Handbook of Machine Learning Applications for Genomics PDF Download

Author: Sanjiban Sekhar Roy
Publisher: Springer Nature
ISBN: 9811691584
Category : Technology & Engineering
Languages : en
Pages : 222

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Book Description
Currently, machine learning is playing a pivotal role in the progress of genomics. The applications of machine learning are helping all to understand the emerging trends and the future scope of genomics. This book provides comprehensive coverage of machine learning applications such as DNN, CNN, and RNN, for predicting the sequence of DNA and RNA binding proteins, expression of the gene, and splicing control. In addition, the book addresses the effect of multiomics data analysis of cancers using tensor decomposition, machine learning techniques for protein engineering, CNN applications on genomics, challenges of long noncoding RNAs in human disease diagnosis, and how machine learning can be used as a tool to shape the future of medicine. More importantly, it gives a comparative analysis and validates the outcomes of machine learning methods on genomic data to the functional laboratory tests or by formal clinical assessment. The topics of this book will cater interest to academicians, practitioners working in the field of functional genomics, and machine learning. Also, this book shall guide comprehensively the graduate, postgraduates, and Ph.D. scholars working in these fields.

Author: Upendra Kumar Devisetty
Publisher: Packt Publishing Ltd
ISBN: 1804613010
Category : Computers
Languages : en
Pages : 270

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Book Description
Learn concepts, methodologies, and applications of deep learning for building predictive models from complex genomics data sets to overcome challenges in the life sciences and biotechnology industries Key FeaturesApply deep learning algorithms to solve real-world problems in the field of genomicsExtract biological insights from deep learning models built from genomic datasetsTrain, tune, evaluate, deploy, and monitor deep learning models for enabling predictions in genomicsBook Description Deep learning has shown remarkable promise in the field of genomics; however, there is a lack of a skilled deep learning workforce in this discipline. This book will help researchers and data scientists to stand out from the rest of the crowd and solve real-world problems in genomics by developing the necessary skill set. Starting with an introduction to the essential concepts, this book highlights the power of deep learning in handling big data in genomics. First, you'll learn about conventional genomics analysis, then transition to state-of-the-art machine learning-based genomics applications, and finally dive into deep learning approaches for genomics. The book covers all of the important deep learning algorithms commonly used by the research community and goes into the details of what they are, how they work, and their practical applications in genomics. The book dedicates an entire section to operationalizing deep learning models, which will provide the necessary hands-on tutorials for researchers and any deep learning practitioners to build, tune, interpret, deploy, evaluate, and monitor deep learning models from genomics big data sets. By the end of this book, you'll have learned about the challenges, best practices, and pitfalls of deep learning for genomics. What you will learnDiscover the machine learning applications for genomicsExplore deep learning concepts and methodologies for genomics applicationsUnderstand supervised deep learning algorithms for genomics applicationsGet to grips with unsupervised deep learning with autoencodersImprove deep learning models using generative modelsOperationalize deep learning models from genomics datasetsVisualize and interpret deep learning modelsUnderstand deep learning challenges, pitfalls, and best practicesWho this book is for This deep learning book is for machine learning engineers, data scientists, and academicians practicing in the field of genomics. It assumes that readers have intermediate Python programming knowledge, basic knowledge of Python libraries such as NumPy and Pandas to manipulate and parse data, Matplotlib, and Seaborn for visualizing data, along with a base in genomics and genomic analysis concepts.

Author: Shailza Singh
Publisher: Springer Nature
ISBN: 9811659931
Category : Science
Languages : en
Pages : 239

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Book Description
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.

Author: Bharath Ramsundar
Publisher: "O'Reilly Media, Inc."
ISBN: 1492039780
Category : Science
Languages : en
Pages : 244

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Book Description
Deep learning has already achieved remarkable results in many fields. Now it’s making waves throughout the sciences broadly and the life sciences in particular. This practical book teaches developers and scientists how to use deep learning for genomics, chemistry, biophysics, microscopy, medical analysis, and other fields. Ideal for practicing developers and scientists ready to apply their skills to scientific applications such as biology, genetics, and drug discovery, this book introduces several deep network primitives. You’ll follow a case study on the problem of designing new therapeutics that ties together physics, chemistry, biology, and medicine—an example that represents one of science’s greatest challenges. Learn the basics of performing machine learning on molecular data Understand why deep learning is a powerful tool for genetics and genomics Apply deep learning to understand biophysical systems Get a brief introduction to machine learning with DeepChem Use deep learning to analyze microscopic images Analyze medical scans using deep learning techniques Learn about variational autoencoders and generative adversarial networks Interpret what your model is doing and how it’s working

Author: Altuna Akalin
Publisher: CRC Press
ISBN: 1498781861
Category : Mathematics
Languages : en
Pages : 462

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Book Description
Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.

Author: Sanjiban Sekhar Roy
Publisher: Springer Nature
ISBN: 9819937841
Category : Technology & Engineering
Languages : en
Pages : 218

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Book Description
This book provides state-of-the-art coverage of deep learning applications in image analysis. The book demonstrates various deep learning algorithms that can offer practical solutions for various image-related problems; also how these algorithms are used by scientists and scholars in industry and academia. This includes autoencoder and deep convolutional generative adversarial network in improving classification performance of Bangla handwritten characters, dealing with deep learning-based approaches using feature selection methods for automatic diagnosis of covid-19 disease from x-ray images, imbalance image data sets of classification, image captioning using deep transfer learning, developing a vehicle over speed detection system, creating an intelligent system for video-based proximity analysis, building a melanoma cancer detection system using deep learning, plant diseases classification using AlexNet, dealing with hyperspectral images using deep learning, chest x-ray image classification of pneumonia disease using efficient net and inceptionv3. The book also addresses the difficulty of implementing deep learning in terms of computation time and the complexity of reasoning and modelling different types of data where information is currently encoded. Each chapter has the application of various new or existing deep learning models such as Deep Neural Network (DNN) and Deep Convolutional Neural Networks (DCNN). The detailed utilization of deep learning packages that are available in MATLAB, Python and R programming environments have also been discussed, therefore, the readers will get to know about the practical implementation of deep learning as well. The content of this book is presented in a simple and lucid style for professionals, nonprofessionals, scientists, and students interested in the research area of deep learning applications in image analysis.

Author: Abedalrhman Alkhateeb
Publisher: Springer Nature
ISBN: 303136502X
Category : Science
Languages : en
Pages : 171

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Book Description
The advancement of biomedical engineering has enabled the generation of multi-omics data by developing high-throughput technologies, such as next-generation sequencing, mass spectrometry, and microarrays. Large-scale data sets for multiple omics platforms, including genomics, transcriptomics, proteomics, and metabolomics, have become more accessible and cost-effective over time. Integrating multi-omics data has become increasingly important in many research fields, such as bioinformatics, genomics, and systems biology. This integration allows researchers to understand complex interactions between biological molecules and pathways. It enables us to comprehensively understand complex biological systems, leading to new insights into disease mechanisms, drug discovery, and personalized medicine. Still, integrating various heterogeneous data types into a single learning model also comes with challenges. In this regard, learning algorithms have been vital in analyzing and integrating these large-scale heterogeneous data sets into one learning model. This book overviews the latest multi-omics technologies, machine learning techniques for data integration, and multi-omics databases for validation. It covers different types of learning for supervised and unsupervised learning techniques, including standard classifiers, deep learning, tensor factorization, ensemble learning, and clustering, among others. The book categorizes different levels of integrations, ranging from early, middle, or late-stage among multi-view models. The underlying models target different objectives, such as knowledge discovery, pattern recognition, disease-related biomarkers, and validation tools for multi-omics data. Finally, the book emphasizes practical applications and case studies, making it an essential resource for researchers and practitioners looking to apply machine learning to their multi-omics data sets. The book covers data preprocessing, feature selection, and model evaluation, providing readers with a practical guide to implementing machine learning techniques on various multi-omics data sets.

Author: K. G. Srinivasa
Publisher: Springer Nature
ISBN: 9811524459
Category : Technology & Engineering
Languages : en
Pages : 318

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Book Description
This book discusses topics related to bioinformatics, statistics, and machine learning, presenting the latest research in various areas of bioinformatics. It also highlights the role of computing and machine learning in knowledge extraction from biological data, and how this knowledge can be applied in fields such as drug design, health supplements, gene therapy, proteomics and agriculture.

Author: Loveleen Gaur
Publisher: CRC Press
ISBN: 100046301X
Category : Technology & Engineering
Languages : en
Pages : 220

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Book Description
The advanced AI techniques are essential for resolving various problematic aspects emerging in the field of bioinformatics. This book covers the recent approaches in artificial intelligence and machine learning methods and their applications in Genome and Gene editing, cancer drug discovery classification, and the protein folding algorithms among others. Deep learning, which is widely used in image processing, is also applicable in bioinformatics as one of the most popular artificial intelligence approaches. The wide range of applications discussed in this book are an indispensable resource for computer scientists, engineers, biologists, mathematicians, physicians, and medical informaticists. Features: Focusses on the cross-disciplinary relation between computer science and biology and the role of machine learning methods in resolving complex problems in bioinformatics Provides a comprehensive and balanced blend of topics and applications using various advanced algorithms Presents cutting-edge research methodologies in the area of AI methods when applied to bioinformatics and innovative solutions Discusses the AI/ML techniques, their use, and their potential for use in common and future bioinformatics applications Includes recent achievements in AI and bioinformatics contributed by a global team of researchers

Author: Pierre Baldi
Publisher: MIT Press
ISBN: 9780262025065
Category : Computers
Languages : en
Pages : 492

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Book Description
A guide to machine learning approaches and their application to the analysis of biological data. An unprecedented wealth of data is being generated by genome sequencing projects and other experimental efforts to determine the structure and function of biological molecules. The demands and opportunities for interpreting these data are expanding rapidly. Bioinformatics is the development and application of computer methods for management, analysis, interpretation, and prediction, as well as for the design of experiments. Machine learning approaches (e.g., neural networks, hidden Markov models, and belief networks) are ideally suited for areas where there is a lot of data but little theory, which is the situation in molecular biology. The goal in machine learning is to extract useful information from a body of data by building good probabilistic models—and to automate the process as much as possible. In this book Pierre Baldi and Søren Brunak present the key machine learning approaches and apply them to the computational problems encountered in the analysis of biological data. The book is aimed both at biologists and biochemists who need to understand new data-driven algorithms and at those with a primary background in physics, mathematics, statistics, or computer science who need to know more about applications in molecular biology. This new second edition contains expanded coverage of probabilistic graphical models and of the applications of neural networks, as well as a new chapter on microarrays and gene expression. The entire text has been extensively revised.