NiftyNet: a deep-learning platform for medical imaging

Medical image analysis and computer-assisted intervention problems are increasingly being addressed with deep-learning-based solutions. Established deep-learning platforms are flexible but do not provide specific functionality for medical image analysis and adapting them for this application requires substantial implementation effort. Thus, there has been substantial duplication of effort and incompatible infrastructure developed across many research groups. This work presents the open-source NiftyNet platform for deep learning in medical imaging. The ambition of NiftyNet is to accelerate and simplify the development of these solutions, and to provide a common mechanism for disseminating research outputs for the community to use, adapt and build upon. NiftyNet provides a modular deep-learning pipeline for a range of medical imaging applications including segmentation, regression, image generation and representation learning applications. Components of the NiftyNet pipeline including data loading, data augmentation, network architectures, loss functions and evaluation metrics are tailored to, and take advantage of, the idiosyncracies of medical image analysis and computer-assisted intervention. NiftyNet is built on TensorFlow and supports TensorBoard visualization of 2D and 3D images and computational graphs by default. We present 3 illustrative medical image analysis applications built using NiftyNet: (1) segmentation of multiple abdominal organs from computed tomography; (2) image regression to predict computed tomography attenuation maps from brain magnetic resonance images; and (3) generation of simulated ultrasound images for specified anatomical poses. NiftyNet enables researchers to rapidly develop and distribute deep learning solutions for segmentation, regression, image generation and representation learning applications, or extend the platform to new applications.Comment: Wenqi Li and Eli Gibson contributed equally to this work. M. Jorge Cardoso and Tom Vercauteren contributed equally to this work. 26 pages, 6 figures; Update includes additional applications, updated author list and formatting for journal submissio

Analyzing satellite images by apply deep learning instance segmentation of agricultural fields

This novel research focuses on multi-exposure satellite images of agricultural fields using image analysis and deep learning techniques. The development of image edge smoothening system using CNN is in hot pursuit, with special attention being given to the smoothening of all the edges of image. Given its high propensity to meta-size, going hand in hand with severe decreases in preservation rates, and the high inter-edge variability in image appearance, as well as a strong requirement on the training of the physician properly de-noising an image can be considered a daunting task. The purpose of this advance research is to use a deep learning and image analysis pipeline for multi-exposure satellite image for the segmentation of edges in an image using with hybrid techniques in deep learning and imaging. The literature review of different papers was conducted with different imaging model architectures. The CNN custom model was created for the task, and deep learning technique (CNN) was used with different levels of fine tuning of hybrid satellite image analysis techniques. Screening for high edge filter to identify edges at high accuracy has been under debate. The custom deep learning model architectures were designed to represent different depths. Additionally, deep learning CNN model was created to represent traditional automated image analysis approach. The study also attempts to find solutions to practical deep learning challenges such as low training speed and lack of transparency with an accuracy of 98.17% absolutely

Pediatric Bone Age Assessment Using Deep Convolutional Neural Networks

Skeletal bone age assessment is a common clinical practice to diagnose endocrine and metabolic disorders in child development. In this paper, we describe a fully automated deep learning approach to the problem of bone age assessment using data from Pediatric Bone Age Challenge organized by RSNA 2017. The dataset for this competition is consisted of 12.6k radiological images of left hand labeled by the bone age and sex of patients. Our approach utilizes several deep learning architectures: U-Net, ResNet-50, and custom VGG-style neural networks trained end-to-end. We use images of whole hands as well as specific parts of a hand for both training and inference. This approach allows us to measure importance of specific hand bones for the automated bone age analysis. We further evaluate performance of the method in the context of skeletal development stages. Our approach outperforms other common methods for bone age assessment.Comment: 14 pages, 9 figure

Artificial Intelligence & Machine Learning in Computer Vision Applications

Deep learning and machine learning innovations are at the core of the ongoing revolution in Artificial Intelligence for the interpretation and analysis of multimedia data. The convergence of large-scale datasets and more affordable Graphics Processing Unit (GPU) hardware has enabled the development of neural networks for data analysis problems that were previously handled by traditional handcrafted features. Several deep learning architectures such as Convolutional Neural Networks (CNNs), Recurrent Neural Networks (RNNs), Long Short Term Memory (LSTM)/Gated Recurrent Unit (GRU), Deep Believe Networks (DBN), and Deep Stacking Networks (DSNs) have been used with new open source software and libraries options to shape an entirely new scenario in computer vision processing

Nature inspired meta-heuristic algorithms for deep learning: recent progress and novel perspective

Deep learning is presently attracting extra ordinary attention from both the industry and the academia. The application of deep learning in computer vision has recently gain popularity. The optimization of deep learning models through nature inspired algorithms is a subject of debate in computer science. The application areas of the hybrid of natured inspired algorithms and deep learning architecture includes: machine vision and learning, image processing, data science, autonomous vehicles, medical image analysis, biometrics, etc. In this paper, we present recent progress on the application of nature inspired algorithms in deep learning. The survey pointed out recent development issues, strengths, weaknesses and prospects for future research. A new taxonomy is created based on natured inspired algorithms for deep learning. The trend of the publications in this domain is depicted; it shows the research area is growing but slowly. The deep learning architectures not exploit by the nature inspired algorithms for optimization are unveiled. We believed that the survey can facilitate synergy between the nature inspired algorithms and deep learning research communities. As such, massive attention can be expected in a near future

Deep Learning in Single-Cell Analysis

Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high-dimensional, sparse, heterogeneous, and have complicated dependency structures, making analyses using conventional machine learning approaches challenging and impractical. In tackling these challenges, deep learning often demonstrates superior performance compared to traditional machine learning methods. In this work, we give a comprehensive survey on deep learning in single-cell analysis. We first introduce background on single-cell technologies and their development, as well as fundamental concepts of deep learning including the most popular deep architectures. We present an overview of the single-cell analytic pipeline pursued in research applications while noting divergences due to data sources or specific applications. We then review seven popular tasks spanning through different stages of the single-cell analysis pipeline, including multimodal integration, imputation, clustering, spatial domain identification, cell-type deconvolution, cell segmentation, and cell-type annotation. Under each task, we describe the most recent developments in classical and deep learning methods and discuss their advantages and disadvantages. Deep learning tools and benchmark datasets are also summarized for each task. Finally, we discuss the future directions and the most recent challenges. This survey will serve as a reference for biologists and computer scientists, encouraging collaborations.Comment: 77 pages, 11 figures, 15 tables, deep learning, single-cell analysi

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 neural networks architectures from the perspective of manifold learning

Despite significant advances in the field of deep learning in ap-plications to various areas, an explanation of the learning pro-cess of neural network models remains an important open ques-tion. The purpose of this paper is a comprehensive comparison and description of neural network architectures in terms of ge-ometry and topology. We focus on the internal representation of neural networks and on the dynamics of changes in the topology and geometry of a data manifold on different layers. In this paper, we use the concepts of topological data analysis (TDA) and persistent homological fractal dimension. We present a wide range of experiments with various datasets and configurations of convolutional neural network (CNNs) architectures and Transformers in CV and NLP tasks. Our work is a contribution to the development of the important field of explainable and interpretable AI within the framework of geometrical deep learning.Comment: 11 pages, 12 figures, PRAI2023. arXiv admin note: substantial text overlap with arXiv:2204.0862