The Third Gravitational Lensing Accuracy Testing (GREAT3) Challenge Handbook

The GRavitational lEnsing Accuracy Testing 3 (GREAT3) challenge is the third in a series of image analysis challenges, with a goal of testing and facilitating the development of methods for analyzing astronomical images that will be used to measure weak gravitational lensing. This measurement requires extremely precise estimation of very small galaxy shape distortions, in the presence of far larger intrinsic galaxy shapes and distortions due to the blurring kernel caused by the atmosphere, telescope optics, and instrumental effects. The GREAT3 challenge is posed to the astronomy, machine learning, and statistics communities, and includes tests of three specific effects that are of immediate relevance to upcoming weak lensing surveys, two of which have never been tested in a community challenge before. These effects include realistically complex galaxy models based on high-resolution imaging from space; spatially varying, physically-motivated blurring kernel; and combination of multiple different exposures. To facilitate entry by people new to the field, and for use as a diagnostic tool, the simulation software for the challenge is publicly available, though the exact parameters used for the challenge are blinded. Sample scripts to analyze the challenge data using existing methods will also be provided. See http://great3challenge.info and http://great3.projects.phys.ucl.ac.uk/leaderboard/ for more information.Comment: 30 pages, 13 figures, submitted for publication, with minor edits (v2) to address comments from the anonymous referee. Simulated data are available for download and participants can find more information at http://great3.projects.phys.ucl.ac.uk/leaderboard

Gene expression in large pedigrees: analytic approaches.

BackgroundWe currently have the ability to quantify transcript abundance of messenger RNA (mRNA), genome-wide, using microarray technologies. Analyzing genotype, phenotype and expression data from 20 pedigrees, the members of our Genetic Analysis Workshop (GAW) 19 gene expression group published 9 papers, tackling some timely and important problems and questions. To study the complexity and interrelationships of genetics and gene expression, we used established statistical tools, developed newer statistical tools, and developed and applied extensions to these tools.MethodsTo study gene expression correlations in the pedigree members (without incorporating genotype or trait data into the analysis), 2 papers used principal components analysis, weighted gene coexpression network analysis, meta-analyses, gene enrichment analyses, and linear mixed models. To explore the relationship between genetics and gene expression, 2 papers studied expression quantitative trait locus allelic heterogeneity through conditional association analyses, and epistasis through interaction analyses. A third paper assessed the feasibility of applying allele-specific binding to filter potential regulatory single-nucleotide polymorphisms (SNPs). Analytic approaches included linear mixed models based on measured genotypes in pedigrees, permutation tests, and covariance kernels. To incorporate both genotype and phenotype data with gene expression, 4 groups employed linear mixed models, nonparametric weighted U statistics, structural equation modeling, Bayesian unified frameworks, and multiple regression.Results and discussionRegarding the analysis of pedigree data, we found that gene expression is familial, indicating that at least 1 factor for pedigree membership or multiple factors for the degree of relationship should be included in analyses, and we developed a method to adjust for familiality prior to conducting weighted co-expression gene network analysis. For SNP association and conditional analyses, we found FaST-LMM (Factored Spectrally Transformed Linear Mixed Model) and SOLAR-MGA (Sequential Oligogenic Linkage Analysis Routines -Major Gene Analysis) have similar type 1 and type 2 errors and can be used almost interchangeably. To improve the power and precision of association tests, prior knowledge of DNase-I hypersensitivity sites or other relevant biological annotations can be incorporated into the analyses. On a biological level, eQTL (expression quantitative trait loci) are genetically complex, exhibiting both allelic heterogeneity and epistasis. Including both genotype and phenotype data together with measurements of gene expression was found to be generally advantageous in terms of generating improved levels of significance and in providing more interpretable biological models.ConclusionsPedigrees can be used to conduct analyses of and enhance gene expression studies

Classifying Pattern Formation in Materials via Machine Learning

Scanning probe experiments such as scanning tunneling microscopy (STM) and atomic force microscopy (AFM) on strongly correlated materials often reveal complex pattern formation that occurs on multiple length scales. We have shown in two disparate correlated materials that the pattern formation is driven by proximity to a disorder-driven critical point. We developed new analysis concepts and techniques that relate the observed pattern formation to critical exponents by analyzing the geometry and statistics of clusters observed in these experiments and converting that information into critical exponents. Machine learning algorithms can be helpful correlating data from scanning probe experiments to theoretical models of pattern formation. We analyze the use of machine learning algorithms for the identification of critical behavior and universality underlying scanning probe data sets taken from correlated materials. This method has complementary strengths to the cluster analysis methods. The cluster techniques have a clear physical interpretation while machine learning algorithms require less expertise from the user and are faster to implement. The complementary nature of the two techniques further facilitates our understanding of correlated materials. The training of machine learning algorithms has been done through artificial neural networks. The neural net was trained using data from theoretical simulations of percolation and Ising models. The trained net had a 3.00% average classification error during testing. This proves that machine learning algorithms can successfully distinguish whether the complex pattern formation of a specific novel material is governed by uncorrelated percolation or by an interaction model fixed point

The use of Petri nets for modeling pipelined processors

This paper discusses the use of Petri Nets for modeling and analyzing pipelined processors. Petri Nets are particularly well-suited to modeling the synchronization, buffering, resource contention and delicate timing so common in pipelined processors. Tools for simulating, animating and analyzing the behavior of the models are described. The usefulness of the tools and the analysis methods they support in evaluating the performance and analyzing the detailed timing of pipelined microprocessors is illustrated through an example

Managing stimulation of regional innovation subjects’ interaction in the digital economy

The reported study was funded by RFBR according to the research project No. 18-01000204_a, No. 16-07-00031_a, No. 18-07-00975_a.Purpose: The article is devoted to solving fundamental scientific problems in the scope of the development of forecasting modeling methods and evaluation of regional company’s innovative development parameters, synthesizing new methods of big data processing and intelligent analysis, as well as methods of knowledge eliciting and forecasting the dynamics of regional innovation developments through benchmarking. Design/Methodology/Approach: For regional economic development, it is required to identify the mechanisms that contribute to (or impede) the innovative economic development of the regions. The synergetic approach to management is based on the fact that there are multiple paths of IS development (scenarios with different probabilities), although it is necessary to reach the required attractor by meeting the management goals. Findings: The present research is focused on obtainment of new knowledge in creating a technique of multi-agent search, collection and processing of data on company’s innovative development indicators, models and methods of intelligent analysis of the collected data. Practical Implications: The author developed recommendations before starting the process of institutional changes in a specific regional innovation system. The article formulates recommendations on the implementation of institutional changes in the region taking into account the sociocultural characteristics of the region’s population. Originality/Value: It is the first time, when a complex of models and methods is based on the use of a convergent model of large data volumes processing is presented.peer-reviewe