Related papers: Constructing and Employing Tree Alignment Graphs f…

Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…

In this paper we show that an account for coordination can be constructed using the derivation structures in a lexicalized Tree Adjoining Grammar (LTAG). We present a notion of derivation in LTAGs that preserves the notion of fixed…

THIS IS A CORRECTED VERSION INCLUDING AN APPENDED CORRIGENDUM. Best match graphs arise naturally as the first processing intermediate in algorithms for orthology detection. Let $T$ be a phylogenetic (gene) tree $T$ and $\sigma$ an…

In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…

The development of lexicalized grammars, particularly Tree-Adjoining Grammar (TAG), has significantly advanced our understanding of syntax and semantics in natural language processing (NLP). While existing syntactic resources like the Penn…

The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…

Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…

'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…

A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…

This paper shows how DATR, a widely used formal language for lexical knowledge representation, can be used to define an LTAG lexicon as an inheritance hierarchy with internal lexical rules. A bottom-up featural encoding is used for LTAG…

Much of the power of probabilistic methods in modelling language comes from their ability to compare several derivations for the same string in the language. An important starting point for the study of such cross-derivational properties is…

Large tree structures are ubiquitous and real-world relational datasets often have information associated with nodes (e.g., labels or other attributes) and edges (e.g., weights or distances) that need to be communicated to the viewers. Yet,…

Semantic parsing is the task of producing a structured meaning representation for natural language utterances or questions. Recent research has pointed out that the commonly-used sequence-to-sequence (seq2seq) semantic parsers struggle to…

Designing well-connected graphs is a fundamental problem that frequently arises in various contexts across science and engineering. The weighted number of spanning trees, as a connectivity measure, emerges in numerous problems and plays a…

Merge trees are fundamental structures in topological data analysis. Interleaving distance is a widely accepted metric for comparing merge trees, with applications in visualization and scientific computing. While a greedy algorithm exists…

Identifying implicit discourse relations between text spans is a challenging task because it requires understanding the meaning of the text. To tackle this task, recent studies have tried several deep learning methods but few of them…

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…

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…

Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…

A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…