17,051 research outputs found
Use of pre-transformation to cope with outlying values in important candidate genes
Outlying values in predictors often strongly affect the results of statistical analyses in high-dimensional settings. Although they frequently occur with most high-throughput techniques, the problem is often ignored in the literature. We suggest to use a very simple transformation, proposed before in a different context by Royston and Sauerbrei, as an intermediary step between array normalization and high-level statistical analysis. This straightforward univariate transformation identifies extreme values and reduces the influence of outlying values considerably in all further steps of statistical analysis without eliminating the incriminated observation or feature. The use of the transformation and its effects are demonstrated for diverse univariate and multivariate statistical analyses using nine publicly available microarray data sets
A lexicographic multi-objective genetic algorithm for multi-label correlation-based feature selection
This paper proposes a new Lexicographic multi-objective Genetic Algorithm for Multi-Label Correlation-based Feature Selection (LexGA-ML-CFS), which is an extension of the previous single-objective Genetic Algorithm for Multi-label Correlation-based Feature Selection (GA-ML-CFS). This extension uses a LexGA as a global search method for generating candidate feature subsets. In our experiments, we compare the results obtained by LexGA-ML-CFS with the results obtained by the original hill climbing-based ML-CFS, the single-objective GA-ML-CFS and a baseline Binary Relevance method, using ML-kNN as the multi-label classifier. The results from our experiments show that LexGA-ML-CFS improved predictive accuracy, by comparison with other methods, in some cases, but in general there was no statistically significant different between the results of LexGA-ML-CFS and other methods
ExplainIt! -- A declarative root-cause analysis engine for time series data (extended version)
We present ExplainIt!, a declarative, unsupervised root-cause analysis engine
that uses time series monitoring data from large complex systems such as data
centres. ExplainIt! empowers operators to succinctly specify a large number of
causal hypotheses to search for causes of interesting events. ExplainIt! then
ranks these hypotheses, reducing the number of causal dependencies from
hundreds of thousands to a handful for human understanding. We show how a
declarative language, such as SQL, can be effective in declaratively
enumerating hypotheses that probe the structure of an unknown probabilistic
graphical causal model of the underlying system. Our thesis is that databases
are in a unique position to enable users to rapidly explore the possible causal
mechanisms in data collected from diverse sources. We empirically demonstrate
how ExplainIt! had helped us resolve over 30 performance issues in a commercial
product since late 2014, of which we discuss a few cases in detail.Comment: SIGMOD Industry Track 201
PLS dimension reduction for classification of microarray data
PLS dimension reduction is known to give good prediction accuracy in the context of classification with high-dimensional microarray data. In this paper, PLS is compared with some of the best state-of-the-art classification methods. In addition, a simple procedure to choose the number of components is suggested. The connection between PLS dimension reduction and gene selection is examined and a property of the first PLS component for binary classification is proven. PLS can also be used as a visualization tool for high-dimensional data in the classification framework. The whole study is based on 9 real microarray cancer data sets
Sparse reduced-rank regression for imaging genetics studies: models and applications
We present a novel statistical technique; the sparse reduced rank regression (sRRR) model
which is a strategy for multivariate modelling of high-dimensional imaging responses and
genetic predictors. By adopting penalisation techniques, the model is able to enforce sparsity
in the regression coefficients, identifying subsets of genetic markers that best explain
the variability observed in subsets of the phenotypes. To properly exploit the rich structure
present in each of the imaging and genetics domains, we additionally propose the use of
several structured penalties within the sRRR model. Using simulation procedures that accurately
reflect realistic imaging genetics data, we present detailed evaluations of the sRRR
method in comparison with the more traditional univariate linear modelling approach. In
all settings considered, we show that sRRR possesses better power to detect the deleterious
genetic variants. Moreover, using a simple genetic model, we demonstrate the potential
benefits, in terms of statistical power, of carrying out voxel-wise searches as opposed to
extracting averages over regions of interest in the brain. Since this entails the use of phenotypic
vectors of enormous dimensionality, we suggest the use of a sparse classification
model as a de-noising step, prior to the imaging genetics study. Finally, we present the
application of a data re-sampling technique within the sRRR model for model selection.
Using this approach we are able to rank the genetic markers in order of importance of association
to the phenotypes, and similarly rank the phenotypes in order of importance to
the genetic markers. In the very end, we illustrate the application perspective of the proposed
statistical models in three real imaging genetics datasets and highlight some potential
associations
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Statistical Workflow for Feature Selection in Human Metabolomics Data.
High-throughput metabolomics investigations, when conducted in large human cohorts, represent a potentially powerful tool for elucidating the biochemical diversity underlying human health and disease. Large-scale metabolomics data sources, generated using either targeted or nontargeted platforms, are becoming more common. Appropriate statistical analysis of these complex high-dimensional data will be critical for extracting meaningful results from such large-scale human metabolomics studies. Therefore, we consider the statistical analytical approaches that have been employed in prior human metabolomics studies. Based on the lessons learned and collective experience to date in the field, we offer a step-by-step framework for pursuing statistical analyses of cohort-based human metabolomics data, with a focus on feature selection. We discuss the range of options and approaches that may be employed at each stage of data management, analysis, and interpretation and offer guidance on the analytical decisions that need to be considered over the course of implementing a data analysis workflow. Certain pervasive analytical challenges facing the field warrant ongoing focused research. Addressing these challenges, particularly those related to analyzing human metabolomics data, will allow for more standardization of as well as advances in how research in the field is practiced. In turn, such major analytical advances will lead to substantial improvements in the overall contributions of human metabolomics investigations
Algorithmic Thomas Decomposition of Algebraic and Differential Systems
In this paper, we consider systems of algebraic and non-linear partial
differential equations and inequations. We decompose these systems into
so-called simple subsystems and thereby partition the set of solutions. For
algebraic systems, simplicity means triangularity, square-freeness and
non-vanishing initials. Differential simplicity extends algebraic simplicity
with involutivity. We build upon the constructive ideas of J. M. Thomas and
develop them into a new algorithm for disjoint decomposition. The given paper
is a revised version of a previous paper and includes the proofs of correctness
and termination of our decomposition algorithm. In addition, we illustrate the
algorithm with further instructive examples and describe its Maple
implementation together with an experimental comparison to some other
triangular decomposition algorithms.Comment: arXiv admin note: substantial text overlap with arXiv:1008.376
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