相关论文: Evaluation of tools for differential gene expressi…
The probability density function (PDF) plays a central role in statistical and machine learning modeling. Real-world data often deviates from Gaussian assumptions, exhibiting skewness and exponential decay. To evaluate how well different…
Retrieval-augmented generation (RAG) enhances large language models (LLMs) by incorporating external knowledge, but existing approaches indiscriminately trigger retrieval and rely on single-path evidence construction, often introducing…
Unit testing attempts to validate the correctness of basic units of the software system under test and has a crucial role in software development and testing. Very recent work proposes a retrieve-and-edit approach to generate unit test…
The use of Thin-foil Proton Recoil (TPR) spectrometers for application in neutron spectroscopy is of high relevance for future fusion devices such as ITER, where neutron spectroscopy will play a crucial role in fuel content monitoring.…
Qualifying gene and isoform expression is one of the primary tasks for RNA-Seq experiments. Given a sequence of counts representing numbers of reads mapped to different positions (exons and junctions) of isoforms, methods based on Poisson…
The main goal of Systems Biology research is to reconstruct biological networks for its topological analysis so that reconstructed networks can be used for the identification of various kinds of disease. The availability of high-throughput…
Whole transcriptome sequencing is increasingly being used as a functional genomics tool to study non- model organisms. However, when the reference transcriptome used to calculate differential expression is incomplete, significant error in…
Single-cell RNA-sequencing (scRNA-seq) stands as a powerful tool for deciphering cellular heterogeneity and exploring gene expression profiles at high resolution. However, its high cost renders it impractical for extensive sample cohorts…
The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4]…
Biologists use random transposon mutagenesis to construct knockout libraries for bacteria. Random mutagenesis offers cost and efficiency benefits over the standard site directed mutagenesis, but one can no longer ensure that all the…
Assessing the personality of software engineers may help to match individual traits with the characteristics of development activities such as code review and testing, as well as support managers in team composition. However,…
Next-generation sequencing technology enables the identification of thousands of gene regulatory sequences in many cell types and organisms. We consider the problem of testing if two such sequences differ in their number of binding site…
While Retrieval-Augmented Generation (RAG) is increasingly adopted to ground Large Language Models (LLMs) in software artifacts, the optimal configuration of its components remains an open question for software engineering (SE) tasks. The…
The proliferation of misinformation necessitates robust yet computationally efficient fact verification systems. While current state-of-the-art approaches leverage Large Language Models (LLMs) for generating explanatory rationales, these…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
In multi-stage recommender systems, reranking optimizes overall utility by capturing intra-list contextual dependencies, yet its central challenge lies in exploring optimal sequences within an exponentially large permutation space. Recent…
RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput…
As single-cell RNA sequencing datasets grow in adoption, scale, and complexity, data analysis remains a bottleneck for many research groups. Although frontier AI agents have improved dramatically at software engineering and general data…
Algorithms that ensure reproducible findings from large-scale, high-dimensional data are pivotal in numerous signal processing applications. In recent years, multivariate false discovery rate (FDR) controlling methods have emerged,…
Public data repositories have enabled researchers to compare results across multiple genomic studies in order to replicate findings. A common approach is to first rank genes according to an hypothesis of interest within each study. Then,…