Related papers: Commet: comparing and combining multiple metagenom…
Our view of the microbial world and its impact on human health is changing radically with the ability to sequence uncultured or unculturable microbes sampled directly from their habitats, ability made possible by fast and cheap next…
Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of…
In recent years, many methods have been developed for detecting causal relationships in observational data. Some of them have the potential to tackle large data sets. However, these methods fail to discover a combined cause, i.e. a…
Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these…
The Big Data landscape poses challenges in managing diverse data formats, requiring efficient storage and processing for high-quality analysis. Effective metadata management is crucial for organizing, accessing, and reusing data within…
Dataset Condensation is a newly emerging technique aiming at learning a tiny dataset that captures the rich information encoded in the original dataset. As the size of datasets contemporary machine learning models rely on becomes…
The Web today has millions of datasets, and the number of datasets continues to grow at a rapid pace. These datasets are not standalone entities; rather, they are intricately connected through complex relationships. Semantic relationships…
Metagenomics is the study of environments through genetic sampling of their microbiota. Metagenomic studies produce large datasets that are estimated to grow at a faster rate than the available computational capacity. A key step in the…
MetaScope is a fast and accurate tool for analyzing (host-associated) metagenome datasets. Sequence alignment of reads against the host genome (if requested) and against microbial Genbank is performed using a new DNA aligner called SASS.…
Modern Deep Learning (DL) models have grown to sizes requiring massive clusters of specialized, high-end nodes to train. Designing such clusters to maximize both performance and utilization--to amortize their steep cost--is a challenging…
Background: In the metagenome assembly of a microbiome community, we may think abundant species would be easier to assemble due to their deeper coverage. However, this conjucture is rarely tested. We often do not know how many abundant…
Genome-scale metabolic models (GEMs) are essential tools for systems biology and rational chassis design, but conventional top-down reconstruction depends heavily on sequence homology and often leaves unknown enzymes and metabolic dark…
Motivation: The rapid growth of diverse biological data allows us to consider interactions between a variety of objects, such as genes, chemicals, molecular signatures, diseases, pathways and environmental exposures. Often, any pair of…
Semantic segmentation of remote sensing images plays a vital role in a wide range of Earth Observation applications, such as land use land cover mapping, environment monitoring, and sustainable development. Driven by rapid developments in…
Beyond the Transformer, it is important to explore how to exploit the capacity of the MetaFormer, an architecture that is fundamental to the performance improvements of the Transformer. Previous studies have exploited it only for the…
The automatic generation of high-quality mathematical problems is practically valuable in many educational scenarios. Large multimodal model provides a novel technical approach for the mathematical problem generation because of its wide…
Meta-analysis is routinely performed in many scientific disciplines. This analysis is attractive since discoveries are possible even when all the individual studies are underpowered. However, the meta-analytic discoveries may be entirely…
Cancer is a heterogeneous disease with different combinations of genetic and epigenetic alterations driving the development of cancer in different individuals. While these alterations are believed to converge on genes in key cellular…
In biological experiments researchers often have information in the form of a graph that supplements observed numerical data. Incorporating the knowledge contained in these graphs into an analysis of the numerical data is an important and…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…