Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Medical imaging analysis with artificial neural networks

Given that neural networks have been widely reported in the research community of medical imaging, we provide a focused literature survey on recent neural network developments in computer-aided diagnosis, medical image segmentation and edge detection towards visual content analysis, and medical image registration for its pre-processing and post-processing, with the aims of increasing awareness of how neural networks can be applied to these areas and to provide a foundation for further research and practical development. Representative techniques and algorithms are explained in detail to provide inspiring examples illustrating: (i) how a known neural network with fixed structure and training procedure could be applied to resolve a medical imaging problem; (ii) how medical images could be analysed, processed, and characterised by neural networks; and (iii) how neural networks could be expanded further to resolve problems relevant to medical imaging. In the concluding section, a highlight of comparisons among many neural network applications is included to provide a global view on computational intelligence with neural networks in medical imaging

GLOBAL OPTIMIZATION METHODS

Training a neural network is a difficult optimization problem because of numerous local minimums. Many global search algorithms have been used to train neural networks. However, local search algorithms are more efficient with computational resources, and therefore numerous random restarts with a local algorithm may be more effective than a global algorithm. This study uses Monte-Carlo simulations to determine the relative efficiency of a local search algorithm to 9 stochastic global algorithms. The computational requirements of the global algorithms are several times higher than the local algorithm and there is little gain in using the global algorithms to train neural networks.Research Methods/ Statistical Methods,

Sparse Modeling for Image and Vision Processing

In recent years, a large amount of multi-disciplinary research has been conducted on sparse models and their applications. In statistics and machine learning, the sparsity principle is used to perform model selection---that is, automatically selecting a simple model among a large collection of them. In signal processing, sparse coding consists of representing data with linear combinations of a few dictionary elements. Subsequently, the corresponding tools have been widely adopted by several scientific communities such as neuroscience, bioinformatics, or computer vision. The goal of this monograph is to offer a self-contained view of sparse modeling for visual recognition and image processing. More specifically, we focus on applications where the dictionary is learned and adapted to data, yielding a compact representation that has been successful in various contexts.Comment: 205 pages, to appear in Foundations and Trends in Computer Graphics and Visio

Storage Capacity Estimation of Commercial Scale Injection and Storage of CO2 in the Jacksonburg-Stringtown Oil Field, West Virginia

Geological capture, utilization and storage (CCUS) of carbon dioxide (CO2) in depleted oil and gas reservoirs is one method to reduce greenhouse gas emissions with enhanced oil recovery (EOR) and extending the life of the field. Therefore CCUS coupled with EOR is considered to be an economic approach to demonstration of commercial-scale injection and storage of anthropogenic CO2. Several critical issues should be taken into account prior to injecting large volumes of CO2, such as storage capacity, project duration and long-term containment. Reservoir characterization and 3D geological modeling are the best way to estimate the theoretical CO 2 storage capacity in mature oil fields. The Jacksonburg-Stringtown field, located in northwestern West Virginia, has produced over 22 million barrels of oil (MMBO) since 1895. The sandstone of the Late Devonian Gordon Stray is the primary reservoir.;The Upper Devonian fluvial sandstone reservoirs in Jacksonburg-Stringtown oil field, which has produced over 22 million barrels of oil since 1895, are an ideal candidate for CO2 sequestration coupled with EOR. Supercritical depth (\u3e2500 ft.), minimum miscible pressure (941 psi), favorable API gravity (46.5°) and good water flood response are indicators that facilitate CO 2-EOR operations. Moreover, Jacksonburg-Stringtown oil field is adjacent to a large concentration of CO2 sources located along the Ohio River that could potentially supply enough CO2 for sequestration and EOR without constructing new pipeline facilities.;Permeability evaluation is a critical parameter to understand the subsurface fluid flow and reservoir management for primary and enhanced hydrocarbon recovery and efficient carbon storage. In this study, a rapid, robust and cost-effective artificial neural network (ANN) model is constructed to predict permeability using the model\u27s strong ability to recognize the possible interrelationships between input and output variables. Two commonly available conventional well logs, gamma ray and bulk density, and three logs derived variables, the slope of GR, the slope of bulk density and Vsh were selected as input parameters and permeability was selected as desired output parameter to train and test an artificial neural network. The results indicate that the ANN model can be applied effectively in permeability prediction.;Porosity is another fundamental property that characterizes the storage capability of fluid and gas bearing formations in a reservoir. In this study, a support vector machine (SVM) with mixed kernels function (MKF) is utilized to construct the relationship between limited conventional well log suites and sparse core data. The input parameters for SVM model consist of core porosity values and the same log suite as ANN\u27s input parameters, and porosity is the desired output. Compared with results from the SVM model with a single kernel function, mixed kernel function based SVM model provide more accurate porosity prediction values.;Base on the well log analysis, four reservoir subunits within a marine-dominated estuarine depositional system are defined: barrier sand, central bay shale, tidal channels and fluvial channel subunits. A 3-D geological model, which is used to estimate theoretical CO2 sequestration capacity, is constructed with the integration of core data, wireline log data and geological background knowledge. Depending on the proposed 3-D geological model, the best regions for coupled CCUS-EOR are located in southern portions of the field, and the estimated CO2 theoretical storage capacity for Jacksonburg-Stringtown oil field vary between 24 to 383 million metric tons. The estimation results of CO2 sequestration and EOR potential indicate that the Jacksonburg-Stringtown oilfield has significant potential for CO2 storage and value-added EOR