Related papers: PhaBOX: A web server for identifying and character…
\textbf{Introduction:} Accurate prediction of Phage Virion Proteins (PVP) is essential for genomic studies due to their crucial role as structural elements in bacteriophages. Computational tools, particularly machine learning, have emerged…
Even todays most advanced machine learning models are easily fooled by almost imperceptible perturbations of their inputs. Foolbox is a new Python package to generate such adversarial perturbations and to quantify and compare the robustness…
Viral fusion proteins are attached to the membrane of enveloped viruses (a group that includes Coronaviruses, Dengue, HIV and Influenza) and catalyze fusion between the viral and host membranes, enabling the virus to insert its genetic…
Advances in next-generation metagenome sequencing have the potential to revolutionize the point-of-care diagnosis of novel pathogen infections, which could help prevent potential widespread transmission of diseases. Given the high volume of…
In real-world information-seeking scenarios, users have dynamic and diverse needs, requiring RAG systems to demonstrate adaptable resilience. To comprehensively evaluate the resilience of current RAG methods, we introduce HawkBench, a…
Meta-Black-Box Optimization (MetaBBO) streamlines the automation of optimization algorithm design through meta-learning. It typically employs a bi-level structure: the meta-level policy undergoes meta-training to reduce the manual effort…
Infections depend on interactions between pathogen and host proteins, but comprehensively mapping these interactions is challenging and labor intensive. Many biological networks have hierarchical, scale-free structure, so we developed a…
Microbiome functions are encoded within the genes of the community-wide metagenome. A natural question is whether properties of a microbial community can be predicted just from knowing the raw DNA sequences of its members. In this work, we…
Summary: Accurate phenotype prediction from genomic sequences is a highly coveted task in biological and medical research. While machine-learning holds the key to accurate prediction in a variety of fields, the complexity of biological data…
Online malware scanners are one of the best weapons in the arsenal of cybersecurity companies and researchers. A fundamental part of such systems is the sandbox that provides an instrumented and isolated environment (virtualized or…
The requirement of supporting both latency sensitive and computing intensive Internet of Things (IoT) applications is consistently boosting the necessity for integrating Edge, Fog and Cloud infrastructure. Although there are a number of…
Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and interpret the tsunami of metagenomic sequencing data generated by high-throughput sequencing. Compared to alternative (e. g., similarity-based)…
Metabolite structure identification has become the major bottleneck of the mass spectrometry based metabolomics research. Till now, number of mass spectra databases and search algorithms have been developed to address this issue. However,…
Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions-including those that have yet to be…
We introduce the ParClusterers Benchmark Suite (PCBS) -- a collection of highly scalable parallel graph clustering algorithms and benchmarking tools that streamline comparing different graph clustering algorithms and implementations. The…
Modern embedded Linux devices, such as routers, IP cameras, and IoT gateways, rely on complex software stacks where numerous daemons interact to provide services. Testing these devices is crucial from a security perspective since vendors…
Fuzzing has contributed to automatically identifying bugs and vulnerabilities in the software testing field. Although it can efficiently generate crashing inputs, these inputs are usually analyzed manually. Several root cause analysis (RCA)…
Modern online mass spectrometry generates multi-terabyte data streams critical for understanding Earth's environmental systems. However, extracting actionable chemical insights from these repositories is impeded by a computational…
This paper proposes a faceted information exploration model that supports coarse-grained and fine-grained focusing of geographic maps by offering a graphical representation of data attributes within interactive widgets. The proposed…
As edge and fog computing become central to modern distributed systems, there's growing interest in combining serverless architectures with privacy-preserving machine learning techniques like federated learning (FL). However, current…