BeamGA Median: A Hybrid Heuristic Search Approach

The median problem is significantly applied to derive the most reasonable rearrangement phylogenetic tree for many species. More specifically, the problem is concerned with finding a permutation that minimizes the sum of distances between itself and a set of three signed permutations. Genomes with equal number of genes but different order can be represented as permutations. In this paper, an algorithm, namely BeamGA median, is proposed that combines a heuristic search approach (local beam) as an initialization step to generate a number of solutions, and then a Genetic Algorithm (GA) is applied in order to refine the solutions, aiming to achieve a better median with the smallest possible reversal distance from the three original permutations. In this approach, any genome rearrangement distance can be applied. In this paper, we use the reversal distance. To the best of our knowledge, the proposed approach was not applied before for solving the median problem. Our approach considers true biological evolution scenario by applying the concept of common intervals during the GA optimization process. This allows us to imitate a true biological behavior and enhance genetic approach time convergence. We were able to handle permutations with a large number of genes, within an acceptable time performance and with same or better accuracy as compared to existing algorithms

Multichromosomal median and halving problems under different genomic distances

<p>Abstract</p> <p>Background</p> <p>Genome median and genome halving are combinatorial optimization problems that aim at reconstructing ancestral genomes as well as the evolutionary events leading from the ancestor to extant species. Exploring complexity issues is a first step towards devising efficient algorithms. The complexity of the median problem for unichromosomal genomes (permutations) has been settled for both the breakpoint distance and the reversal distance. Although the multichromosomal case has often been assumed to be a simple generalization of the unichromosomal case, it is also a relaxation so that complexity in this context does not follow from existing results, and is open for all distances.</p> <p>Results</p> <p>We settle here the complexity of several genome median and halving problems, including a surprising polynomial result for the breakpoint median and guided halving problems in genomes with circular and linear chromosomes, showing that the multichromosomal problem is actually easier than the unichromosomal problem. Still other variants of these problems are NP-complete, including the DCJ double distance problem, previously mentioned as an open question. We list the remaining open problems.</p> <p>Conclusion</p> <p>This theoretical study clears up a wide swathe of the algorithmical study of genome rearrangements with multiple multichromosomal genomes.</p

CURRENT ACCOUNT ADJUSTMENTS IN SELECTED TRANSITION COUNTRIES

The paper investigates sharp reductions seen in current account deficits in selected transition countries in the 1992- 2003 period. The analysis focuses on three important aspects of these current account reversals: a) to examine those factors that might have triggered the reversals and to provide some insights into the current account adjustment process; b) to reveal some characteristics of persistent current account deficits; and c) to investigate the direct impact of these reversals on economic growth in the region. Results suggest that restrictively defined reversals seem to be closely related to factors such as domestic savings, real export growth, international reserves and external indebtedness as well as with the budget and trade balances. While the role of exchange rate depreciation seems ambiguous, we found that the sharp current account reversals are systematically associated with a gradual GDP growth slowdown in the pre-reversal period and with robust GDP growth impetus afterwards. Indeed, less restrictively defined reversals show that reversals are associated with an increase of output by around 1.20 percentage points in the second year of recovery. Finally, the results suggest the significant possibility that persistent current account deficits, which on average last more than five years, are consumption-driven in the transition countries.http://deepblue.lib.umich.edu/bitstream/2027.42/40199/3/wp813.pd

Continuous-time perpetuities and time reversal of diffusions

We consider the problem of estimating the joint distribution of a continuous-time perpetuity and the underlying factors which govern the cash flow rate, in an ergodic Markov model. Two approaches are used to obtain the distribution. The first identifies a partial differential equation for the conditional cumulative distribution function of the perpetuity given the initial factor value, which under certain conditions ensures the existence of a density for the perpetuity. The second (and more general) approach, identifies the joint law as the stationary distribution of an ergodic multi-dimensional diffusion using techniques of time reversal. This later approach allows for efficient use of Monte-Carlo simulation when estimating the distribution, as the distribution is obtained by sampling a single path of the reversed process.Comment: 42 pages; added numerical exampl

PageRank and rank-reversal dependence on the damping factor

PageRank (PR) is an algorithm originally developed by Google to evaluate the importance of web pages. Considering how deeply rooted Google's PR algorithm is to gathering relevant information or to the success of modern businesses, the question of rank-stability and choice of the damping factor (a parameter in the algorithm) is clearly important. We investigate PR as a function of the damping factor d on a network obtained from a domain of the World Wide Web, finding that rank-reversal happens frequently over a broad range of PR (and of d). We use three different correlation measures, Pearson, Spearman, and Kendall, to study rank-reversal as d changes, and show that the correlation of PR vectors drops rapidly as d changes from its frequently cited value, $d_0=0.85$. Rank-reversal is also observed by measuring the Spearman and Kendall rank correlation, which evaluate relative ranks rather than absolute PR. Rank-reversal happens not only in directed networks containing rank-sinks but also in a single strongly connected component, which by definition does not contain any sinks. We relate rank-reversals to rank-pockets and bottlenecks in the directed network structure. For the network studied, the relative rank is more stable by our measures around $d=0.65$ than at $d=d_0$.Comment: 14 pages, 9 figure

Avoiding the rating bounce : why rating agencies are slow to react to new information

Rating agencies state that they take a rating action only when it is unlikely to be reversed shortly afterwards. Based on a formal representation of the rating process, I show that such a policy provides a good explanation for the empirical evidence: Rating changes occur relatively seldom, exhibit serial dependence, and lag changes in the issuers’ default risk. In terms of informational losses, avoiding rating reversals can be more harmful than monitoring credit quality only twice per year