Related papers: RACS: Rapid Analysis of ChIP-Seq data for contig b…

Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call…

Genomic datasets generated with massively parallel sequencing methods have the potential to propel systematics in new and exciting directions, but selecting appropriate markers and methods is not straightforward. We applied two approaches…

Cyber threat intelligence (CTI) analysts must answer complex questions over large collections of narrative security reports. Retrieval-augmented generation (RAG) systems help language models access external knowledge, but traditional vector…

Genome sequence analysis, which examines the DNA sequences of organisms, drives advances in many critical medical and biotechnological fields. Given its importance and the exponentially growing volumes of genomic sequence data, there are…

The accelerating growth of scientific publications has intensified the need for scalable, trustworthy systems to synthesize knowledge across diverse literature. While recent retrieval-augmented generation (RAG) methods have improved access…

In digital pathology tasks, transformers have achieved state-of-the-art results, surpassing convolutional neural networks (CNNs). However, transformers are usually complex and resource intensive. In this study, we developed a novel and…

Integrated sensing and communication (ISAC) is a key feature of future cellular systems, enabling applications such as intruder detection, monitoring, and tracking using the same infrastructure. However, its potential for structural health…

Retrieval-augmented generation (RAG) has emerged as a powerful framework for enhancing large language models (LLMs) with external knowledge, particularly in scientific domains that demand specialized and dynamic information. Despite its…

Retrieval-Augmented Generation (RAG) has become a foundational component of modern AI systems, yet it introduces significant privacy risks by exposing user queries to service providers. To address this, we introduce PIR-RAG, a practical…

Segmentation and genome annotation (SAGA) algorithms are widely used to understand genome activity and gene regulation. These algorithms take as input epigenomic datasets, such as chromatin immunoprecipitation-sequencing (ChIP-seq)…

Due to its specificity, fluorescence microscopy (FM) has become a quintessential imaging tool in cell biology. However, photobleaching, phototoxicity, and related artifacts continue to limit FM's utility. Recently, it has been shown that…

One essential component in the construction of patent landscapes in biomedical research and development (R&D) is identifying the most seminal patents. Hitherto, the identification of seminal patents required subject matter experts within…

Sepsis is an organ dysfunction caused by a deregulated immune response to an infection. Early sepsis prediction and identification allow for timely intervention, leading to improved clinical outcomes. Clinical calculators (e.g., the…

The IRIS-HEP Analysis Grand Challenge (AGC) is designed to be a realistic environment for investigating how analysis methods scale to the demands of the HL-LHC. The analysis task is based on publicly available Open Data and allows for…

In clinical applications, the utility of segmentation models is often based on the accuracy of derived downstream metrics such as organ size, rather than by the pixel-level accuracy of the segmentation masks themselves. Thus, uncertainty…

Large-scale, high-quality data is essential for advancing the reasoning capabilities of large language models (LLMs). As publicly available Internet data becomes increasingly scarce, synthetic data has emerged as a crucial research…

Recently, the intervention calculus when the DAG is absent (IDA) method was developed to estimate lower bounds of causal effects from observational high-dimensional data. Originally it was introduced to assess the effect of baseline…

Radiology reports are detailed text descriptions of the content of medical scans. Each report describes the presence/absence and location of relevant clinical findings, commonly including comparison with prior exams of the same patient to…

We present a new algorithm for the identification of bound regions from ChIP-seq experiments. Our method for identifying statistically significant peaks from read coverage is inspired by the notion of persistence in topological data…

Retrieval-Augmented Generation (RAG) encounters efficiency challenges when scaling to massive knowledge bases while preserving contextual relevance. We propose Hash-RAG, a framework that integrates deep hashing techniques with systematic…