Cellular Neural Networks with Switching Connections

Artificial neural networks are widely used for parallel processing of data analysis and visual information. The most prominent example of artificial neural networks is a cellular neural network (CNN), composed from two-dimensional arrays of simple first-order dynamical systems (“cells”) that are interconnected by wires. The information, to be processed by a CNN, represents the initial state of the network, and the parallel information processing is performed by converging to one of the stable spatial equilibrium states of the multi-stable CNN. This thesis studies a specific type of CNNs designed to perform the winner-take-all function of finding the largest among the n numbers, using the network dynamics. In a wider context, this amounts to automatically detecting a target spot in the given visual picture. The research, reported in this thesis, demonstrates that the addition of fast on-off switching (blinking) connections significantly improves the functionality of winner-take-all CNNs. Numerical calculations are performed to reveal the dependence of the probability, that the CNN correctly classifies the largest number, on the switching frequency

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

Pushing the Boundaries of Biomolecule Characterization through Deep Learning

The importance of studying biological molecules in living organisms can hardly be overstated as they regulate crucial processes in living matter of all kinds.Their ubiquitous nature makes them relevant for disease diagnosis, drug development, and for our fundamental understanding of the complex systems of biology.However, due to their small size, they scatter too little light on their own to be directly visible and available for study.Thus, it is necessary to develop characterization methods which enable their elucidation even in the regime of very faint signals. Optical systems, utilizing the relatively low intrusiveness of visible light, constitute one such approach of characterization. However, the optical systems currently capable of analyzing single molecules in the nano-sized regime today either require the species of interest to be tagged with visible labels like fluorescence or chemically restrained on a surface to be analyzed.Ergo, there exist effectively no methods of characterizing very small biomolecules under naturally relevant conditions through unobtrusive probing. Nanofluidic Scattering Microscopy is a method introduced in this thesis which bridges this gap by enabling the real-time label-free size-and-weight determination of freely diffusing molecules directly in small nano-sized channels. However, the molecule signals are so faint, and the background noise so complex with high spatial and temporal variation, that standard methods of data analysis are incapable of elucidating the molecules\u27 properties of relevance in any but the least challenging conditions.To remedy the weak signal, and realize the method\u27s full potential, this thesis\u27 focus is the development of a versatile deep-learning based computer-vision platform to overcome the bottleneck of data analysis. We find that said platform has considerably increased speed, accuracy, precision and limit of detection compared to standard methods, constituting even a lower detection limit than any other method of label-free optical characterization currently available. In this regime, hitherto elusive species of biomolecules become accessible for study, potentially opening up entirely new avenues of biological research. These results, along with many others in the context of deep learning for optical microscopy in biological applications, suggest that deep learning is likely to be pivotal in solving the complex image analysis problems of the present and enabling new regimes of study within microscopy-based research in the near future

Neural-network-aided automatic modulation classification

Automatic modulation classification (AMC) is a pattern matching problem which significantly impacts divers telecommunication systems, with significant applications in military and civilian contexts alike. Although its appearance in the literature is far from novel, recent developments in machine learning technologies have triggered an increased interest in this area of research. In the first part of this thesis, an AMC system is studied where, in addition to the typical point-to-point setup of one receiver and one transmitter, a second transmitter is also present, which is considered an interfering device. A convolutional neural network (CNN) is used for classification. In addition to studying the effect of interference strength, we propose a modification attempting to leverage some of the debilitating results of interference, and also study the effect of signal quantisation upon classification performance. Consequently, we assess a cooperative setting of AMC, namely one where the receiver features multiple antennas, and receives different versions of the same signal from the single-antenna transmitter. Through the combination of data from different antennas, it is evidenced that this cooperative approach leads to notable performance improvements over the established baseline. Finally, the cooperative scenario is expanded to a more complicated setting, where a realistic geographic distribution of four receiving nodes is modelled, and furthermore, the decision-making mechanism with regard to the identity of a signal resides in a fusion centre independent of the receivers, connected to them over finite-bandwidth backhaul links. In addition to the common concerns over classification accuracy and inference time, data reduction methods of various types (including “trained” lossy compression) are implemented with the objective of minimising the data load placed upon the backhaul links.Open Acces

Advanced machine learning methods for oncological image analysis

Cancer is a major public health problem, accounting for an estimated 10 million deaths worldwide in 2020 alone. Rapid advances in the field of image acquisition and hardware development over the past three decades have resulted in the development of modern medical imaging modalities that can capture high-resolution anatomical, physiological, functional, and metabolic quantitative information from cancerous organs. Therefore, the applications of medical imaging have become increasingly crucial in the clinical routines of oncology, providing screening, diagnosis, treatment monitoring, and non/minimally- invasive evaluation of disease prognosis. The essential need for medical images, however, has resulted in the acquisition of a tremendous number of imaging scans. Considering the growing role of medical imaging data on one side and the challenges of manually examining such an abundance of data on the other side, the development of computerized tools to automatically or semi-automatically examine the image data has attracted considerable interest. Hence, a variety of machine learning tools have been developed for oncological image analysis, aiming to assist clinicians with repetitive tasks in their workflow. This thesis aims to contribute to the field of oncological image analysis by proposing new ways of quantifying tumor characteristics from medical image data. Specifically, this thesis consists of six studies, the first two of which focus on introducing novel methods for tumor segmentation. The last four studies aim to develop quantitative imaging biomarkers for cancer diagnosis and prognosis. The main objective of Study I is to develop a deep learning pipeline capable of capturing the appearance of lung pathologies, including lung tumors, and integrating this pipeline into the segmentation networks to leverage the segmentation accuracy. The proposed pipeline was tested on several comprehensive datasets, and the numerical quantifications show the superiority of the proposed prior-aware DL framework compared to the state of the art. Study II aims to address a crucial challenge faced by supervised segmentation models: dependency on the large-scale labeled dataset. In this study, an unsupervised segmentation approach is proposed based on the concept of image inpainting to segment lung and head- neck tumors in images from single and multiple modalities. The proposed autoinpainting pipeline shows great potential in synthesizing high-quality tumor-free images and outperforms a family of well-established unsupervised models in terms of segmentation accuracy. Studies III and IV aim to automatically discriminate the benign from the malignant pulmonary nodules by analyzing the low-dose computed tomography (LDCT) scans. In Study III, a dual-pathway deep classification framework is proposed to simultaneously take into account the local intra-nodule heterogeneities and the global contextual information. Study IV seeks to compare the discriminative power of a series of carefully selected conventional radiomics methods, end-to-end Deep Learning (DL) models, and deep features-based radiomics analysis on the same dataset. The numerical analyses show the potential of fusing the learned deep features into radiomic features for boosting the classification power. Study V focuses on the early assessment of lung tumor response to the applied treatments by proposing a novel feature set that can be interpreted physiologically. This feature set was employed to quantify the changes in the tumor characteristics from longitudinal PET-CT scans in order to predict the overall survival status of the patients two years after the last session of treatments. The discriminative power of the introduced imaging biomarkers was compared against the conventional radiomics, and the quantitative evaluations verified the superiority of the proposed feature set. Whereas Study V focuses on a binary survival prediction task, Study VI addresses the prediction of survival rate in patients diagnosed with lung and head-neck cancer by investigating the potential of spherical convolutional neural networks and comparing their performance against other types of features, including radiomics. While comparable results were achieved in intra- dataset analyses, the proposed spherical-based features show more predictive power in inter-dataset analyses. In summary, the six studies incorporate different imaging modalities and a wide range of image processing and machine-learning techniques in the methods developed for the quantitative assessment of tumor characteristics and contribute to the essential procedures of cancer diagnosis and prognosis

Unveiling the frontiers of deep learning: innovations shaping diverse domains

Deep learning (DL) enables the development of computer models that are capable of learning, visualizing, optimizing, refining, and predicting data. In recent years, DL has been applied in a range of fields, including audio-visual data processing, agriculture, transportation prediction, natural language, biomedicine, disaster management, bioinformatics, drug design, genomics, face recognition, and ecology. To explore the current state of deep learning, it is necessary to investigate the latest developments and applications of deep learning in these disciplines. However, the literature is lacking in exploring the applications of deep learning in all potential sectors. This paper thus extensively investigates the potential applications of deep learning across all major fields of study as well as the associated benefits and challenges. As evidenced in the literature, DL exhibits accuracy in prediction and analysis, makes it a powerful computational tool, and has the ability to articulate itself and optimize, making it effective in processing data with no prior training. Given its independence from training data, deep learning necessitates massive amounts of data for effective analysis and processing, much like data volume. To handle the challenge of compiling huge amounts of medical, scientific, healthcare, and environmental data for use in deep learning, gated architectures like LSTMs and GRUs can be utilized. For multimodal learning, shared neurons in the neural network for all activities and specialized neurons for particular tasks are necessary.Comment: 64 pages, 3 figures, 3 table

Deep learning tools for outcome prediction in a trial fibrilation from cardiac MRI

Tese de mestrado integrado em Engenharia Biomédica e Biofísica (Engenharia Clínica e Instrumentação Médica), Universidade de Lisboa, Faculdade de Ciências, 2021Atrial fibrillation (AF), is the most frequent sustained cardiac arrhythmia, described by an irregular and rapid contraction of the two upper chambers of the heart (the atria). AF development is promoted and predisposed by atrial dilation, which is a consequence of atria adaptation to AF. However, it is not clear whether atrial dilation appears similarly over the cardiac cycle and how it affects ventricular volumes. Catheter ablation is arguably the AF gold standard treatment. In their current form, ablations are capable of directly terminating AF in selected patients but are only first-time effective in approximately 50% of the cases. In the first part of this work, volumetric functional markers of the left atrium (LA) and left ventricle (LV) of AF patients were studied. More precisely, a customised convolutional neural network (CNN) was proposed to segment, across the cardiac cycle, the LA from short axis CINE MRI images acquired with full cardiac coverage in AF patients. Using the proposed automatic LA segmentation, volumetric time curves were plotted and ejection fractions (EF) were automatically calculated for both chambers. The second part of the project was dedicated to developing classification models based on cardiac MR images. The EMIDEC STACOM 2020 challenge was used as an initial project and basis to create binary classifiers based on fully automatic classification neural networks (NNs), since it presented a relatively simple binary classification task (presence/absence of disease) and a large dataset. For the challenge, a deep learning NN was proposed to automatically classify myocardial disease from delayed enhancement cardiac MR (DE-CMR) and patient clinical information. The highest classification accuracy (100%) was achieved with Clinic-NET+, a NN that used information from images, segmentations and clinical annotations. For the final goal of this project, the previously referred NNs were re-trained to predict AF recurrence after catheter ablation (CA) in AF patients using pre-ablation LA short axis in CINE MRI images. In this task, the best overall performance was achieved by Clinic-NET+ with a test accuracy of 88%. This work shown the potential of NNs to interpret and extract clinical information from cardiac MRI. If more data is available, in the future, these methods can potentially be used to help and guide clinical AF prognosis and diagnosis