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Interpretable Machine Learning In Plant Genomes
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Book Synopsis Interpretable Machine Learning by : Christoph Molnar
Download or read book Interpretable Machine Learning written by Christoph Molnar and published by Lulu.com. This book was released on 2020 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is about making machine learning models and their decisions interpretable. After exploring the concepts of interpretability, you will learn about simple, interpretable models such as decision trees, decision rules and linear regression. Later chapters focus on general model-agnostic methods for interpreting black box models like feature importance and accumulated local effects and explaining individual predictions with Shapley values and LIME. All interpretation methods are explained in depth and discussed critically. How do they work under the hood? What are their strengths and weaknesses? How can their outputs be interpreted? This book will enable you to select and correctly apply the interpretation method that is most suitable for your machine learning project.
Book Synopsis Genomics-Assisted Crop Improvement by : R.K. Varshney
Download or read book Genomics-Assisted Crop Improvement written by R.K. Varshney and published by Springer Science & Business Media. This book was released on 2007-12-12 with total page 405 pages. Available in PDF, EPUB and Kindle. Book excerpt: This superb volume provides a critical assessment of genomics tools and approaches for crop breeding. Volume 1 presents the status and availability of genomic resources and platforms, and also devises strategies and approaches for effectively exploiting genomics research. Volume 2 goes into detail on a number of case studies of several important crop and plant species that summarize both the achievements and limitations of genomics research for crop improvement.
Book Synopsis Elements of Causal Inference by : Jonas Peters
Download or read book Elements of Causal Inference written by Jonas Peters and published by MIT Press. This book was released on 2017-11-29 with total page 289 pages. Available in PDF, EPUB and Kindle. Book excerpt: A concise and self-contained introduction to causal inference, increasingly important in data science and machine learning. The mathematization of causality is a relatively recent development, and has become increasingly important in data science and machine learning. This book offers a self-contained and concise introduction to causal models and how to learn them from data. After explaining the need for causal models and discussing some of the principles underlying causal inference, the book teaches readers how to use causal models: how to compute intervention distributions, how to infer causal models from observational and interventional data, and how causal ideas could be exploited for classical machine learning problems. All of these topics are discussed first in terms of two variables and then in the more general multivariate case. The bivariate case turns out to be a particularly hard problem for causal learning because there are no conditional independences as used by classical methods for solving multivariate cases. The authors consider analyzing statistical asymmetries between cause and effect to be highly instructive, and they report on their decade of intensive research into this problem. The book is accessible to readers with a background in machine learning or statistics, and can be used in graduate courses or as a reference for researchers. The text includes code snippets that can be copied and pasted, exercises, and an appendix with a summary of the most important technical concepts.
Book Synopsis Pan-genomics: Applications, Challenges, and Future Prospects by : Debmalya Barh
Download or read book Pan-genomics: Applications, Challenges, and Future Prospects written by Debmalya Barh and published by Academic Press. This book was released on 2020-03-06 with total page 476 pages. Available in PDF, EPUB and Kindle. Book excerpt: Pan-genomics: Applications, Challenges, and Future Prospects covers current approaches, challenges and future prospects of pan-genomics. The book discusses bioinformatics tools and their applications and focuses on bacterial comparative genomics in order to leverage the development of precise drugs and treatments for specific organisms. The book is divided into three sections: the first, an "overview of pan-genomics and common approaches, brings the main concepts and current approaches on pan-genomics research; the second, "case studies in pan-genomics, thoroughly discusses twelve case, and the last, "current approaches and future prospects in pan-multiomics, encompasses the developments on omics studies to be applied on bacteria related studies. This book is a valuable source for bioinformaticians, genomics researchers and several members of biomedical field interested in understanding further bacterial organisms and their relationship to human health. - Covers the entire spectrum of pangenomics, highlighting the use of specific approaches, case studies and future perspectives - Discusses current bioinformatics tools and strategies for exploiting pangenomics data - Presents twelve case studies with different organisms in order to provide the audience with real examples of pangenomics applicability
Book Synopsis The Maize Genome by : Jeffrey Bennetzen
Download or read book The Maize Genome written by Jeffrey Bennetzen and published by Springer. This book was released on 2018-11-24 with total page 390 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses advances in our understanding of the structure and function of the maize genome since publication of the original B73 reference genome in 2009, and the progress in translating this knowledge into basic biology and trait improvement. Maize is an extremely important crop, providing a large proportion of the world’s human caloric intake and animal feed, and serving as a model species for basic and applied research. The exceptionally high level of genetic diversity within maize presents opportunities and challenges in all aspects of maize genetics, from sequencing and genotyping to linking genotypes to phenotypes. Topics covered in this timely book range from (i) genome sequencing and genotyping techniques, (ii) genome features such as centromeres and epigenetic regulation, (iii) tools and resources available for trait genomics, to (iv) applications of allele mining and genomics-assisted breeding. This book is a valuable resource for researchers and students interested in maize genetics and genomics.
Book Synopsis Explainable AI: Interpreting, Explaining and Visualizing Deep Learning by : Wojciech Samek
Download or read book Explainable AI: Interpreting, Explaining and Visualizing Deep Learning written by Wojciech Samek and published by Springer Nature. This book was released on 2019-09-10 with total page 435 pages. Available in PDF, EPUB and Kindle. Book excerpt: The development of “intelligent” systems that can take decisions and perform autonomously might lead to faster and more consistent decisions. A limiting factor for a broader adoption of AI technology is the inherent risks that come with giving up human control and oversight to “intelligent” machines. For sensitive tasks involving critical infrastructures and affecting human well-being or health, it is crucial to limit the possibility of improper, non-robust and unsafe decisions and actions. Before deploying an AI system, we see a strong need to validate its behavior, and thus establish guarantees that it will continue to perform as expected when deployed in a real-world environment. In pursuit of that objective, ways for humans to verify the agreement between the AI decision structure and their own ground-truth knowledge have been explored. Explainable AI (XAI) has developed as a subfield of AI, focused on exposing complex AI models to humans in a systematic and interpretable manner. The 22 chapters included in this book provide a timely snapshot of algorithms, theory, and applications of interpretable and explainable AI and AI techniques that have been proposed recently reflecting the current discourse in this field and providing directions of future development. The book is organized in six parts: towards AI transparency; methods for interpreting AI systems; explaining the decisions of AI systems; evaluating interpretability and explanations; applications of explainable AI; and software for explainable AI.
Book Synopsis Multivariate Statistical Machine Learning Methods for Genomic Prediction by : Osval Antonio Montesinos López
Download or read book Multivariate Statistical Machine Learning Methods for Genomic Prediction written by Osval Antonio Montesinos López and published by Springer Nature. This book was released on 2022-02-14 with total page 707 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is open access under a CC BY 4.0 license This open access book brings together the latest genome base prediction models currently being used by statisticians, breeders and data scientists. It provides an accessible way to understand the theory behind each statistical learning tool, the required pre-processing, the basics of model building, how to train statistical learning methods, the basic R scripts needed to implement each statistical learning tool, and the output of each tool. To do so, for each tool the book provides background theory, some elements of the R statistical software for its implementation, the conceptual underpinnings, and at least two illustrative examples with data from real-world genomic selection experiments. Lastly, worked-out examples help readers check their own comprehension.The book will greatly appeal to readers in plant (and animal) breeding, geneticists and statisticians, as it provides in a very accessible way the necessary theory, the appropriate R code, and illustrative examples for a complete understanding of each statistical learning tool. In addition, it weighs the advantages and disadvantages of each tool.
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 Likelihood, Bayesian, and MCMC Methods in Quantitative Genetics by : Daniel Sorensen
Download or read book Likelihood, Bayesian, and MCMC Methods in Quantitative Genetics written by Daniel Sorensen and published by Springer Science & Business Media. This book was released on 2007-03-22 with total page 745 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book, suitable for numerate biologists and for applied statisticians, provides the foundations of likelihood, Bayesian and MCMC methods in the context of genetic analysis of quantitative traits. Although a number of excellent texts in these areas have become available in recent years, the basic ideas and tools are typically described in a technically demanding style and contain much more detail than necessary. Here, an effort has been made to relate biological to statistical parameters throughout, and the book includes extensive examples that illustrate the developing argument.
Book Synopsis Explainable and Interpretable Models in Computer Vision and Machine Learning by : Hugo Jair Escalante
Download or read book Explainable and Interpretable Models in Computer Vision and Machine Learning written by Hugo Jair Escalante and published by Springer. This book was released on 2018-11-29 with total page 305 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book compiles leading research on the development of explainable and interpretable machine learning methods in the context of computer vision and machine learning. Research progress in computer vision and pattern recognition has led to a variety of modeling techniques with almost human-like performance. Although these models have obtained astounding results, they are limited in their explainability and interpretability: what is the rationale behind the decision made? what in the model structure explains its functioning? Hence, while good performance is a critical required characteristic for learning machines, explainability and interpretability capabilities are needed to take learning machines to the next step to include them in decision support systems involving human supervision. This book, written by leading international researchers, addresses key topics of explainability and interpretability, including the following: · Evaluation and Generalization in Interpretable Machine Learning · Explanation Methods in Deep Learning · Learning Functional Causal Models with Generative Neural Networks · Learning Interpreatable Rules for Multi-Label Classification · Structuring Neural Networks for More Explainable Predictions · Generating Post Hoc Rationales of Deep Visual Classification Decisions · Ensembling Visual Explanations · Explainable Deep Driving by Visualizing Causal Attention · Interdisciplinary Perspective on Algorithmic Job Candidate Search · Multimodal Personality Trait Analysis for Explainable Modeling of Job Interview Decisions · Inherent Explainability Pattern Theory-based Video Event Interpretations
Book Synopsis Building Machine Learning and Deep Learning Models on Google Cloud Platform by : Ekaba Bisong
Download or read book Building Machine Learning and Deep Learning Models on Google Cloud Platform written by Ekaba Bisong and published by Apress. This book was released on 2019-09-27 with total page 703 pages. Available in PDF, EPUB and Kindle. Book excerpt: Take a systematic approach to understanding the fundamentals of machine learning and deep learning from the ground up and how they are applied in practice. You will use this comprehensive guide for building and deploying learning models to address complex use cases while leveraging the computational resources of Google Cloud Platform. Author Ekaba Bisong shows you how machine learning tools and techniques are used to predict or classify events based on a set of interactions between variables known as features or attributes in a particular dataset. He teaches you how deep learning extends the machine learning algorithm of neural networks to learn complex tasks that are difficult for computers to perform, such as recognizing faces and understanding languages. And you will know how to leverage cloud computing to accelerate data science and machine learning deployments. Building Machine Learning and Deep Learning Models on Google Cloud Platform is divided into eight parts that cover the fundamentals of machine learning and deep learning, the concept of data science and cloud services, programming for data science using the Python stack, Google Cloud Platform (GCP) infrastructure and products, advanced analytics on GCP, and deploying end-to-end machine learning solution pipelines on GCP. What You’ll Learn Understand the principles and fundamentals of machine learning and deep learning, the algorithms, how to use them, when to use them, and how to interpret your resultsKnow the programming concepts relevant to machine and deep learning design and development using the Python stack Build and interpret machine and deep learning models Use Google Cloud Platform tools and services to develop and deploy large-scale machine learning and deep learning products Be aware of the different facets and design choices to consider when modeling a learning problem Productionalize machine learning models into software products Who This Book Is For Beginners to the practice of data science and applied machine learning, data scientists at all levels, machine learning engineers, Google Cloud Platform data engineers/architects, and software developers
Book Synopsis Deep Learning Applications, Volume 2 by : M. Arif Wani
Download or read book Deep Learning Applications, Volume 2 written by M. Arif Wani and published by Springer. This book was released on 2020-12-14 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents selected papers from the 18th IEEE International Conference on Machine Learning and Applications (IEEE ICMLA 2019). It focuses on deep learning networks and their application in domains such as healthcare, security and threat detection, fault diagnosis and accident analysis, and robotic control in industrial environments, and highlights novel ways of using deep neural networks to solve real-world problems. Also offering insights into deep learning architectures and algorithms, it is an essential reference guide for academic researchers, professionals, software engineers in industry, and innovative product developers.
Book Synopsis Genome-Wide Association Studies and Genomic Prediction by : Cedric Gondro
Download or read book Genome-Wide Association Studies and Genomic Prediction written by Cedric Gondro and published by Humana Press. This book was released on 2013-06-12 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the detailed genomic information that is now becoming available, we have a plethora of data that allows researchers to address questions in a variety of areas. Genome-wide association studies (GWAS) have become a vital approach to identify candidate regions associated with complex diseases in human medicine, production traits in agriculture, and variation in wild populations. Genomic prediction goes a step further, attempting to predict phenotypic variation in these traits from genomic information. Genome-Wide Association Studies and Genomic Prediction pulls together expert contributions to address this important area of study. The volume begins with a section covering the phenotypes of interest as well as design issues for GWAS, then moves on to discuss efficient computational methods to store and handle large datasets, quality control measures, phasing, haplotype inference, and imputation. Later chapters deal with statistical approaches to data analysis where the experimental objective is either to confirm the biology by identifying genomic regions associated to a trait or to use the data to make genomic predictions about a future phenotypic outcome (e.g. predict onset of disease). As part of the Methods in Molecular Biology series, chapters provide helpful, real-world implementation advice.
Book Synopsis Achievements of the National Plant Genome Initiative and New Horizons in Plant Biology by : National Research Council
Download or read book Achievements of the National Plant Genome Initiative and New Horizons in Plant Biology written by National Research Council and published by National Academies Press. This book was released on 2008-04-20 with total page 183 pages. Available in PDF, EPUB and Kindle. Book excerpt: Life on Earth would be impossible without plants. Humans rely on plants for most clothing, furniture, food, as well as for many pharmaceuticals and other products. Plant genome sciences are essential to understanding how plants function and how to develop desirable plant characteristics. For example, plant genomic science can contribute to the development of plants that are drought-resistant, those that require less fertilizer, and those that are optimized for conversion to fuels such as ethanol and biodiesel. The National Plant Genome Initiative (NPGI) is a unique, cross-agency funding enterprise that has been funding and coordinating plant genome research successfully for nine years. Research breakthroughs from NPGI and the National Science Foundation (NSF) Arabidopsis 2010 Project, such as how the plant immune system controls pathogen defense, demonstrate that the plant genome science community is vibrant and capable of driving technological advancement. This book from the National Research Council concludes that these programs should continue so that applied programs on agriculture, bioenergy, and others will always be built on a strong foundation of fundamental plant biology research.
Book Synopsis Unraveling New Frontiers and Advances in Bioinformatics by : Amit Chaudhary
Download or read book Unraveling New Frontiers and Advances in Bioinformatics written by Amit Chaudhary and published by Springer Nature. This book was released on with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Genomic Prediction of Complex Traits by : Nourollah Ahmadi
Download or read book Genomic Prediction of Complex Traits written by Nourollah Ahmadi and published by Springer Nature. This book was released on 2022-04-22 with total page 651 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores the conceptual framework and the practical issues related to genomic prediction of complex traits in human medicine and in animal and plant breeding. The book is organized into five parts. Part One reminds molecular genetics approaches intending to predict phenotypic variations. Part Two presents the principles of genomic prediction of complex traits, and reviews factors that affect its reliability. Part Three describes genomic prediction methods, including machine-learning approaches, accounting for different degree of biological complexity, and reviews the associated computer-packages. Part Four reports on emerging trends such as phenomic prediction and incorporation into genomic prediction models of “omics” data and crop growth models. Part Five is dedicated to lessons learned from cases studies in the fields of human health and animal and plant breeding, and to methods for analysis of the economic effectiveness of genomic prediction. Written in the highly successful Methods in Molecular Biology series format, the book provides theoretical bases and practical guidelines for an informed decision making of practitioners and identifies pertinent routes for further methodological researches. Cutting-edge and thorough, Complex Trait Predictions: Methods and Protocols is a valuable resource for scientists and researchers who are interested in learning more about this important and developing field. Chapters 3, 9, 13, 14, and 21 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Book Synopsis Rule Extraction from Support Vector Machines by : Joachim Diederich
Download or read book Rule Extraction from Support Vector Machines written by Joachim Diederich and published by Springer. This book was released on 2007-12-27 with total page 267 pages. Available in PDF, EPUB and Kindle. Book excerpt: Support vector machines (SVMs) are one of the most active research areas in machine learning. SVMs have shown good performance in a number of applications, including text and image classification. However, the learning capability of SVMs comes at a cost – an inherent inability to explain in a comprehensible form, the process by which a learning result was reached. Hence, the situation is similar to neural networks, where the apparent lack of an explanation capability has led to various approaches aiming at extracting symbolic rules from neural networks. For SVMs to gain a wider degree of acceptance in fields such as medical diagnosis and security sensitive areas, it is desirable to offer an explanation capability. User explanation is often a legal requirement, because it is necessary to explain how a decision was reached or why it was made. This book provides an overview of the field and introduces a number of different approaches to extracting rules from support vector machines developed by key researchers. In addition, successful applications are outlined and future research opportunities are discussed. The book is an important reference for researchers and graduate students, and since it provides an introduction to the topic, it will be important in the classroom as well. Because of the significance of both SVMs and user explanation, the book is of relevance to data mining practitioners and data analysts.
