Related papers: Genome-wide inference of ancestral recombination g…
Purpose: To develop a retrieval-augmented generation (RAG) system powered by LLaMA-4 109B for automated, protocol-aware, and interpretable evaluation of radiotherapy treatment plans. Methods and Materials: We curated a multi-protocol…
Retrieval-Augmented Generation (RAG) improves factual grounding in large language models but suffers from substantial latency due to synchronous retrieval. While recent work explores asynchronous retrieval, existing approaches rely on…
In the analysis of complex traits, genetic effects are frequently modelled as either fixed or random effects. Such assumptions serve as a foundation of defining heritability and relatedness using genome-wide single nucleotide polymorphism…
Accurate and efficient access to laboratory protocols is essential in Anatomical Pathology (AP), where up to 70% of medical decisions depend on laboratory diagnoses. However, static documentation such as printed manuals or PDFs is often…
We introduce \emph{Adaptive RAG Memory} (ARM), a retrieval-augmented generation (RAG) framework that replaces a static vector index with a \emph{dynamic} memory substrate governed by selective remembrance and decay. Frequently retrieved…
Community detection in complex networks is a topic of considerable recent interest within the scientific community. For dealing with the problem that genetic algorithm are hardly applied to community detection, we propose a genetic…
Advancements in model algorithms, the growth of foundational models, and access to high-quality datasets have propelled the evolution of Artificial Intelligence Generated Content (AIGC). Despite its notable successes, AIGC still faces…
In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…
Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from…
Bayesian phylogenetics typically estimates a posterior distribution, or aspects thereof, using Markov chain Monte Carlo methods. These methods integrate over tree space by applying local rearrangements to move a tree through its space as a…
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…
Rapid growth of high-dimensional datasets in fields such as single-cell RNA sequencing and spatial genomics has led to unprecedented opportunities for scientific discovery, but it also presents unique computational and statistical…
The advent of accessible ancient DNA technology now allows the direct ascertainment of allele frequencies in ancestral populations, thereby enabling the use of allele frequency time series to detect and estimate natural selection. Such…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
We develop a general methodological framework for probabilistic inference in discrete- and continuous-time stochastic processes evolving on directed acyclic graphs (DAGs). The process is observed only at the leaf nodes, and the challenge is…
Research question answering requires accurate retrieval and contextual understanding of scientific literature. However, current Retrieval-Augmented Generation (RAG) methods often struggle to balance complex document relationships with…
Graph retrieval-augmented generation (GRAG) places high demands on graph-specific retrievers. However, existing retrievers often rely on language models pretrained on plain text, limiting their effectiveness due to domain misalignment and…
Nanopore sequencing enables real-time long-read DNA sequencing with reads exceeding 10 kilobases, but inherent error rates of 12-15 percent present significant computational challenges for read alignment. The critical seed chaining step…
Retrieval-augmented generation (RAG) empowers large language models to access external and private corpus, enabling factually consistent responses in specific domains. By exploiting the inherent structure of the corpus, graph-based RAG…
The deterministic selection-recombination equation describes the evolution of the genetic type composition of a population under selection and recombination in a law of large numbers regime. So far, an explicit solution has seemed out of…