Related papers: Beyond cognacy
We present a novel Auxiliary Truth enhanced Genetic Algorithm (GA) that uses logical or mathematical constraints as a means of data augmentation as well as to compute loss (in conjunction with the traditional MSE), with the aim of…
Semantic similarity measures are a key component in natural language processing tasks such as document analysis, requirement matching, and user input interpretation. However, the performance of individual measures varies considerably across…
Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in…
Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is…
It is reasonable to hypothesize that the divergence patterns formulated by historical linguists and typologists reflect constraints on human languages, and are thus consistent with Second Language Acquisition (SLA) in a certain way. In this…
Causal discovery in multi-omic datasets is crucial for understanding the bigger picture of gene regulatory mechanisms, but remains challenging due to high dimensionality, differentiation of direct from indirect relationships, and hidden…
Inference of the marginal likelihood of sample allele configurations using backward algorithms yields identical results with the Kingman coalescent, the Moran model, and the diffusion model (up to a scaling of time). For inference of…
Phylogenetic tree inference using deep DNA sequencing is reshaping our understanding of rapidly evolving systems, such as the within-host battle between viruses and the immune system. Densely sampled phylogenetic trees can contain special…
This paper establishes logical and expression-based characterizations for the class of languages recognized by nondeterministic register automata with guessing (NRA) over infinite alphabets. We introduce Scoped MSO, a logic featuring a…
Phylogenetic stochastic mapping is a method for reconstructing the history of trait changes on a phylogenetic tree relating species/organisms carrying the trait. State-of-the-art methods assume that the trait evolves according to a…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…
English proficiency assessments have become a necessary metric for filtering and selecting prospective candidates for both academia and industry. With the rise in demand for such assessments, it has become increasingly necessary to have the…
The construction of high-quality parallel corpora for translation research has increasingly evolved from simple sentence alignment to complex, multi-layered annotation tasks. This methodological shift presents significant challenges for…
Semantics, morphology and syntax are strongly interdependent. However, the majority of computational methods for semantic change detection use distributional word representations which encode mostly semantics. We investigate an alternative…
We propose a novel framework for generating causal graphs from narrative texts, bridging high-level causality and detailed event-specific relationships. Our method first extracts concise, agent-centered vertices using large language model…
Large Language Models (LLMs) excel at generating synthetic data, but ensuring its quality and diversity remains challenging. We propose Genetic Prompt, a novel framework that combines genetic algorithms with LLMs to augment synthetic data…
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…
Designing plausible network models typically requires scholars to form a priori intuitions on the key drivers of network formation. Oftentimes, these intuitions are supported by the statistical estimation of a selection of network evolution…
Large Language Models (LLMs) have achieved significant progress across various fields and have exhibited strong potential in evolutionary computation, such as generating new solutions and automating algorithm design. Surrogate-assisted…