Related papers: CoverM: Read alignment statistics for metagenomics
Computed tomography (CT) is routinely used in clinical practice to evaluate a wide variety of medical conditions. While CT scans provide diagnoses, they also offer the ability to extract quantitative body composition metrics to analyze…
Unsupervised region representation learning aims to extract dense and effective features from unlabeled urban data. While some efforts have been made for solving this problem based on multiple views, existing methods are still insufficient…
Microbial communities play important roles in the function and maintenance of various biosystems, ranging from human body to the environment. Current methods for analysis of microbial communities are typically based on taxonomic…
Method: We develop CNN-based methods for automatic ICD coding based on clinical text from intensive care unit (ICU) stays. We come up with the Shallow and Wide Attention convolutional Mechanism (SWAM), which allows our model to learn local…
Simulated microbial communities are used in benchmarking microbial abundance estimators and other bioinformatic utilities. To match current data scales, large simulated samples are needed, and many. The speed of current implementations…
Melanoma is a fatal skin cancer that is curable and has dramatically increasing survival rate when diagnosed at early stages. Learning-based methods hold significant promise for the detection of melanoma from dermoscopic images. However,…
Motivation: Seed filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. Read mappers 1) quickly…
We developed a low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region. Amplified PCR products are sequenced using an Illumina paired-end protocol…
Conformal inference has played a pivotal role in providing uncertainty quantification for black-box ML prediction algorithms with finite sample guarantees. Traditionally, conformal prediction inference requires a data-independent…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
Over the recent years, the field of whole metagenome shotgun sequencing has witnessed significant growth due to the high-throughput sequencing technologies that allow sequencing genomic samples cheaper, faster, and with better coverage than…
Metagenomics has lowered the barrier to microbial discovery--enabling the identification of novel microbes without isolation--but cultures remain imperative for the deep study of microbes. Cultivation and isolation of non-model microbes…
In a "publish-or-perish culture", the ranking of scientific journals plays a central role in assessing performance in the current research environment. With a wide range of existing methods and approaches to deriving journal rankings,…
Recent work identified the fundamental limits on the information requirements in terms of read length and coverage depth required for successful de novo genome reconstruction from shotgun sequencing data, based on the idealistic assumption…
The yaglm package aims to make the broader ecosystem of modern generalized linear models accessible to data analysts and researchers. This ecosystem encompasses a range of loss functions (e.g. linear, logistic, quantile regression),…
Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from…
Conformal prediction provides prediction sets with finite-sample marginal coverage, but many applications require coverage guarantees that adapt to individual test points, a subpopulation, or a structural component of the data. Existing…
Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. It also can reliably identify barcodes and assign the reads to the original samples.…
Automatic melanoma segmentation in dermoscopic images is essential in computer-aided diagnosis of skin cancer. Existing methods may suffer from the hole and shrink problems with limited segmentation performance. To tackle these issues, we…
Code documentation can, if written precisely, help developers better understand the code they accompany. However, unlike code, code documentation cannot be automatically verified via execution, potentially leading to inconsistencies between…