Related papers: CoverM: Read alignment statistics for metagenomics

Empirical research on code review processes is increasingly central to understanding software quality and collaboration. However, collecting and analyzing review data remains a time-consuming and technically intensive task. Most researchers…

The modern code review process is an integral part of the current software development practice. Considerable effort is given here to inspect code changes, find defects, suggest an improvement, and address the suggestions of the reviewers.…

Incidental detection and quantification of coronary calcium in CT scans could lead to the early introduction of lifesaving clinical interventions. However, over-reporting could negatively affect patient wellbeing and unnecessarily burden…

Analyses of targeted genomic sequencing data from next-generation-sequencing (NGS) technologies typically involves mapping reads to a reference sequence or clustering reads. For a number of species a reference genome is not available so the…

Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…

Metaproteomics are becoming widely used in microbiome research for gaining insights into the functional state of the microbial community. Current metaproteomics studies are generally based on high-throughput tandem mass spectrometry (MS/MS)…

The first step in any genome assembly algorithm entails the conversion from the domain of strings and overlaps to the language of graphs and paths, typically using one of the two conventional methods: de Bruijn graphs or overlap graphs.…

This is the first detailed study on the coverage of Microsoft Academic (MA). Based on the complete and verified publication list of a university, the coverage of MA was assessed and compared with two benchmark databases, Scopus and Web of…

In modern high-throughput applications, it is important to identify pairwise associations between variables, and desirable to use methods that are powerful and sensitive to a variety of association relationships. We describe RankCover, a…

Automated skin lesion classification using deep learning has shown remarkable accuracy, yet clinical adoption remains limited due to the "black box" nature of these models. We present MelanomaNet, an explainable deep learning system for…

Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational…

The malfunction of safety-critical systems may cause damage to people and the environment. Software within those systems is rigorously designed and verified according to domain specific guidance, such as ISO26262 for automotive safety. This…

(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…

Dense pixel-specific representation learning at scale has been bottlenecked due to the unavailability of large-scale multi-view datasets. Current methods for building effective pretraining datasets heavily rely on annotated 3D meshes, point…

Automated radiology report drafting (ARRD) using vision-language models (VLMs) has advanced rapidly, yet most systems lack explicit uncertainty estimates, limiting trust and safe clinical deployment. We propose CONRep, a model-agnostic…

Conformal prediction is a non-parametric technique for constructing prediction intervals or sets from arbitrary predictive models under the assumption that the data is exchangeable. It is popular as it comes with theoretical guarantees on…

Accurate breast lesion risk estimation can significantly reduce unnecessary biopsies and help doctors decide optimal treatment plans. Most existing computer-aided systems rely solely on mammogram features to classify breast lesions. While…

Conformal prediction is widely used to equip black-box machine learning models with uncertainty quantification, offering formal coverage guarantees under exchangeable data. However, these guarantees fail when faced with subpopulation…

Reproducibility of research is essential for science. However, in the way modern computational biology research is done, it is easy to lose track of small, but extremely critical, details. Key details, such as the specific version of a…

Just as in eukaryotes, high-throughput chromosome conformation capture (Hi-C) data have revealed nested organizations of bacterial chromosomes into overlapping interaction domains. In this chapter, we present a multiscale analysis framework…