Related papers: Counting, generating and sampling tree alignments

Tandem duplication is an evolutionary process whereby a segment of DNA is replicated and proximally inserted. The different configurations that can arise from this process give rise to some interesting combinatorial questions. Firstly, we…

We propose a novel architecture for Graph Neural Networks that is inspired by the idea behind Tree Kernels of measuring similarity between trees by taking into account their common substructures, named fragments. By imposing a series of…

The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…

A common approach to aggregate classification estimates in an ensemble of decision trees is to either use voting or to average the probabilities for each class. The latter takes uncertainty into account, but not the reliability of the…

Working with tree graphs is always easier than with loopy ones and spanning trees are the closest tree-like structures to a given graph. We find a correspondence between the solutions of random K-satisfiability problem and those of spanning…

In many situations, the choice of an adequate similarity measure or metric on the feature space dramatically determines the performance of machine learning methods. Building automatically such measures is the specific purpose of…

A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…

The computational complexity of the isomorphism problem for regular trees, regular linear orders, and regular words is analyzed. A tree is regular if it is isomorphic to the prefix order on a regular language. In case regular languages are…

Binary trees are fundamental objects in models of evolutionary biology and population genetics. Here, we discuss some of their combinatorial and structural properties as they depend on the tree class considered. Furthermore, the process by…

Tree kernels are fundamental tools that have been leveraged in many applications, particularly those based on machine learning for Natural Language Processing tasks. In this paper, we devise a parallel implementation of the sequential…

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…

The precise formulation of derivation for tree-adjoining grammars has important ramifications for a wide variety of uses of the formalism, from syntactic analysis to semantic interpretation and statistical language modeling. We argue that…

Alignments, i.e., position-wise comparisons of two or more strings or ordered lists are of utmost practical importance in computational biology and a host of other fields, including historical linguistics and emerging areas of research in…

We give a 2-approximation algorithm for the Maximum Agreement Forest problem on two rooted binary trees. This NP-hard problem has been studied extensively in the past two decades, since it can be used to compute the rooted Subtree…

Ensembles of decision trees perform well on many problems, but are not interpretable. In contrast to existing approaches in interpretability that focus on explaining relationships between features and predictions, we propose an alternative…

In this paper, we propose the TBCNN-pair model to recognize entailment and contradiction between two sentences. In our model, a tree-based convolutional neural network (TBCNN) captures sentence-level semantics; then heuristic matching…

It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…

For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…

Tree trace reconstruction aims to learn the binary node labels of a tree, given independent samples of the tree passed through an appropriately defined deletion channel. In recent work, Davies, R\'acz, and Rashtchian used combinatorial…

We describe an attentive encoder that combines tree-structured recursive neural networks and sequential recurrent neural networks for modelling sentence pairs. Since existing attentive models exert attention on the sequential structure, we…