相关论文: Parsimony via concensus

How many permutations of the natural numbers are needed so that every conditionally convergent series of real numbers can be rearranged to no longer converge to the same sum? We define the \emph{rearrangement number}, a new cardinal…

In this paper we review some recent results that shed light on a fundamental question in molecular systematics: how much phylogenetic `signal' can we expect from characters that have evolved under some Markov process? There are many sides…

Ranking individuals based on their performance in different coalitions is a problem emerging in various domains (teams sports, scientific evaluation, argumentation, etc.). Often, for practical reasons, the number of comparable coalitions is…

This paper derives a unifying theorem establishing consistency results for a broad class of tree-based algorithms. It improves current results in two aspects. First of all, it can be applied to algorithms that vary from traditional Random…

Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…

Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…

When making simultaneous decisions, our preference for the outcomes on one subset can depend on the outcomes on a disjoint subset. In referendum elections, this gives rise to the separability problem, where a voter must predict the outcome…

Consensus methods provide a useful strategy for combining information from a collection of gene trees. An important application of consensus methods is to combine gene trees to estimate a species tree. To investigate the theoretical…

Phylogenetic trees are frequently used to model evolution. Such trees are typically reconstructed from data like DNA, RNA, or protein alignments using methods based on criteria like maximum parsimony (amongst others). Maximum parsimony has…

Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…

Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…

Repetitions within a given genealogical tree provides some information about the degree of consanguineity of a population. They can be analyzed with techniques usually employed in statistical physics when dealing with fixed point…

Rooted phylogenetic networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate…

Post-hoc global/local feature attribution methods are progressively being employed to understand the decisions of complex machine learning models. Yet, because of limited amounts of data, it is possible to obtain a diversity of models with…

Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence of reversals that do not break any…

As an alternative to parsimony analyses, stochastic models have been proposed (Lewis, 2001), (Nylander, et al., 2004) for morphological characters, so that maximum likelihood or Bayesian analyses may be used for phylogenetic inference. A…

The motivation for this paper is the study of the phase transition for recurrence/transience of a class of self-interacting random walks on trees, which includes the once-reinforced random walk. For this purpose, we define a quantity, that…

The purpose of this paper is to analyze certain statistics of a recently introduced non-uniform random tree model, biased recursive trees. This model is based on constructing a random tree by establishing a correspondence with non-uniform…

In comparison to phylogenetic trees, phylogenetic networks are more suitable to represent complex evolutionary histories of species whose past includes reticulation such as hybridisation or lateral gene transfer. However, the reconstruction…

We study the complexity and expressive power of conjunctive queries over unranked labeled trees represented using a variety of structure relations such as ``child'', ``descendant'', and ``following'' as well as unary relations for node…