Graph Representation Learning

Graph Representation Learning

Author: William L. William L. Hamilton

Publisher: Springer Nature

Published: 2022-06-01

Total Pages: 141

ISBN-13: 3031015886

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Graph-structured data is ubiquitous throughout the natural and social sciences, from telecommunication networks to quantum chemistry. Building relational inductive biases into deep learning architectures is crucial for creating systems that can learn, reason, and generalize from this kind of data. Recent years have seen a surge in research on graph representation learning, including techniques for deep graph embeddings, generalizations of convolutional neural networks to graph-structured data, and neural message-passing approaches inspired by belief propagation. These advances in graph representation learning have led to new state-of-the-art results in numerous domains, including chemical synthesis, 3D vision, recommender systems, question answering, and social network analysis. This book provides a synthesis and overview of graph representation learning. It begins with a discussion of the goals of graph representation learning as well as key methodological foundations in graph theory and network analysis. Following this, the book introduces and reviews methods for learning node embeddings, including random-walk-based methods and applications to knowledge graphs. It then provides a technical synthesis and introduction to the highly successful graph neural network (GNN) formalism, which has become a dominant and fast-growing paradigm for deep learning with graph data. The book concludes with a synthesis of recent advancements in deep generative models for graphs—a nascent but quickly growing subset of graph representation learning.


Computational Stem Cell Biology

Computational Stem Cell Biology

Author: Patrick Cahan

Publisher: Humana

Published: 2019-05-07

Total Pages: 0

ISBN-13: 9781493992232

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This volume details methods and protocols to further the study of stem cells within the computational stem cell biology (CSCB) field. Chapters are divided into four sections covering the theory and practice of modeling of stem cell behavior, analyzing single cell genome-scale measurements, reconstructing gene regulatory networks, and metabolomics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Stem Cell Biology: Methods and Protocols will be an invaluable guide to researchers as they explore stem cells from the perspective of computational biology.


Gene Network Inference

Gene Network Inference

Author: Alberto Fuente

Publisher: Springer Science & Business Media

Published: 2014-01-03

Total Pages: 135

ISBN-13: 3642451616

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This book presents recent methods for Systems Genetics (SG) data analysis, applying them to a suite of simulated SG benchmark datasets. Each of the chapter authors received the same datasets to evaluate the performance of their method to better understand which algorithms are most useful for obtaining reliable models from SG datasets. The knowledge gained from this benchmarking study will ultimately allow these algorithms to be used with confidence for SG studies e.g. of complex human diseases or food crop improvement. The book is primarily intended for researchers with a background in the life sciences, not for computer scientists or statisticians.


Towards a Theory of Development

Towards a Theory of Development

Author: Alessandro Minelli

Publisher: Oxford University Press, USA

Published: 2014

Total Pages: 299

ISBN-13: 0199671435

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Is it possible to explain and predict the development of living things? What is development? Articulate answers to these seemingly innocuous questions are far from straightforward. To date, no systematic, targeted effort has been made to construct a unifying theory of development. This novel work offers a unique exploration of the foundations of ontogeny by asking how the development of living things should be understood. It explores the key concepts of developmental biology, asks whether general principles of development can be discovered, and examines the role of models and theories. The two editors (one a biologist with long interest in the theoretical aspects of his discipline, the other a philosopher of science who has mainly worked on biological systems) have assembled a team of leading contributors who are representative of the scientific and philosophical community within which a diversity of thoughts are growing, and out of which a theory of development may eventually emerge. They analyse a wealth of approaches to concepts, models and theories of development, such as gene regulatory networks, accounts based on systems biology and on physics of soft matter, the different articulations of evolution and development, symbiont-induced development, as well as the widely discussed concepts of positional information and morphogenetic field, the idea of a 'programme' of development and its critiques, and the long-standing opposition between preformationist and epigenetic conceptions of development. Towards a Theory of Development is primarily aimed at students and researchers in the fields of 'evo-devo', developmental biology, theoretical biology, systems biology, biophysics, and the philosophy of science.


Computational Methods for Single-Cell Data Analysis

Computational Methods for Single-Cell Data Analysis

Author: Guo-Cheng Yuan

Publisher: Humana Press

Published: 2019-02-14

Total Pages: 271

ISBN-13: 9781493990566

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This detailed book provides state-of-art computational approaches to further explore the exciting opportunities presented by single-cell technologies. Chapters each detail a computational toolbox aimed to overcome a specific challenge in single-cell analysis, such as data normalization, rare cell-type identification, and spatial transcriptomics analysis, all with a focus on hands-on implementation of computational methods for analyzing experimental data. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Methods for Single-Cell Data Analysis aims to cover a wide range of tasks and serves as a vital handbook for single-cell data analysis.


The Regulatory Genome

The Regulatory Genome

Author: Eric H. Davidson

Publisher: Elsevier

Published: 2010-07-19

Total Pages: 303

ISBN-13: 0080455573

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Gene regulatory networks are the most complex, extensive control systems found in nature. The interaction between biology and evolution has been the subject of great interest in recent years. The author, Eric Davidson, has been instrumental in elucidating this relationship. He is a world renowned scientist and a major contributor to the field of developmental biology. The Regulatory Genome beautifully explains the control of animal development in terms of structure/function relations of inherited regulatory DNA sequence, and the emergent properties of the gene regulatory networks composed of these sequences. New insights into the mechanisms of body plan evolution are derived from considerations of the consequences of change in developmental gene regulatory networks. Examples of crucial evidence underscore each major concept. The clear writing style explains regulatory causality without requiring a sophisticated background in descriptive developmental biology. This unique text supersedes anything currently available in the market. - The only book in the market that is solely devoted to the genomic regulatory code for animal development - Written at a conceptual level, including many novel synthetic concepts that ultimately simplify understanding - Presents a comprehensive treatment of molecular control elements that determine the function of genes - Provides a comparative treatment of development, based on principles rather than description of developmental processes - Considers the evolutionary processes in terms of the structural properties of gene regulatory networks - Includes 42 full-color descriptive figures and diagrams


Peterson's Graduate Programs in Computer Science & Information Technology, Electrical & Computer Engineering, and Energy & Power Engineering 2011

Peterson's Graduate Programs in Computer Science & Information Technology, Electrical & Computer Engineering, and Energy & Power Engineering 2011

Author: Peterson's

Publisher: Peterson's

Published: 2011-05-01

Total Pages: 658

ISBN-13: 0768934818

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Peterson's Graduate Programs in Computer Science & Information Technology, Electrical & Computer Engineering, and Energy & Power Engineering contains a wealth of information on colleges and universities that offer graduate work these exciting fields. The profiled institutions include those in the United States, Canada and abroad that are accredited by U.S. accrediting bodies. Up-to-date data, collected through Peterson's Annual Survey of Graduate and Professional Institutions, provides valuable information on degree offerings, professional accreditation, jointly offered degrees, part-time and evening/weekend programs, postbaccalaureate distance degrees, faculty, students, degree requirements, entrance requirements, expenses, financial support, faculty research, and unit head and application contact information. Readers will find helpful links to in-depth descriptions that offer additional detailed information about a specific program or department, faculty members and their research, and much more. In addition, there are valuable articles on financial assistance, the graduate admissions process, advice for international and minority students, and facts about accreditation, with a current list of accrediting agencies.


Handbook of Statistical Genomics

Handbook of Statistical Genomics

Author: David J. Balding

Publisher: John Wiley & Sons

Published: 2019-07-09

Total Pages: 1740

ISBN-13: 1119429250

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A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.


Relative Distribution Methods in the Social Sciences

Relative Distribution Methods in the Social Sciences

Author: Mark S. Handcock

Publisher: Springer Science & Business Media

Published: 2006-05-10

Total Pages: 272

ISBN-13: 0387226583

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This monograph presents methods for full comparative distributional analysis based on the relative distribution. This provides a general integrated framework for analysis, a graphical component that simplifies exploratory data analysis and display, a statistically valid basis for the development of hypothesis-driven summary measures, and the potential for decomposition - enabling the examination of complex hypotheses regarding the origins of distributional changes within and between groups. Written for data analysts and those interested in measurement, the text can also serve as a textbook for a course on distributional methods.


The SAGE Handbook of Quantitative Methods in Psychology

The SAGE Handbook of Quantitative Methods in Psychology

Author: Roger E Millsap

Publisher: SAGE Publications

Published: 2009-08-05

Total Pages: 801

ISBN-13: 141293091X

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`I often... wonder to myself whether the field needs another book, handbook, or encyclopedia on this topic. In this case I think that the answer is truly yes. The handbook is well focused on important issues in the field, and the chapters are written by recognized authorities in their fields. The book should appeal to anyone who wants an understanding of important topics that frequently go uncovered in graduate education in psychology' - David C Howell, Professor Emeritus, University of Vermont Quantitative psychology is arguably one of the oldest disciplines within the field of psychology and nearly all psychologists are exposed to quantitative psychology in some form. While textbooks in statistics, research methods and psychological measurement exist, none offer a unified treatment of quantitative psychology. The SAGE Handbook of Quantitative Methods in Psychology does just that. Each chapter covers a methodological topic with equal attention paid to established theory and the challenges facing methodologists as they address new research questions using that particular methodology. The reader will come away from each chapter with a greater understanding of the methodology being addressed as well as an understanding of the directions for future developments within that methodological area. Drawing on a global scholarship, the Handbook is divided into seven parts: Part One: Design and Inference: addresses issues in the inference of causal relations from experimental and non-experimental research, along with the design of true experiments and quasi-experiments, and the problem of missing data due to various influences such as attrition or non-compliance. Part Two: Measurement Theory: begins with a chapter on classical test theory, followed by the common factor analysis model as a model for psychological measurement. The models for continuous latent variables in item-response theory are covered next, followed by a chapter on discrete latent variable models as represented in latent class analysis. Part Three: Scaling Methods: covers metric and non-metric scaling methods as developed in multidimensional scaling, followed by consideration of the scaling of discrete measures as found in dual scaling and correspondence analysis. Models for preference data such as those found in random utility theory are covered next. Part Four: Data Analysis: includes chapters on regression models, categorical data analysis, multilevel or hierarchical models, resampling methods, robust data analysis, meta-analysis, Bayesian data analysis, and cluster analysis. Part Five: Structural Equation Models: addresses topics in general structural equation modeling, nonlinear structural equation models, mixture models, and multilevel structural equation models. Part Six: Longitudinal Models: covers the analysis of longitudinal data via mixed modeling, time series analysis and event history analysis. Part Seven: Specialized Models: covers specific topics including the analysis of neuro-imaging data and functional data-analysis.