Noise resistant generalized parametric validity index of clustering for gene expression data

This article has been made available through the Brunel Open Access Publishing Fund.Validity indices have been investigated for decades. However, since there is no study of noise-resistance performance of these indices in the literature, there is no guideline for determining the best clustering in noisy data sets, especially microarray data sets. In this paper, we propose a generalized parametric validity (GPV) index which employs two tunable parameters α and β to control the proportions of objects being considered to calculate the dissimilarities. The greatest advantage of the proposed GPV index is its noise-resistance ability, which results from the flexibility of tuning the parameters. Several rules are set to guide the selection of parameter values. To illustrate the noise-resistance performance of the proposed index, we evaluate the GPV index for assessing five clustering algorithms in two gene expression data simulation models with different noise levels and compare the ability of determining the number of clusters with eight existing indices. We also test the GPV in three groups of real gene expression data sets. The experimental results suggest that the proposed GPV index has superior noise-resistance ability and provides fairly accurate judgements

Reduced-Rank STAP Schemes for Airborne Radar Based on Switched Joint Interpolation, Decimation and Filtering Algorithm

In this paper, we propose a reduced-rank space-time adaptive processing (STAP) technique for airborne phased array radar applications. The proposed STAP method performs dimensionality reduction by using a reduced-rank switched joint interpolation, decimation and filtering algorithm (RR-SJIDF). In this scheme, a multiple-processing-branch (MPB) framework, which contains a set of jointly optimized interpolation, decimation and filtering units, is proposed to adaptively process the observations and suppress jammers and clutter. The output is switched to the branch with the best performance according to the minimum variance criterion. In order to design the decimation unit, we present an optimal decimation scheme and a low-complexity decimation scheme. We also develop two adaptive implementations for the proposed scheme, one based on a recursive least squares (RLS) algorithm and the other on a constrained conjugate gradient (CCG) algorithm. The proposed adaptive algorithms are tested with simulated radar data. The simulation results show that the proposed RR-SJIDF STAP schemes with both the RLS and the CCG algorithms converge at a very fast speed and provide a considerable SINR improvement over the state-of-the-art reduced-rank schemes

Finite-element modeling of liquid-crystal hydrodynamics with a variable degree of order

A finite-element model of liquid-crystal hydrodynamics based on the Qian and Sheng formulation has been developed. This formulation is a generalization of the Ericksen-Leslie theory to include variations in the order parameter, allowing for a proper description of disclinations. The present implementation is well suited to treat properly the various length scales necessary to model large regions yet resolve the rapid variations in the order parameter in proximity to disclinations

Dual-layer network representation exploiting information characterization

In this paper, a logical dual-layer representation approach is proposed to facilitate the analysis of directed and weighted complex networks. Unlike the single logical layer structure, which was widely used for the directed and weighted flow graph, the proposed approach replaces the single layer with a dual-layer structure, which introduces a provider layer and a requester layer. The new structure provides the characterization of the nodes by the information, which they provide to and they request from the network. Its features are explained and its implementation and visualization are also detailed. We also design two clustering methods with different strategies respectively, which provide the analysis from different points of view. The effectiveness of the proposed approach is demonstrated using a simplified example. By comparing the graph layout with the conventional directed graph, the new dual-layer representation reveals deeper insight into the complex networks and provides more opportunities for versatile clustering analysis.The National Institute for Health Research (NIHR) under its Programme Grants for Applied Research Programme (Grant Reference Number RP-PG-0310-1004)

Modeling of weak anisotropic anchoring of nematic liquid crystals in the Landau-de Gennes theory

The anisotropic anchoring effect of a treated solid surface on a nematic liquid crystal is described in the Landau-de Gennes theory using a power expansion on the tensor-order parameter and two mutually orthogonal unit vectors. The expression has three degrees of freedom, allowing for independent assignment of polar and azimuthal anchoring strengths and a preferred value of the surface-order parameter. It is shown that in the limit for a uniaxial constant-order parameter, the expression simplifies to the anisotropic generalization of the Rapini-Papoular anchoring energy density proposed by Zhao et al. Experimentally measurable values with a physical meaning in the Oseen-Frank theory can be scaled and assigned to the scalar coefficients of the tensor-order-parameter expansion. Results of numerical experiments comparing the anchoring according to the study of Zhao et al. in the Oseen-Frank theory and the power expansion in the Landau-de Gennes theory are presented and shown to agree well

Yeast gene CMR1/YDL156W is consistently co-expressed with genes participating in DNA-metabolic processes in a variety of stringent clustering experiments

© 2013 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/3.0/, which permits unrestricted use, provided the original author and source are credited.The binarization of consensus partition matrices (Bi-CoPaM) method has, among its unique features, the ability to perform ensemble clustering over the same set of genes from multiple microarray datasets by using various clustering methods in order to generate tunable tight clusters. Therefore, we have used the Bi-CoPaM method to the most synchronized 500 cell-cycle-regulated yeast genes from different microarray datasets to produce four tight, specific and exclusive clusters of co-expressed genes. We found 19 genes formed the tightest of the four clusters and this included the gene CMR1/YDL156W, which was an uncharacterized gene at the time of our investigations. Two very recent proteomic and biochemical studies have independently revealed many facets of CMR1 protein, although the precise functions of the protein remain to be elucidated. Our computational results complement these biological results and add more evidence to their recent findings of CMR1 as potentially participating in many of the DNA-metabolism processes such as replication, repair and transcription. Interestingly, our results demonstrate the close co-expressions of CMR1 and the replication protein A (RPA), the cohesion complex and the DNA polymerases α, δ and ɛ, as well as suggest functional relationships between CMR1 and the respective proteins. In addition, the analysis provides further substantial evidence that the expression of the CMR1 gene could be regulated by the MBF complex. In summary, the application of a novel analytic technique in large biological datasets has provided supporting evidence for a gene of previously unknown function, further hypotheses to test, and a more general demonstration of the value of sophisticated methods to explore new large datasets now so readily generated in biological experiments.National Institute for Health Researc

Vortex structures of rotating spin-orbit coupled Bose-Einstein condensates

We consider the quasi-2D two-component Bose-Einstein condensates with Rashba spin-orbit (SO) coupling in a rotating trap. An external Zeeman term favoring spin polarization along the radial direction is also considered, which has the same form as the non-canonical part of the mechanical angular momentum. The rotating condensate exhibits rich structures as varying the strengths of trapping potential and interaction. With a strong trapping potential, the condensate exhibits a half-quantum vortex-lattice configuration. Such a configuration is driven to the normal one by introducing the external radial Zeeman field. In the case of a weak trap potential, the condensate exhibits a multi-domain pattern of plane-wave states under the external radial Zeeman field.Comment: 8 pages, 7 figures, two figures are adde

Using Self-Adaptive Evolutionary Algorithms to Evolve Dynamism-Oriented Maps for a Real Time Strategy Game

9th International Conference on Large Scale Scientific Computations. The final publication is available at link.springer.comThis work presents a procedural content generation system that uses an evolutionary algorithm in order to generate interesting maps for a real-time strategy game, called Planet Wars. Interestingness is here captured by the dynamism of games (i.e., the extent to which they are action-packed). We consider two different approaches to measure the dynamism of the games resulting from these generated maps, one based on fluctuations in the resources controlled by either player and another one based on their confrontations. Both approaches rely on conducting several games on the map under scrutiny using top artificial intelligence (AI) bots for the game. Statistic gathered during these games are then transferred to a fuzzy system that determines the map's level of dynamism. We use an evolutionary algorithm featuring self-adaptation of mutation parameters and variable-length chromosomes (which means maps of different sizes) to produce increasingly dynamic maps.TIN2011-28627-C04-01, P10-TIC-608

Bulk-fragment and tube-like structures of AuN (N=2-26)

Using the relativistic all-electron density-functional calculations on the AuN (N=2-26) in the generalized gradient approximation, combined with the guided simulated annealing, we have found that the two- to three-dimensional structural transition for AuN occurs between N=13 and 15, and the AuN (16<= N <=25) prefer also the pyramid-based bulk fragment structures in addition to the Au20. More importantly, the tubelike structures are found to be the most stable for Au24 and Au26, offering another powerful structure competitor with other isomers, e.g., amorphous, bulk fragment, and gold fullerene. The mechanism to cause these unusual AuN may be attributed to the stronger s-d hybridization and the d-d interaction enhanced by the relativistic effects.Comment: 12 pages and 3 figure