Related papers: Moonshine.jl: a Julia package for genome-scale mod…

There is little debate about the importance of the ancestral recombination graph in population genetics. An important theoretical tool, the main obstacle to its widespread usage is the computational cost required to match the…

The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG), a complete record of coalescence and recombination events in the history of the sample.…

In the presence of recombination, the evolutionary relationships between a set of sampled genomes cannot be described by a single genealogical tree. Instead, the genomes are related by a complex, interwoven collection of genealogies…

Ancestral recombination graphs (ARGs) encode the complete genealogical history of a population of recombining lineages. ARGs, and their succinct representation, tree sequences, are increasingly central to modern population genetics methods,…

Summary: Ancestral recombination graphs (ARGs) are a complete representation of the genetic relationships between recombining lineages and are of central importance in population genetics. Recent breakthroughs in simulation and inference…

Microstructure.jl is a Julia package designed for probabilistic estimation of tissue microstructural parameters from diffusion or combined diffusion-relaxometry MRI data. It provides a flexible and extensible framework for defining…

Ancestral recombination graphs (ARGs) are an increasingly important component of population and statistical genetics. The tskit library has become key infrastructure for the field, providing an expressive and general representation of ARGs…

Retrieval-Augmented Generation (RAG) has proven effective in integrating external knowledge into large language models (LLMs) for solving question-answer (QA) tasks. The state-of-the-art RAG approaches often use the graph data as the…

The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene…

Large language models (LLMs) have demonstrated remarkable capabilities in a wide range of tasks, yet their application to specialized domains remains challenging due to the need for deep expertise. Retrieval-Augmented generation (RAG) has…

Retrieval-Augmented Generation (RAG) was introduced to enhance the capabilities of Large Language Models (LLMs) beyond their encoded prior knowledge. This is achieved by providing LLMs with an external source of knowledge, which helps…

The reconstruction of possible histories given a sample of genetic data in the presence of recombination and recurrent mutation is a challenging problem, but can provide key insights into the evolution of a population. We present KwARG,…

Retrieval-augmented generation (RAG) extends large language models (LLMs) with external data sources to enhance factual correctness and domain coverage. Modern RAG pipelines rely on large datastores, creating a significant system challenge:…

Recent advances in graph learning have paved the way for innovative retrieval-augmented generation (RAG) systems that leverage the inherent relational structures in graph data. However, many existing approaches suffer from rigid, fixed…

The BioModels database is one of the premier databases for computational models in systems biology. The database contains over 1000 curated models and an even larger number of non-curated models. All the models are stored in the…

Recently, haplo-identical transplantation with multiple HLA mismatches has become a viable option for system cell transplants. Haplotype sharing detection requires imputation of donor and recipient. We show that even in high-resolution…

Recently, Retrieval-Augmented Generation (RAG) has achieved remarkable success in addressing the challenges of Large Language Models (LLMs) without necessitating retraining. By referencing an external knowledge base, RAG refines LLM…

Retrieval-Augmented Generation (RAG) is an effective approach to enhance the factual accuracy of large language models (LLMs) by retrieving information from external databases, which are typically composed of diverse sources, to supplement…

In this paper, a nonlinear symbolic regression technique using an evolutionary algorithm known as multi-gene genetic programming (MGGP) is applied for a data-driven modelling between the dependent and the independent variables. The…

Geometric computing with chain complexes allows for the computation of the whole chain of linear spaces and (co)boundary operators generated by a space decomposition into a cell complex. The space decomposition is stored and handled with…