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

Treatment approaches for colorectal cancer (CRC) are highly dependent on the molecular subtype, as immunotherapy has shown efficacy in cases with microsatellite instability (MSI) but is ineffective for the microsatellite stable (MSS)…

The composed image retrieval (CIR) task is to retrieve target images given a reference image and a modification text. Recent methods for CIR leverage large pretrained vision-language models (VLMs) and achieve good performance on…

Automating radiology report generation can significantly alleviate radiologists' workloads. Previous research has primarily focused on realizing highly concise observations while neglecting the precise attributes that determine the severity…

Assessing the quality of automatic image segmentation is crucial in clinical practice, but often very challenging due to the limited availability of ground truth annotations. Reverse Classification Accuracy (RCA) is an approach that…

Retrieval-Augmented Generation (RAG) helps large language models (LLMs) answer knowledge-intensive and time-sensitive questions by conditioning generation on external evidence. However, most RAG systems still retrieve unstructured chunks…

Retrieval-Augmented Generation (RAG) systems lose retrieval accuracy when similar documents coexist in the vector database, causing unnecessary information, hallucinations, and factual errors. To alleviate this issue, we propose CHOP, a…

Retrieval-augmented generation (RAG) has emerged as one of the most prominent applications of vector databases. By integrating documents retrieved from a database into the prompt of a large language model (LLM), RAG enables more reliable…

Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…

Locating lesions is important in the computer-aided diagnosis of X-ray images. However, box-level annotation is time-consuming and laborious. How to locate lesions accurately with few, or even without careful annotations is an urgent…

Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…

Conventional multi-stage cell tracking approaches rely heavily on detection or segmentation in each frame as a prerequisite, requiring substantial resources for high-quality segmentation masks and increasing the overall prediction time. To…

The cost of DNA sequencing has dropped exponentially over the past decade, making genomic data accessible to a growing number of scientists. In bioinformatics, localization of short DNA sequences (reads) within large genomic sequences is…

We devise a novel inference algorithm to effectively solve the cancer progression model reconstruction problem. Our empirical analysis of the accuracy and convergence rate of our algorithm, CAncer PRogression Inference (CAPRI), shows that…

A large number of inorganic and organic compounds are able to bind DNA and form complexes, among which drug-related molecules are important. Chromatin accessibility changes not only directly affects drug-DNA interactions, but also promote…

The marine environment is one of the most important sources for microbial biodiversity on the planet. These microbes are drivers for many biogeochemical processes, and their enormous genetic potential is still not fully explored or…

Background. Dramatic increases in RNA structural data have made it possible to recognize its conformational preferences much better than a decade ago. This has created an opportunity to use discrete restraint-based conformational sampling…

Reconfigurable intelligent surface (RIS) technology is a promising enabler for next-generation (NextG) wireless systems, capable of dynamically shaping the propagation environment. Integrating RIS within the open radio access network…

Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene…

This study aims to improve knowledge-based question-answering (QA) systems by overcoming the limitations of existing Retrieval-Augmented Generation (RAG) models and implementing an advanced RAG system based on Graph technology to develop…

Biosciences have been revolutionized by next generation sequencing (NGS) technologies in last years, leading to new perspectives in medical, industrial and environmental applications. And although our motivation comes from biosciences, the…