Related papers: Syntactic Phylogenetic Trees
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…
Syntactic language models (SLMs) enhance Transformers by incorporating syntactic biases through the modeling of linearized syntactic parse trees alongside surface sentences. This paper focuses on compositional SLMs that are based on…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…
The concept of a temporal phylogenetic network is a mathematical model of evolution of a family of natural languages. It takes into account the fact that languages can trade their characteristics with each other when linguistic communities…
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…
In real practice, questions are typically complex and knowledge-intensive, requiring Large Language Models (LLMs) to recognize the multifaceted nature of the question and reason across multiple information sources. Iterative and adaptive…
Phylogenetic methods have broad potential in linguistics beyond tree inference. Here, we show how a phylogenetic approach opens the possibility of gaining historical insights from entirely new kinds of linguistic data--in this instance,…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
Syntactic Language Models (SLMs) can be trained efficiently to reach relatively high performance; however, they have trouble with inference efficiency due to the explicit generation of syntactic structures. In this paper, we propose a new…
The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe…
Accurate syntactic representations are essential for robust generalization in natural language. Recent work has found that pre-training can teach language models to rely on hierarchical syntactic features - as opposed to incorrect linear…
The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…
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…
It is commonly believed that knowledge of syntactic structure should improve language modeling. However, effectively and computationally efficiently incorporating syntactic structure into neural language models has been a challenging topic.…
Computational phylogenetics has become an established tool in historical linguistics, with many language families now analyzed using likelihood-based inference. However, standard approaches rely on expert-annotated cognate sets, which are…