Related papers: Genome-wide inference of ancestral recombination g…

This paper presents a comprehensive study of Retrieval-Augmented Generation (RAG), tracing its evolution from foundational concepts to the current state of the art. RAG combines retrieval mechanisms with generative language models to…

Genealogical networks, also known as family trees or population pedigrees, are commonly studied by genealogists wanting to know about their ancestry, but they also provide a valuable resource for disciplines such as digital demography,…

Ancestral inference for branching processes in random environments involves determining the ancestor distribution parameters using the population sizes of descendant generations. In this paper, we introduce a new methodology for ancestral…

Samples of multiple complete genome sequences contain vast amounts of information about the evolutionary history of populations, much of it in the associations among polymorphisms at different loci. Current methods that take advantage of…

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…

This study aims to optimize the existing retrieval-augmented generation model (RAG) by introducing a graph structure to improve the performance of the model in dealing with complex knowledge reasoning tasks. The traditional RAG model has…

Retrieval-Augmented Generation (RAG) has gained significant attention in recent years for its potential to enhance natural language understanding and generation by combining large-scale retrieval systems with generative models. RAG…

Retrieval-Augmented Generation (RAG) is increasingly employed in generative AI-driven scientific workflows to integrate rapidly evolving scientific knowledge bases, yet its reliability is frequently compromised by non-determinism in their…

Retrieval-Augmented Generation (RAG) is a prevalent approach to infuse a private knowledge base of documents with Large Language Models (LLM) to build Generative Q\&A (Question-Answering) systems. However, RAG accuracy becomes increasingly…

This study introduces a novel approach for inferring social network structures using Aggregate Relational Data (ARD), addressing the challenge of limited detailed network data availability. By integrating ARD with variational approximation…

A method based on mapping a symbolic sequence into a set of patterns (strings resulting from the sequence parsing) is proposed as a tool for the reconstruction of ancestral sequences. The set union of patterns comprises all the patterns…

In this work, the human parsing task, namely decomposing a human image into semantic fashion/body regions, is formulated as an Active Template Regression (ATR) problem, where the normalized mask of each fashion/body item is expressed as the…

The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…

Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…

We introduce Autoregressive Retrieval Augmentation (AR-RAG), a novel paradigm that enhances image generation by autoregressively incorporating knearest neighbor retrievals at the patch level. Unlike prior methods that perform a single,…

Ancestral sequence reconstruction (ASR) aims to infer extinct protein sequences at internal nodes of a phylogenetic tree. Classical ASR methods are typically based on continuous-time Markov substitution models, but they treat sites largely…

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…

Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…

Retrieval-Augmented Generation (RAG) has become a standard approach for enhancing large language models (LLMs) with external knowledge, mitigating hallucinations, and improving factuality. However, existing systems rely on generating…

Retrieval-augmented generation (RAG) has become a cornerstone for knowledge-intensive tasks. However, the efficacy of RAG is often bottlenecked by the ``one-size-fits-all'' retrieval paradigm, as different queries exhibit distinct…