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Book
Systems Analytics and Integration of Big Omics Data
Author:
ISBN: 3039287451 3039287443 Year: 2020 Publisher: MDPI - Multidisciplinary Digital Publishing Institute

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Abstract

A “genotype"" is essentially an organism's full hereditary information which is obtained from its parents. A ""phenotype"" is an organism's actual observed physical and behavioral properties. These may include traits such as morphology, size, height, eye color, metabolism, etc. One of the pressing challenges in computational and systems biology is genotype-to-phenotype prediction. This is challenging given the amount of data generated by modern Omics technologies. This “Big Data” is so large and complex that traditional data processing applications are not up to the task. Challenges arise in collection, analysis, mining, sharing, transfer, visualization, archiving, and integration of these data. In this Special Issue, there is a focus on the systems-level analysis of Omics data, recent developments in gene ontology annotation, and advances in biological pathways and network biology. The integration of Omics data with clinical and biomedical data using machine learning is explored. This Special Issue covers new methodologies in the context of gene–environment interactions, tissue-specific gene expression, and how external factors or host genetics impact the microbiome.

Keywords

precision medicine informatics --- n/a --- drug sensitivity --- chromatin modification --- cell lines --- biocuration --- neurodegeneration --- multivariate analysis --- artificial intelligence --- epigenetics --- missing data --- sequencing --- clinical data --- class imbalance --- integrative analytics --- algorithm development for network integration --- deep phenotype --- non-omics data --- feature selection --- Gene Ontology --- miRNA–gene expression networks --- omics data --- plot visualization --- Alzheimer’s disease --- tissue classification --- epidemiological data --- proteomic analysis --- genotype --- RNA expression --- indirect effect --- multi-omics --- dementia --- multiomics integration --- data integration --- phenomics --- network topology analysis --- challenges --- transcriptome --- enrichment analysis --- regulatory genomics --- scalability --- heterogeneous data --- systemic lupus erythematosus --- database --- microtubule-associated protein tau --- disease variants --- genomics --- joint modeling --- distance correlation --- annotation --- phenotype --- direct effect --- curse of dimensionality --- gene–environment interactions --- logic forest --- machine learning --- KEGG pathways --- multivariate causal mediation --- amyloid-beta --- bioinformatics pipelines --- support vector machine --- pharmacogenomics --- candidate genes --- tissue-specific expressed genes --- cognitive impairment --- causal inference --- miRNA-gene expression networks --- Alzheimer's disease --- gene-environment interactions


Book
Robust optimization
Authors: --- ---
ISBN: 1282259288 9786612259289 1400831059 0691143684 9780691143682 9781400831050 9781282259287 6612259280 Year: 2009 Publisher: Princeton, NJ : Princeton University Press,

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Abstract

Robust optimization is still a relatively new approach to optimization problems affected by uncertainty, but it has already proved so useful in real applications that it is difficult to tackle such problems today without considering this powerful methodology. Written by the principal developers of robust optimization, and describing the main achievements of a decade of research, this is the first book to provide a comprehensive and up-to-date account of the subject. Robust optimization is designed to meet some major challenges associated with uncertainty-affected optimization problems: to operate under lack of full information on the nature of uncertainty; to model the problem in a form that can be solved efficiently; and to provide guarantees about the performance of the solution. The book starts with a relatively simple treatment of uncertain linear programming, proceeding with a deep analysis of the interconnections between the construction of appropriate uncertainty sets and the classical chance constraints (probabilistic) approach. It then develops the robust optimization theory for uncertain conic quadratic and semidefinite optimization problems and dynamic (multistage) problems. The theory is supported by numerous examples and computational illustrations. An essential book for anyone working on optimization and decision making under uncertainty, Robust Optimization also makes an ideal graduate textbook on the subject.

Keywords

Robust optimization. --- Linear programming. --- 519.8 --- 681.3*G16 --- 681.3*G16 Optimization: constrained optimization; gradient methods; integer programming; least squares methods; linear programming; nonlinear programming (Numericalanalysis) --- Optimization: constrained optimization; gradient methods; integer programming; least squares methods; linear programming; nonlinear programming (Numericalanalysis) --- 519.8 Operational research --- Operational research --- Robust optimization --- Linear programming --- Optimisation robuste --- Programmation linéaire --- Optimization, Robust --- RO (Robust optimization) --- Mathematical optimization --- Production scheduling --- Programming (Mathematics) --- 0O. --- Accuracy and precision. --- Additive model. --- Almost surely. --- Approximation algorithm. --- Approximation. --- Best, worst and average case. --- Bifurcation theory. --- Big O notation. --- Candidate solution. --- Central limit theorem. --- Chaos theory. --- Coefficient. --- Computational complexity theory. --- Constrained optimization. --- Convex hull. --- Convex optimization. --- Convex set. --- Cumulative distribution function. --- Curse of dimensionality. --- Decision problem. --- Decision rule. --- Degeneracy (mathematics). --- Diagram (category theory). --- Duality (optimization). --- Dynamic programming. --- Exponential function. --- Feasible region. --- Floor and ceiling functions. --- For All Practical Purposes. --- Free product. --- Ideal solution. --- Identity matrix. --- Inequality (mathematics). --- Infimum and supremum. --- Integer programming. --- Law of large numbers. --- Likelihood-ratio test. --- Linear dynamical system. --- Linear inequality. --- Linear map. --- Linear matrix inequality. --- Linear regression. --- Loss function. --- Margin classifier. --- Markov chain. --- Markov decision process. --- Mathematical optimization. --- Max-plus algebra. --- Maxima and minima. --- Multivariate normal distribution. --- NP-hardness. --- Norm (mathematics). --- Normal distribution. --- Optimal control. --- Optimization problem. --- Orientability. --- P versus NP problem. --- Pairwise. --- Parameter. --- Parametric family. --- Probability distribution. --- Probability. --- Proportionality (mathematics). --- Quantity. --- Random variable. --- Relative interior. --- Robust control. --- Robust decision-making. --- Semi-infinite. --- Sensitivity analysis. --- Simple set. --- Singular value. --- Skew-symmetric matrix. --- Slack variable. --- Special case. --- Spherical model. --- Spline (mathematics). --- State variable. --- Stochastic calculus. --- Stochastic control. --- Stochastic optimization. --- Stochastic programming. --- Stochastic. --- Strong duality. --- Support vector machine. --- Theorem. --- Time complexity. --- Uncertainty. --- Uniform distribution (discrete). --- Unimodality. --- Upper and lower bounds. --- Variable (mathematics). --- Virtual displacement. --- Weak duality. --- Wiener filter. --- With high probability. --- Without loss of generality.

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