Related papers: PhaBOX: A web server for identifying and character…
Federated learning leverages data across institutions to improve clinical discovery while complying with data-sharing restrictions and protecting patient privacy. This paper provides a gentle introduction to this approach in bioinformatics,…
The recent rise of cryo-EM and X-ray high-throughput techniques is providing a wealth of new structures trapped in different conformations. Understanding how proteins transition between different conformers, and how they relate to each…
We introduce functional adaptive shrinkage (FASH), an empirical Bayes method for joint analysis of observation units in which each unit estimates an effect function at several values of a continuous condition variable. The ideas in this…
Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on…
Designing flexible graph kernels that can run well on various platforms is a crucial research problem due to the frequent usage of graphs for modeling data and recent architectural advances and variety. In this work, we propose a novel…
Pathology foundation models (PFMs) have rapidly advanced and are becoming a common backbone for downstream clinical tasks, offering strong transferability across tissues and institutions. However, for dense prediction (e.g., segmentation),…
Motivation: In this paper we present the latest release of EBIC, a next-generation biclustering algorithm for mining genetic data. The major contribution of this paper is adding support for big data, making it possible to efficiently run…
Biogeographical regions (bioregions) reveal how different sets of species are spatially grouped and therefore are important units for conservation, historical biogeography, ecology and evolution. Several methods have been developed to…
Biologists study Diatoms, a fundamental algae, to assess the health of aquatic systems. Diatom specimens have traditionally been preserved on analog slides, where a single slide can contain thousands of these microscopic organisms.…
Phytoplankton, a crucial component of aquatic ecosystems, requires efficient monitoring to understand marine ecological processes and environmental conditions. Traditional phytoplankton monitoring methods, relying on non-in situ…
Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this…
Biological data sets are often high-dimensional, noisy, and governed by complex interactions among sparse signals. This poses major challenges for interpretability and reliable feature selection. Tasks such as identifying motif interactions…
Background: Cancers are highly heterogeneous with different subtypes. These subtypes often possess different genetic variants, present different pathological phenotypes, and most importantly, show various clinical outcomes such as varied…
Research increasingly relies on computational methods to analyze experimental data and predict molecular properties. Current approaches often require researchers to use a variety of tools for statistical analysis and machine learning,…
Modern processor advancements have introduced security risks, particularly in the form of microarchitectural timing attacks. High-profile attacks such as Meltdown and Spectre have revealed critical flaws, compromising the entire system's…
Feature based steganalysis, an emerging branch in information forensics, aims at identifying the presence of a covert communication by employing the statistical features of the cover and stego image as clues/evidences. Due to the large…
Future warehouses will be made of modular embedded entities with communication ability and energy aware operation attached to the traditional materials handling and warehousing objects. This advancement is mainly to fulfill the flexibility…
Rapid environmental change and advances in data-driven analysis highlight the need not only to use computational tools, but also to foster understanding of the natural world and inspire creativity. Photosynthesis, the process that fuels…
The human body consists of microbiomes associated with the development and prevention of several diseases. These microbial organisms form several complex interactions that are informative to the scientific community for explaining disease…
Asterias (\url{http://www.asterias.info}) is an integrated collection of freely-accessible web tools for the analysis of gene expression and aCGH data. Most of the tools use parallel computing (via MPI). Most of our applications allow the…