learning, electrical stimulation). Similarly, advancements in methodological approaches to validate measures have been introduced (e.g., item response theory using Rasch analysis), prompting the need to develop new, robust measures for use in clinics and intervention studies. Against this backdrop, this Special Issue focuses on studies aiming to improve early diagnostics of laryngological disorders and its management. This issue also welcomes the submission of studies on diagnostic accuracy and psychometrics performance of existing and newly developed measures. This includes but is not limited to studies investigating screening tools with sound diagnostic accuracy and robust psychometric properties. Furthermore, interventions with high levels of evidence in relation to clinical outcome using robust methodology (e.g., sophisticated meta-analytic approaches) are of great interest. This issue provides an overview of the latest advances in voice and swallowing disorders

Wearable and Nearable Biosensors and Systems for Healthcare

Biosensors and systems in the form of wearables and “nearables” (i.e., everyday sensorized objects with transmitting capabilities such as smartphones) are rapidly evolving for use in healthcare. Unlike conventional approaches, these technologies can enable seamless or on-demand physiological monitoring, anytime and anywhere. Such monitoring can help transform healthcare from the current reactive, one-size-fits-all, hospital-centered approach into a future proactive, personalized, decentralized structure. Wearable and nearable biosensors and systems have been made possible through integrated innovations in sensor design, electronics, data transmission, power management, and signal processing. Although much progress has been made in this field, many open challenges for the scientific community remain, especially for those applications requiring high accuracy. This book contains the 12 papers that constituted a recent Special Issue of Sensors sharing the same title. The aim of the initiative was to provide a collection of state-of-the-art investigations on wearables and nearables, in order to stimulate technological advances and the use of the technology to benefit healthcare. The topics covered by the book offer both depth and breadth pertaining to wearable and nearable technology. They include new biosensors and data transmission techniques, studies on accelerometers, signal processing, and cardiovascular monitoring, clinical applications, and validation of commercial devices