Related papers: A polynomial time algorithm for calculating the pr…

Query plans are compared according to multiple cost metrics in multi-objective query optimization. The goal is to find the set of Pareto plans realizing optimal cost tradeoffs for a given query. So far, only algorithms with exponential…

In this paper we give a linear time algorithm for computing the number of spanninig trees in double nested graphs.

Species trees represent the historical divergences of populations or species, while gene trees trace the ancestry of individual gene copies sampled within those populations. In cases involving rapid speciation, gene trees with topologies…

The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…

In this paper we consider the problem of connected edge searching of weighted trees. It is shown that there exists a polynomial-time algorithm for finding optimal connected search strategy for bounded degree trees with arbitrary weights on…

We present a polynomial-time algorithm that determines, given some choice rule, whether there exists an obviously strategy-proof mechanism for that choice rule.

We consider weighted particle systems in which new generations are re-sampled from current particles with probabilities proportional to their weights. This covers a broad class of sequential Monte Carlo methods, widely used in applied…

We study probability distributions over free algebras of trees. Probability distributions can be seen as particular (formal power) tree series [Berstel et al 82, Esik et al 03], i.e. mappings from trees to a semiring K . A widely studied…

The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…

In this article we consider several probabilistic processes defining random grapha. One of these processes appeared recently in connection with a factorization problem in the symmetric group. For each of the probabilistic processes, we…

Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…

Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…

When considering the number of subtrees of trees, the extremal structures which maximize this number among binary trees and trees with a given maximum degree lead to some interesting facts that correlate to other graphical indices in…

We consider the creation conditions of diverse hierarchical trees both analytically and numerically. A connection between the probabilities to create hierarchical levels and the probability to associate these levels into a united structure…

Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…

This paper presents our studies on the rearrangement of links from the structure of websites for the purpose of improving the valuation of a page or group of pages as established by a ranking function as Google's PageRank. We build our…

We consider a Gibbs distribution over all spanning trees of an undirected, edge weighted finite graph, where, up to normalization, the probability of each tree is given by the product of its edge weights. Defining the weighted degree of a…

Many real-world problems require making sequences of decisions where the outcomes of each decision are probabilistic and uncertain, and the availability of different actions is constrained by the outcomes of previous actions. There is a…

Recent work has shown that not only decision trees (DTs) may not be interpretable but also proposed a polynomial-time algorithm for computing one PI-explanation of a DT. This paper shows that for a wide range of classifiers, globally…

We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…