102,869 research outputs found
Information visualization for DNA microarray data analysis: A critical review
Graphical representation may provide effective means of making sense of the complexity and sheer volume of data produced by DNA microarray experiments that monitor the expression patterns of thousands of genes simultaneously. The ability to use ldquoabstractrdquo graphical representation to draw attention to areas of interest, and more in-depth visualizations to answer focused questions, would enable biologists to move from a large amount of data to particular records they are interested in, and therefore, gain deeper insights in understanding the microarray experiment results. This paper starts by providing some background knowledge of microarray experiments, and then, explains how graphical representation can be applied in general to this problem domain, followed by exploring the role of visualization in gene expression data analysis. Having set the problem scene, the paper then examines various multivariate data visualization techniques that have been applied to microarray data analysis. These techniques are critically reviewed so that the strengths and weaknesses of each technique can be tabulated. Finally, several key problem areas as well as possible solutions to them are discussed as being a source for future work
Causal graphical models in systems genetics: A unified framework for joint inference of causal network and genetic architecture for correlated phenotypes
Causal inference approaches in systems genetics exploit quantitative trait
loci (QTL) genotypes to infer causal relationships among phenotypes. The
genetic architecture of each phenotype may be complex, and poorly estimated
genetic architectures may compromise the inference of causal relationships
among phenotypes. Existing methods assume QTLs are known or inferred without
regard to the phenotype network structure. In this paper we develop a
QTL-driven phenotype network method (QTLnet) to jointly infer a causal
phenotype network and associated genetic architecture for sets of correlated
phenotypes. Randomization of alleles during meiosis and the unidirectional
influence of genotype on phenotype allow the inference of QTLs causal to
phenotypes. Causal relationships among phenotypes can be inferred using these
QTL nodes, enabling us to distinguish among phenotype networks that would
otherwise be distribution equivalent. We jointly model phenotypes and QTLs
using homogeneous conditional Gaussian regression models, and we derive a
graphical criterion for distribution equivalence. We validate the QTLnet
approach in a simulation study. Finally, we illustrate with simulated data and
a real example how QTLnet can be used to infer both direct and indirect effects
of QTLs and phenotypes that co-map to a genomic region.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS288 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Modeling dependent gene expression
In this paper we propose a Bayesian approach for inference about dependence
of high throughput gene expression. Our goals are to use prior knowledge about
pathways to anchor inference about dependence among genes; to account for this
dependence while making inferences about differences in mean expression across
phenotypes; and to explore differences in the dependence itself across
phenotypes. Useful features of the proposed approach are a model-based
parsimonious representation of expression as an ordinal outcome, a novel and
flexible representation of prior information on the nature of dependencies, and
the use of a coherent probability model over both the structure and strength of
the dependencies of interest. We evaluate our approach through simulations and
in the analysis of data on expression of genes in the Complement and
Coagulation Cascade pathway in ovarian cancer.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS525 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
A sparse conditional Gaussian graphical model for analysis of genetical genomics data
Genetical genomics experiments have now been routinely conducted to measure
both the genetic markers and gene expression data on the same subjects. The
gene expression levels are often treated as quantitative traits and are subject
to standard genetic analysis in order to identify the gene expression
quantitative loci (eQTL). However, the genetic architecture for many gene
expressions may be complex, and poorly estimated genetic architecture may
compromise the inferences of the dependency structures of the genes at the
transcriptional level. In this paper we introduce a sparse conditional Gaussian
graphical model for studying the conditional independent relationships among a
set of gene expressions adjusting for possible genetic effects where the gene
expressions are modeled with seemingly unrelated regressions. We present an
efficient coordinate descent algorithm to obtain the penalized estimation of
both the regression coefficients and the sparse concentration matrix. The
corresponding graph can be used to determine the conditional independence among
a group of genes while adjusting for shared genetic effects. Simulation
experiments and asymptotic convergence rates and sparsistency are used to
justify our proposed methods. By sparsistency, we mean the property that all
parameters that are zero are actually estimated as zero with probability
tending to one. We apply our methods to the analysis of a yeast eQTL data set
and demonstrate that the conditional Gaussian graphical model leads to a more
interpretable gene network than a standard Gaussian graphical model based on
gene expression data alone.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS494 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Model-driven engineering approach to design and implementation of robot control system
In this paper we apply a model-driven engineering approach to designing
domain-specific solutions for robot control system development. We present a
case study of the complete process, including identification of the domain
meta-model, graphical notation definition and source code generation for
subsumption architecture -- a well-known example of robot control architecture.
Our goal is to show that both the definition of the robot-control architecture
and its supporting tools fits well into the typical workflow of model-driven
engineering development.Comment: Presented at DSLRob 2011 (arXiv:cs/1212.3308
Communication Theoretic Data Analytics
Widespread use of the Internet and social networks invokes the generation of
big data, which is proving to be useful in a number of applications. To deal
with explosively growing amounts of data, data analytics has emerged as a
critical technology related to computing, signal processing, and information
networking. In this paper, a formalism is considered in which data is modeled
as a generalized social network and communication theory and information theory
are thereby extended to data analytics. First, the creation of an equalizer to
optimize information transfer between two data variables is considered, and
financial data is used to demonstrate the advantages. Then, an information
coupling approach based on information geometry is applied for dimensionality
reduction, with a pattern recognition example to illustrate the effectiveness.
These initial trials suggest the potential of communication theoretic data
analytics for a wide range of applications.Comment: Published in IEEE Journal on Selected Areas in Communications, Jan.
201
Ship product modelling
This paper is a fundamental review of ship product modeling techniques with a focus on determining the state of the art, to identify any shortcomings and propose future directions. The review addresses ship product data representations, product modeling techniques and integration issues, and life phase issues. The most significant development has been the construction of the ship Standard for the Exchange of Product Data (STEP) application protocols. However, difficulty has been observed with respect to the general uptake of the standards, in particular with the application to legacy systems, often resulting in embellishments to the standards and limiting the ability to further exchange the product data. The EXPRESS modeling language is increasingly being superseded by the extensible mark-up language (XML) as a method to map the STEP data, due to its wider support throughout the information technology industry and its more obvious structure and hierarchy. The associated XML files are, however, larger than those produced using the EXPRESS language and make further demands on the already considerable storage required for the ship product model. Seamless integration between legacy applications appears to be difficult to achieve using the current technologies, which often rely on manual interaction for the translation of files. The paper concludes with a discussion of future directions that aim to either solve or alleviate these issues
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