Related papers: The Cognate Data Bottleneck in Language Phylogenet…

We present a computational analysis of cognate effects on the spontaneous linguistic productions of advanced non-native speakers. Introducing a large corpus of highly competent non-native English speakers, and using a set of carefully…

Large language models hallucinate factual claims and struggle to ground their outputs in retrievable evidence, particularly in non-English languages. Existing resources impose a trade-off: structured knowledge bases lack textual grounding,…

In 2006, Warnow, Evans, Ringe, and Nakhleh proposed a stochastic model (hereafter, the WERN 2006 model) of multi-state linguistic character evolution that allowed for homoplasy and borrowing. They proved that if there is no borrowing…

A major factor in the recent success of large language models is the use of enormous and ever-growing text datasets for unsupervised pre-training. However, naively training a model on all available data may not be optimal (or feasible), as…

Ensuring data quality in large tabular datasets is a critical challenge, typically addressed through data wrangling tasks. Traditional statistical methods, though efficient, cannot often understand the semantic context and deep learning…

Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer)…

Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in…

Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…

Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…

Search typically relies on keyword queries, but these are often semantically ambiguous. We propose to overcome this by offering users natural language questions, based on their keyword queries, to disambiguate their intent. This…

Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…

Exploiting cognates for transfer learning in under-resourced languages is an exciting opportunity for language understanding tasks, including unsupervised machine translation, named entity recognition and information retrieval. Previous…

A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…

Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…

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…

Phylogenetics, the inference of evolutionary trees from molecular sequence data such as DNA, is an enterprise that yields valuable evolutionary understanding of many biological systems. Bayesian phylogenetic algorithms, which approximate a…

Probabilistic programming frameworks are powerful tools for statistical modelling and inference. They are not immediately generalisable to phylogenetic problems due to the particular computational properties of the phylogenetic tree object.…

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…

Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…

In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular…