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Advanced Interpretable Machine Learning Methods For Clinical Ngs Big Data Of Complex Hereditary Diseases Volume Ii
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Book Synopsis Advanced interpretable machine learning methods for clinical NGS big data of complex hereditary diseases – volume II by : Yudong Cai
Download or read book Advanced interpretable machine learning methods for clinical NGS big data of complex hereditary diseases – volume II written by Yudong Cai and published by Frontiers Media SA. This book was released on 2023-02-13 with total page 194 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Advanced Interpretable Machine Learning Methods for Clinical NGS Big Data of Complex Hereditary Diseases, 2nd Edition by : Yudong Cai
Download or read book Advanced Interpretable Machine Learning Methods for Clinical NGS Big Data of Complex Hereditary Diseases, 2nd Edition written by Yudong Cai and published by Frontiers Media SA. This book was released on 2021-07-01 with total page 219 pages. Available in PDF, EPUB and Kindle. Book excerpt: Publisher’s note: This is a 2nd edition due to an article retraction
Book Synopsis Big Data in Omics and Imaging by : Momiao Xiong
Download or read book Big Data in Omics and Imaging written by Momiao Xiong and published by CRC Press. This book was released on 2017-12-01 with total page 668 pages. Available in PDF, EPUB and Kindle. Book excerpt: Big Data in Omics and Imaging: Association Analysis addresses the recent development of association analysis and machine learning for both population and family genomic data in sequencing era. It is unique in that it presents both hypothesis testing and a data mining approach to holistically dissecting the genetic structure of complex traits and to designing efficient strategies for precision medicine. The general frameworks for association analysis and machine learning, developed in the text, can be applied to genomic, epigenomic and imaging data. FEATURES Bridges the gap between the traditional statistical methods and computational tools for small genetic and epigenetic data analysis and the modern advanced statistical methods for big data Provides tools for high dimensional data reduction Discusses searching algorithms for model and variable selection including randomization algorithms, Proximal methods and matrix subset selection Provides real-world examples and case studies Will have an accompanying website with R code The book is designed for graduate students and researchers in genomics, bioinformatics, and data science. It represents the paradigm shift of genetic studies of complex diseases– from shallow to deep genomic analysis, from low-dimensional to high dimensional, multivariate to functional data analysis with next-generation sequencing (NGS) data, and from homogeneous populations to heterogeneous population and pedigree data analysis. Topics covered are: advanced matrix theory, convex optimization algorithms, generalized low rank models, functional data analysis techniques, deep learning principle and machine learning methods for modern association, interaction, pathway and network analysis of rare and common variants, biomarker identification, disease risk and drug response prediction.
Book Synopsis Machine Learning Advanced Dynamic Omics Data Analysis for Precision Medicine by : Tao Zeng
Download or read book Machine Learning Advanced Dynamic Omics Data Analysis for Precision Medicine written by Tao Zeng and published by . This book was released on 2020 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Precision medicine is being developed as a preventative, diagnostic and treatment tool to combat complex human diseases in a personalized manner. By utilizing high-throughput technologies, dynamic 'omics data including genetics, epi-genetics and even meta-genomics has produced temporal-spatial big biological datasets which can be associated with individual genotypes underlying pathogen progressive phenotypes. It is therefore necessary to investigate how to integrate these multi-scale 'omics datasets to distinguish the novel individual-specific disease causes from conventional cohort-common disease causes. Currently, machine learning plays an important role in biological and biomedical research, especially in the analysis of big 'omics data. However, in contrast to traditional big social data, 'omics datasets are currently always "small-sample-high-dimension", which causes overwhelming application problems and also introduces new challenges: (1) Big 'omics datasets can be extremely unbalanced, due to the difficulty of obtaining enough positive samples of such rare mutations or rare diseases; (2) A large number of machine learning models are "black box," which is enough to apply in social applications. However, in biological or biomedical fields, knowledge of the molecular mechanisms underlying any disease or biological study is necessary to deepen our understanding; (3) The genotype-phenotype association is a "white clue" captured in conventional big data studies. But identification of "causality" rather than association would be more helpful for physicians or biologists, as this can be used to determine an experimental target as the subject of future research. Therefore, to simultaneously improve the phenotype discrimination and genotype interpretability for complex diseases, it is necessary: To design and implement new machine learning technologies to integrate prior-knowledge with new 'omics datasets to provide transferable learning methods by combining multiple sources of data; To develop new network-based theories and methods to balance the trade-off between accuracy and interpretability of machine learning in biomedical and biological domains; To enhance the causality inference on "small-sample high dimension" data to capture the personalized causal relationship.
Book Synopsis Machine Learning in Medicine by : Ton J. Cleophas
Download or read book Machine Learning in Medicine written by Ton J. Cleophas and published by Springer Science & Business Media. This book was released on 2013-05-30 with total page 235 pages. Available in PDF, EPUB and Kindle. Book excerpt: Machine learning is concerned with the analysis of large data and multiple variables. However, it is also often more sensitive than traditional statistical methods to analyze small data. The first volume reviewed subjects like optimal scaling, neural networks, factor analysis, partial least squares, discriminant analysis, canonical analysis, and fuzzy modeling. This second volume includes various clustering models, support vector machines, Bayesian networks, discrete wavelet analysis, genetic programming, association rule learning, anomaly detection, correspondence analysis, and other subjects. Both the theoretical bases and the step by step analyses are described for the benefit of non-mathematical readers. Each chapter can be studied without the need to consult other chapters. Traditional statistical tests are, sometimes, priors to machine learning methods, and they are also, sometimes, used as contrast tests. To those wishing to obtain more knowledge of them, we recommend to additionally study (1) Statistics Applied to Clinical Studies 5th Edition 2012, (2) SPSS for Starters Part One and Two 2012, and (3) Statistical Analysis of Clinical Data on a Pocket Calculator Part One and Two 2012, written by the same authors, and edited by Springer, New York.
Book Synopsis Advanced Prognostic Predictive Modelling in Healthcare Data Analytics by : Sudipta Roy
Download or read book Advanced Prognostic Predictive Modelling in Healthcare Data Analytics written by Sudipta Roy and published by Springer Nature. This book was released on 2021-04-22 with total page 317 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses major technical advancements and research findings in the field of prognostic modelling in healthcare image and data analysis. The use of prognostic modelling as predictive models to solve complex problems of data mining and analysis in health care is the feature of this book. The book examines the recent technologies and studies that reached the practical level and becoming available in preclinical and clinical practices in computational intelligence. The main areas of interest covered in this book are highest quality, original work that contributes to the basic science of processing, analysing and utilizing all aspects of advanced computational prognostic modelling in healthcare image and data analysis.
Book Synopsis Big Data in Omics and Imaging by : Momiao Xiong
Download or read book Big Data in Omics and Imaging written by Momiao Xiong and published by CRC Press. This book was released on 2018-06-14 with total page 736 pages. Available in PDF, EPUB and Kindle. Book excerpt: Big Data in Omics and Imaging: Integrated Analysis and Causal Inference addresses the recent development of integrated genomic, epigenomic and imaging data analysis and causal inference in big data era. Despite significant progress in dissecting the genetic architecture of complex diseases by genome-wide association studies (GWAS), genome-wide expression studies (GWES), and epigenome-wide association studies (EWAS), the overall contribution of the new identified genetic variants is small and a large fraction of genetic variants is still hidden. Understanding the etiology and causal chain of mechanism underlying complex diseases remains elusive. It is time to bring big data, machine learning and causal revolution to developing a new generation of genetic analysis for shifting the current paradigm of genetic analysis from shallow association analysis to deep causal inference and from genetic analysis alone to integrated omics and imaging data analysis for unraveling the mechanism of complex diseases. FEATURES Provides a natural extension and companion volume to Big Data in Omic and Imaging: Association Analysis, but can be read independently. Introduce causal inference theory to genomic, epigenomic and imaging data analysis Develop novel statistics for genome-wide causation studies and epigenome-wide causation studies. Bridge the gap between the traditional association analysis and modern causation analysis Use combinatorial optimization methods and various causal models as a general framework for inferring multilevel omic and image causal networks Present statistical methods and computational algorithms for searching causal paths from genetic variant to disease Develop causal machine learning methods integrating causal inference and machine learning Develop statistics for testing significant difference in directed edge, path, and graphs, and for assessing causal relationships between two networks The book is designed for graduate students and researchers in genomics, epigenomics, medical image, bioinformatics, and data science. Topics covered are: mathematical formulation of causal inference, information geometry for causal inference, topology group and Haar measure, additive noise models, distance correlation, multivariate causal inference and causal networks, dynamic causal networks, multivariate and functional structural equation models, mixed structural equation models, causal inference with confounders, integer programming, deep learning and differential equations for wearable computing, genetic analysis of function-valued traits, RNA-seq data analysis, causal networks for genetic methylation analysis, gene expression and methylation deconvolution, cell –specific causal networks, deep learning for image segmentation and image analysis, imaging and genomic data analysis, integrated multilevel causal genomic, epigenomic and imaging data analysis.
Book Synopsis Machine Learning and Systems Biology in Genomics and Health by : Shailza Singh
Download or read book Machine Learning and Systems Biology in Genomics and Health written by Shailza Singh and published by Springer Nature. This book was released on 2022-02-04 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses the application of machine learning in genomics. Machine Learning offers ample opportunities for Big Data to be assimilated and comprehended effectively using different frameworks. Stratification, diagnosis, classification and survival predictions encompass the different health care regimes representing unique challenges for data pre-processing, model training, refinement of the systems with clinical implications. The book discusses different models for in-depth analysis of different conditions. Machine Learning techniques have revolutionized genomic analysis. Different chapters of the book describe the role of Artificial Intelligence in clinical and genomic diagnostics. It discusses how systems biology is exploited in identifying the genetic markers for drug discovery and disease identification. Myriad number of diseases whether be infectious, metabolic, cancer can be dealt in effectively which combines the different omics data for precision medicine. Major breakthroughs in the field would help reflect more new innovations which are at their pinnacle stage. This book is useful for researchers in the fields of genomics, genetics, computational biology and bioinformatics.
Book Synopsis Biologically Interpretable Machine Learning Methods to Understand Gene Regulation for Disease Phenotypes by : Ting Jin
Download or read book Biologically Interpretable Machine Learning Methods to Understand Gene Regulation for Disease Phenotypes written by Ting Jin and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gene expression and regulation is a key molecular mechanism driving the development of human diseases, particularly at the cell type level, but it remains elusive. For example in many brain diseases, such as Alzheimer's disease (AD), understanding how cell-type gene expression and regulation change across multiple stages of AD progression is still challenging. Moreover, interindividual variability of gene expression and regulation is a known characteristic of the human brain and brain diseases. However, it is still unclear how interindividual variability affects personalized gene regulation in brain diseases including AD, thereby contributing to their heterogeneity. Recent technological advances have enabled the detection of gene regulation activities through multi-omics (i.e., genomics, transcriptomics, epigenomics, proteomics). In particular, emerging single-cell sequencing technologies (e.g., scRNA-seq, scATAC-seq) allow us to study functional genomics and gene regulation at the cell-type level. Moreover, these multi-omics data of populations (e.g., human individuals) provide a unique opportunity to study the underlying regulatory mechanisms occurring in brain disease progression and clinical phenotypes. For instance, PsychAD is a large project generating single-cell multi-omics data including many neuronal and glial cell types, aiming to understand the molecular mechanisms of neuropsychiatric symptoms of multiple brain diseases (e.g., AD, SCZ, ASD, Bipolar) from over 1,000 individuals. However, analyzing and integrating large-scale multi-omics data at the population level, as well as understanding the mechanisms of gene regulation, also remains a challenge. Machine learning is a powerful and emerging tool to decode the unique complexities and heterogeneity of human diseases. For instance, Beebe-Wang, Nicosia, et al. developed MD-AD, a multi-task neural network model to predict various disease phenotypes in AD patients using RNA-seq. Additionally, with advancements in graph neural networks, which possess enhanced capabilities to represent sophisticated gene network structures like gene regulation networks that control gene expression. Efforts have also been made to capture the gene regulation heterogeneity of brain diseases. For instance, Kim SY has applied graph convolutional networks to offer personalized diagnostic insights through population graphs that correspond with disease progression. However, many existing machine learning methods are often limited to constructing accurate models for disease phenotype prediction and frequently lack biological interpretability or personalized insights, especially in gene regulation. Therefore, to address these challenges, my Ph.D. works have developed three machine-learning methods designed to decode the gene regulation mechanisms of human diseases. First, in this dissertation, I will present scGRNom, a computational pipeline that integrates multi-omic data to construct cell-type gene regulatory networks (GRNs) linking non-coding regulatory elements. Next, I will introduce i-BrainMap an interpretable knowledge-guided graph neural network model to prioritize personalized cell type disease genes, regulatory linkages, and modules. Thirdly, I introduce ECMaker, a semi-restricted Boltzmann machine (semi-RBM) method for identifying gene networks to predict diseases and clinical phenotypes. Overall, all our interpretable machine learning models improve phenotype prediction, prioritize key genes and networks associated with disease phenotypes, and are further aimed at enhancing our understanding of gene regulatory mechanisms driving disease progression and clinical phenotypes.
Book Synopsis Bioinformatics and Medical Applications by : A. Suresh
Download or read book Bioinformatics and Medical Applications written by A. Suresh and published by John Wiley & Sons. This book was released on 2022-04-12 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: BIOINFORMATICS AND MEDICAL APPLICATIONS The main topics addressed in this book are big data analytics problems in bioinformatics research such as microarray data analysis, sequence analysis, genomics-based analytics, disease network analysis, techniques for big data analytics, and health information technology. Bioinformatics and Medical Applications: Big Data Using Deep Learning Algorithms analyses massive biological datasets using computational approaches and the latest cutting-edge technologies to capture and interpret biological data. The book delivers various bioinformatics computational methods used to identify diseases at an early stage by assembling cutting-edge resources into a single collection designed to enlighten the reader on topics focusing on computer science, mathematics, and biology. In modern biology and medicine, bioinformatics is critical for data management. This book explains the bioinformatician’s important tools and examines how they are used to evaluate biological data and advance disease knowledge. The editors have curated a distinguished group of perceptive and concise chapters that presents the current state of medical treatments and systems and offers emerging solutions for a more personalized approach to healthcare. Applying deep learning techniques for data-driven solutions in health information allows automated analysis whose method can be more advantageous in supporting the problems arising from medical and health-related information. Audience The primary audience for the book includes specialists, researchers, postgraduates, designers, experts, and engineers, who are occupied with biometric research and security-related issues.
Book Synopsis Data Science and Predictive Analytics by : Ivo D. Dinov
Download or read book Data Science and Predictive Analytics written by Ivo D. Dinov and published by Springer. This book was released on 2024-02-17 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook integrates important mathematical foundations, efficient computational algorithms, applied statistical inference techniques, and cutting-edge machine learning approaches to address a wide range of crucial biomedical informatics, health analytics applications, and decision science challenges. Each concept in the book includes a rigorous symbolic formulation coupled with computational algorithms and complete end-to-end pipeline protocols implemented as functional R electronic markdown notebooks. These workflows support active learning and demonstrate comprehensive data manipulations, interactive visualizations, and sophisticated analytics. The content includes open problems, state-of-the-art scientific knowledge, ethical integration of heterogeneous scientific tools, and procedures for systematic validation and dissemination of reproducible research findings. Complementary to the enormous challenges related to handling, interrogating, and understanding massive amounts of complex structured and unstructured data, there are unique opportunities that come with access to a wealth of feature-rich, high-dimensional, and time-varying information. The topics covered in Data Science and Predictive Analytics address specific knowledge gaps, resolve educational barriers, and mitigate workforce information-readiness and data science deficiencies. Specifically, it provides a transdisciplinary curriculum integrating core mathematical principles, modern computational methods, advanced data science techniques, model-based machine learning, model-free artificial intelligence, and innovative biomedical applications. The book’s fourteen chapters start with an introduction and progressively build foundational skills from visualization to linear modeling, dimensionality reduction, supervised classification, black-box machine learning techniques, qualitative learning methods, unsupervised clustering, model performance assessment, feature selection strategies, longitudinal data analytics, optimization, neural networks, and deep learning. The second edition of the book includes additional learning-based strategies utilizing generative adversarial networks, transfer learning, and synthetic data generation, as well as eight complementary electronic appendices. This textbook is suitable for formal didactic instructor-guided course education, as well as for individual or team-supported self-learning. The material is presented at the upper-division and graduate-level college courses and covers applied and interdisciplinary mathematics, contemporary learning-based data science techniques, computational algorithm development, optimization theory, statistical computing, and biomedical sciences. The analytical techniques and predictive scientific methods described in the book may be useful to a wide range of readers, formal and informal learners, college instructors, researchers, and engineers throughout the academy, industry, government, regulatory, funding, and policy agencies. The supporting book website provides many examples, datasets, functional scripts, complete electronic notebooks, extensive appendices, and additional materials.
Book Synopsis Genomic Medicine by : Dhavendra Kumar
Download or read book Genomic Medicine written by Dhavendra Kumar and published by Oxford Monographs on Medical G. This book was released on 2014-10-15 with total page 853 pages. Available in PDF, EPUB and Kindle. Book excerpt: Preceded by Genomics and clinical medicine / edited by Dhavendra Kumar. [First edition]. 2008.
Book Synopsis Artificial Intelligence in Healthcare by : Adam Bohr
Download or read book Artificial Intelligence in Healthcare written by Adam Bohr and published by Academic Press. This book was released on 2020-06-21 with total page 385 pages. Available in PDF, EPUB and Kindle. Book excerpt: Artificial Intelligence (AI) in Healthcare is more than a comprehensive introduction to artificial intelligence as a tool in the generation and analysis of healthcare data. The book is split into two sections where the first section describes the current healthcare challenges and the rise of AI in this arena. The ten following chapters are written by specialists in each area, covering the whole healthcare ecosystem. First, the AI applications in drug design and drug development are presented followed by its applications in the field of cancer diagnostics, treatment and medical imaging. Subsequently, the application of AI in medical devices and surgery are covered as well as remote patient monitoring. Finally, the book dives into the topics of security, privacy, information sharing, health insurances and legal aspects of AI in healthcare. Highlights different data techniques in healthcare data analysis, including machine learning and data mining Illustrates different applications and challenges across the design, implementation and management of intelligent systems and healthcare data networks Includes applications and case studies across all areas of AI in healthcare data
Author :National Academies of Sciences, Engineering, and Medicine Publisher :National Academies Press ISBN 13 :0309490812 Total Pages :93 pages Book Rating :4.3/5 (94 download)
Book Synopsis Improving Cancer Diagnosis and Care by : National Academies of Sciences, Engineering, and Medicine
Download or read book Improving Cancer Diagnosis and Care written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2019-08-15 with total page 93 pages. Available in PDF, EPUB and Kindle. Book excerpt: A hallmark of high-quality cancer care is the delivery of the right treatment to the right patient at the right time. Precision oncology therapies, which target specific genetic changes in a patient's cancer, are changing the nature of cancer treatment by allowing clinicians to select therapies that are most likely to benefit individual patients. In current clinical practice, oncologists are increasingly formulating cancer treatment plans using results from complex laboratory and imaging tests that characterize the molecular underpinnings of an individual patient's cancer. These molecular fingerprints can be quite complex and heterogeneous, even within a single patient. To enable these molecular tumor characterizations to effectively and safely inform cancer care, the cancer community is working to develop and validate multiparameter omics tests and imaging tests as well as software and computational methods for interpretation of the resulting datasets. To examine opportunities to improve cancer diagnosis and care in the new precision oncology era, the National Cancer Policy Forum developed a two-workshop series. The first workshop focused on patient access to expertise and technologies in oncologic imaging and pathology and was held in February 2018. The second workshop, conducted in collaboration with the Board on Mathematical Sciences and Analytics, was held in October 2018 to examine the use of multidimensional data derived from patients with cancer, and the computational methods that analyze these data to inform cancer treatment decisions. This publication summarizes the presentations and discussions from the second workshop.
Book Synopsis Bioinformatics and Biomedical Engineering by : Ignacio Rojas
Download or read book Bioinformatics and Biomedical Engineering written by Ignacio Rojas and published by Springer. This book was released on 2019-04-30 with total page 605 pages. Available in PDF, EPUB and Kindle. Book excerpt: The two-volume set LNBI 11465 and LNBI 11466 constitutes the proceedings of the 7th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2019, held in Granada, Spain, in May 2019. The total of 97 papers presented in the proceedings, was carefully reviewed and selected from 301 submissions. The papers are organized in topical sections as follows: Part I: High-throughput genomics: bioinformatics tools and medical applications; omics data acquisition, processing, and analysis; bioinformatics approaches for analyzing cancer sequencing data; next generation sequencing and sequence analysis; structural bioinformatics and function; telemedicine for smart homes and remote monitoring; clustering and analysis of biological sequences with optimization algorithms; and computational approaches for drug repurposing and personalized medicine. Part II: Bioinformatics for healthcare and diseases; computational genomics/proteomics; computational systems for modelling biological processes; biomedical engineering; biomedical image analysis; and biomedicine and e-health.
Book Synopsis Applications of Machine Learning by : Prashant Johri
Download or read book Applications of Machine Learning written by Prashant Johri and published by Springer Nature. This book was released on 2020-05-04 with total page 404 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers applications of machine learning in artificial intelligence. The specific topics covered include human language, heterogeneous and streaming data, unmanned systems, neural information processing, marketing and the social sciences, bioinformatics and robotics, etc. It also provides a broad range of techniques that can be successfully applied and adopted in different areas. Accordingly, the book offers an interesting and insightful read for scholars in the areas of computer vision, speech recognition, healthcare, business, marketing, and bioinformatics.
Book Synopsis Detection Systems in Lung Cancer and Imaging, Volume 1 by : Ayman El-Baz
Download or read book Detection Systems in Lung Cancer and Imaging, Volume 1 written by Ayman El-Baz and published by IOP Publishing Limited. This book was released on 2022-01-20 with total page 450 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on major trends and challenges in the detection of lung cancer, presenting work aimed at identifying new techniques and their use in biomedical analysis. This volume covers recent advancements in lung cancer and imaging detection and classification, examining the main applications of Computer aided diagnosis (CAD) relating to lung cancer: lung nodule segmentation, lung nodule classification, and Big Data in lung cancer. Ideal for academics working in lung cancer, data-mining, machine learning, deep learning and reinforcement learning, as well as industry professionals working in the areas of healthcare, lung cancer imaging, machine learning, deep learning and reinforcement learning, this edited collection comprises an essential reference for researchers at the forefront of the field, and provides a high-level entry point for more advanced students. Key Features: -Unique focus on advance work in detection system and classification systems. -An updated reference for lung cancer detection via imaging. -Focus on progressive deep learning and machine learning applications for more effective detection.
