A decision tree-based method for protein contact map prediction

In this paper, we focus on protein contact map prediction. We describe a method where contact maps are predicted using decision tree-based model. The algorithm includes the subsequence information between the couple of analyzed amino acids. In order to evaluate the method generalization capabilities, we carry out an experiment using 173 non-homologous proteins of known structures. Our results indicate that the method can assign protein contacts with an average accuracy of 0.34, superior to the 0.25 obtained by the FNETCSS method. This shows that our algorithm improves the accuracy with respect to the methods compared, especially with the increase of protein lengt

Inferring AS Relationships: Dead End or Lively Beginning?

Recent techniques for inferring business relationships between ASs have yielded maps that have extremely few invalid BGP paths in the terminology of Gao. However, some relationships inferred by these newer algorithms are incorrect, leading to the deduction of unrealistic AS hierarchies. We investigate this problem and discover what causes it. Having obtained such insight, we generalize the problem of AS relationship inference as a multiobjective optimization problem with node-degree-based corrections to the original objective function of minimizing the number of invalid paths. We solve the generalized version of the problem using the semidefinite programming relaxation of the MAX2SAT problem. Keeping the number of invalid paths small, we obtain a more veracious solution than that yielded by recent heuristics

An Algorithm for Preferential Selection of Spectroscopic Targets in LEGUE

We describe a general target selection algorithm that is applicable to any survey in which the number of available candidates is much larger than the number of objects to be observed. This routine aims to achieve a balance between a smoothly-varying, well-understood selection function and the desire to preferentially select certain types of targets. Some target-selection examples are shown that illustrate different possibilities of emphasis functions. Although it is generally applicable, the algorithm was developed specifically for the LAMOST Experiment for Galactic Understanding and Exploration (LEGUE) survey that will be carried out using the Chinese Guo Shou Jing Telescope. In particular, this algorithm was designed for the portion of LEGUE targeting the Galactic halo, in which we attempt to balance a variety of science goals that require stars at fainter magnitudes than can be completely sampled by LAMOST. This algorithm has been implemented for the halo portion of the LAMOST pilot survey, which began in October 2011.Comment: 17 pages, 7 figures, accepted for publication in RA

Enhancing a Search Algorithm to Perform Intelligent Backtracking

This paper illustrates how a Prolog program, using chronological backtracking to find a solution in some search space, can be enhanced to perform intelligent backtracking. The enhancement crucially relies on the impurity of Prolog that allows a program to store information when a dead end is reached. To illustrate the technique, a simple search program is enhanced. To appear in Theory and Practice of Logic Programming. Keywords: intelligent backtracking, dependency-directed backtracking, backjumping, conflict-directed backjumping, nogood sets, look-back.Comment: To appear in Theory and Practice of Logic Programmin

Analysis of a Gibbs sampler method for model based clustering of gene expression data

Over the last decade, a large variety of clustering algorithms have been developed to detect coregulatory relationships among genes from microarray gene expression data. Model based clustering approaches have emerged as statistically well grounded methods, but the properties of these algorithms when applied to large-scale data sets are not always well understood. An in-depth analysis can reveal important insights about the performance of the algorithm, the expected quality of the output clusters, and the possibilities for extracting more relevant information out of a particular data set. We have extended an existing algorithm for model based clustering of genes to simultaneously cluster genes and conditions, and used three large compendia of gene expression data for S. cerevisiae to analyze its properties. The algorithm uses a Bayesian approach and a Gibbs sampling procedure to iteratively update the cluster assignment of each gene and condition. For large-scale data sets, the posterior distribution is strongly peaked on a limited number of equiprobable clusterings. A GO annotation analysis shows that these local maxima are all biologically equally significant, and that simultaneously clustering genes and conditions performs better than only clustering genes and assuming independent conditions. A collection of distinct equivalent clusterings can be summarized as a weighted graph on the set of genes, from which we extract fuzzy, overlapping clusters using a graph spectral method. The cores of these fuzzy clusters contain tight sets of strongly coexpressed genes, while the overlaps exhibit relations between genes showing only partial coexpression.Comment: 8 pages, 7 figure