Artificial neural networks : A comparative study of implementations for human chromosome classification

Artificial neural networks are a popular field of artificial intelligence and have commonly been applied to solve many prediction, classification and diagnostic tasks. One such task is the analysis of human chromosomes. This thesis investigates the use of artificial neural networks (ANNs) as automated chromosome classifiers. The investigation involves the thorough analysis of seven different implementation techniques. These include three techniques using artificial neural networks, two techniques using ANN s supported by another method and two techniques not using ANNs. These seven implementations are evaluated according to the classification accuracy achieved and according to their support of important system measures, such as robustness and validity. The results collected show that ANNs perform relatively well in terms of classification accuracy, though other implementations achieved higher results. However, ANNs provide excellent support of essential system measures. This leads to a well-rounded implementation, consisting of a good balance between accuracy and system features, and thus an effective technique for automated human chromosome classification

U-Net and its variants for medical image segmentation: theory and applications

U-net is an image segmentation technique developed primarily for medical image analysis that can precisely segment images using a scarce amount of training data. These traits provide U-net with a very high utility within the medical imaging community and have resulted in extensive adoption of U-net as the primary tool for segmentation tasks in medical imaging. The success of U-net is evident in its widespread use in all major image modalities from CT scans and MRI to X-rays and microscopy. Furthermore, while U-net is largely a segmentation tool, there have been instances of the use of U-net in other applications. As the potential of U-net is still increasing, in this review we look at the various developments that have been made in the U-net architecture and provide observations on recent trends. We examine the various innovations that have been made in deep learning and discuss how these tools facilitate U-net. Furthermore, we look at image modalities and application areas where U-net has been applied.Comment: 42 pages, in IEEE Acces

SpinX: Time-resolved 3D Analysis of Spindle Dynamics using Deep Learning Techniques and Mathematical Modelling.

PhD ThesesLive-cell movies generate terabytes of data. However, manual analysis of this data is prone to error and can easily exhaust days of research time, thus limiting the insights that can be gleaned from cutting edge microscopes. Automated analysis has been hard because of discontinuities between the distinct frames of 3D live-cell movies. We present SpinX, a comprehensive and extensible computational framework which bridges the gaps between discontinuous frames in time lapse movies by utilising state-of-the-art Deep Learning technologies and modelling for 3D reconstruction of highly mobile subcellular structures. Using SpinX, we are now in a position to precisely track and analyse the movements of multiple subcellular structures within minutes, including the cell cortex, chromosomes and the mitotic spindle. We demonstrate the utility of SpinX by employing it to define the precise roles of spindle movement regulators that ultimately determine the plane of cell division. We illustrate the extensibility of SpinX by showing how it can also be used to infer the regulation of complex cortex-microtubule interactions. Our analyses reveal previously unrecognised roles for the evolutionarily conserved Dynein motor and MARK2/Par1 polarity kinase in regulating the 3D movements of the mitotic spindle. Thus, SpinX provides an exciting opportunity to study spindle dynamics in relation to the cell cortex using hundreds of time-resolved 3D movies in a novel way

Semantic Segmentation of Sorghum Using Hyperspectral Data Identifies Genetic Associations

This study describes the evaluation of a range of approaches to semantic segmentation of hyperspectral images of sorghum plants, classifying each pixel as either nonplant or belonging to one of the three organ types (leaf, stalk, panicle). While many current methods for segmentation focus on separating plant pixels from background, organ-specific segmentation makes it feasible to measure a wider range of plant properties. Manually scored training data for a set of hyperspectral images collected from a sorghum association population was used to train and evaluate a set of supervised classification models. Many algorithms show acceptable accuracy for this classification task. Algorithms trained on sorghum data are able to accurately classify maize leaves and stalks, but fail to accurately classify maize reproductive organs which are not directly equivalent to sorghum panicles. Trait measurements extracted from semantic segmentation of sorghum organs can be used to identify both genes known to be controlling variation in a previously measured phenotypes (e.g., panicle size and plant height) as well as identify signals for genes controlling traits not previously quantified in this population (e.g., stalk/leaf ratio). Organ level semantic segmentation provides opportunities to identify genes controlling variation in a wide range of morphological phenotypes in sorghum, maize, and other related grain crops

Fully Automatic Karyotyping via Deep Convolutional Neural Networks

Chromosome karyotyping is an important yet labor-intensive procedure for diagnosing genetic diseases. Automating such a procedure drastically reduces the manual work of cytologists and increases congenital disease diagnosing precision. Researchers have contributed to chromosome segmentation and classification for decades. However, very few studies integrate the two tasks as a unified, fully automatic procedure or achieved a promising performance. This paper addresses the gap by presenting: 1) A novel chromosome segmentation module named ChrRender, with the idea of rendering the chromosome instances by combining rich global features from the backbone and coarse mask prediction from Mask R-CNN; 2) A devised chromosome classification module named ChrNet4 that pays more attention to channel-wise dependencies from aggregated informative features and calibrating the channel interdependence; 3) An integrated Render-Attention-Architecture to accomplish fully automatic karyotyping with segmentation and classification modules; 4) A strategy for eliminating differences between training data and segmentation output data to be classified. These proposed methods are implemented in three ways on the public Q-band BioImLab dataset and a G-band private dataset. The results indicate promising performance: 1) on the joint karyotyping task, which predicts a karyotype image by first segmenting an original microscopical image, then classifying each segmentation output with a precision of 89.75% and 94.22% on the BioImLab and private dataset, respectively; 2) On the separate task with two datasets, ChrRender obtained AP50 of 96.652% and 96.809% for segmentation, ChrNet4 achieved 95.24% and 94.07% for classification, respectively. The COCO format annotation files of BioImLab used in this paper are available at https://github.com/Alex17swim/BioImLab The study introduces an integrated workflow to predict a karyotyping image from a Microscopical Chromosome Image. With state-of-the-art performance on a public dataset, the proposed Render-Attention-Architecture has accomplished fully automatic chromosome karyotyping

Brain Tumor Characterization Using Radiogenomics in Artificial Intelligence Framework

Brain tumor characterization (BTC) is the process of knowing the underlying cause of brain tumors and their characteristics through various approaches such as tumor segmentation, classification, detection, and risk analysis. The substantial brain tumor characterization includes the identification of the molecular signature of various useful genomes whose alteration causes the brain tumor. The radiomics approach uses the radiological image for disease characterization by extracting quantitative radiomics features in the artificial intelligence (AI) environment. However, when considering a higher level of disease characteristics such as genetic information and mutation status, the combined study of “radiomics and genomics” has been considered under the umbrella of “radiogenomics”. Furthermore, AI in a radiogenomics’ environment offers benefits/advantages such as the finalized outcome of personalized treatment and individualized medicine. The proposed study summarizes the brain tumor’s characterization in the prospect of an emerging field of research, i.e., radiomics and radiogenomics in an AI environment, with the help of statistical observation and risk-of-bias (RoB) analysis. The PRISMA search approach was used to find 121 relevant studies for the proposed review using IEEE, Google Scholar, PubMed, MDPI, and Scopus. Our findings indicate that both radiomics and radiogenomics have been successfully applied aggressively to several oncology applications with numerous advantages. Furthermore, under the AI paradigm, both the conventional and deep radiomics features have made an impact on the favorable outcomes of the radiogenomics approach of BTC. Furthermore, risk-of-bias (RoB) analysis offers a better understanding of the architectures with stronger benefits of AI by providing the bias involved in them

RC-Net: Regression Correction for End-To-End Chromosome Instance Segmentation

Precise segmentation of chromosome in the real image achieved by a microscope is significant for karyotype analysis. The segmentation of image is usually achieved by a pixel-level classification task, which considers different instances as different classes. Many instance segmentation methods predict the Intersection over Union (IoU) through the head branch to correct the classification confidence. Their effectiveness is based on the correlation between branch tasks. However, none of these methods consider the correlation between input and output in branch tasks. Herein, we propose a chromosome instance segmentation network based on regression correction. First, we adopt two head branches to predict two confidences that are more related to localization accuracy and segmentation accuracy to correct the classification confidence, which reduce the omission of predicted boxes in NMS. Furthermore, a NMS algorithm is further designed to screen the target segmentation mask with the IoU of the overlapping instance, which reduces the omission of predicted masks in NMS. Moreover, given the fact that the original IoU loss function is not sensitive to the wrong segmentation, K-IoU loss function is defined to strengthen the penalty of the wrong segmentation, which rationalizes the loss of mis-segmentation and effectively prevents wrong segmentation. Finally, an ablation experiment is designed to evaluate the effectiveness of the chromosome instance segmentation network based on regression correction, which shows that our proposed method can effectively enhance the performance in automatic chromosome segmentation tasks and provide a guarantee for end-to-end karyotype analysis

A Survey on Evolutionary Computation for Computer Vision and Image Analysis: Past, Present, and Future Trends

Computer vision (CV) is a big and important field in artificial intelligence covering a wide range of applications. Image analysis is a major task in CV aiming to extract, analyse and understand the visual content of images. However, imagerelated tasks are very challenging due to many factors, e.g., high variations across images, high dimensionality, domain expertise requirement, and image distortions. Evolutionary computation (EC) approaches have been widely used for image analysis with significant achievement. However, there is no comprehensive survey of existing EC approaches to image analysis. To fill this gap, this paper provides a comprehensive survey covering all essential EC approaches to important image analysis tasks including edge detection, image segmentation, image feature analysis, image classification, object detection, and others. This survey aims to provide a better understanding of evolutionary computer vision (ECV) by discussing the contributions of different approaches and exploring how and why EC is used for CV and image analysis. The applications, challenges, issues, and trends associated to this research field are also discussed and summarised to provide further guidelines and opportunities for future research

Genetic architecture of 11 organ traits derived from abdominal MRI using deep learning.

Cardiometabolic diseases are an increasing global health burden. While socioeconomic, environmental, behavioural, and genetic risk factors have been identified, a better understanding of the underlying mechanisms is required to develop more effective interventions. Magnetic resonance imaging (MRI) has been used to assess organ health, but biobank-scale studies are still in their infancy. Using over 38,000 abdominal MRI scans in the UK Biobank, we used deep learning to quantify volume, fat, and iron in seven organs and tissues, and demonstrate that imaging-derived phenotypes reflect health status. We show that these traits have a substantial heritable component (8-44%) and identify 93 independent genome-wide significant associations, including four associations with liver traits that have not previously been reported. Our work demonstrates the tractability of deep learning to systematically quantify health parameters from high-throughput MRI across a range of organs and tissues, and use the largest-ever study of its kind to generate new insights into the genetic architecture of these traits