Related papers: VARIANT: Web Server for Decoding and Analyzing Vir…
Genome variants which re-occur independently across evolutionary lineages are key molecular signatures of adaptation. Inferring the dynamics of such genetic changes from pandemic-scale genomic datasets is now possible, which opens up…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
It is estimated that approximately 15% of cancers worldwide can be linked to viral infections. The viruses that can cause or increase the risk of cancer include human papillomavirus, hepatitis B and C viruses, Epstein-Barr virus, and human…
In this paper we present VART, a tool for automatically revealing regression faults missed by regression test suites. Interestingly, VART is not limited to faults causing crashing or exceptions, but can reveal faults that cause the…
Multimodal learning combining pathology images and genomic sequences enhances cancer survival analysis but faces clinical implementation barriers due to limited access to genomic sequencing in under-resourced regions. To enable survival…
The Third-Generation in DNA sequencing has emerged in the last few years using new technologies that allow the production of long-read sequences. Applications of the Third-Generation sequencing enable real-time and on-site data production,…
In order to prevent detection and evade signature-based scanning methods, which are normally exploited by antivirus software, metamorphic viruses use several various obfuscation approaches. They transform their code in new instances as look…
RNA viruses form genetically diverse populations structured as mutant spectra, or quasispecies, whose internal organization influences their evolutionary and adaptive dynamics. While genetic diversity has been extensively characterized, the…
Variant calling is a fundamental task in genomic research, essential for detecting genetic variations such as single nucleotide polymorphisms (SNPs) and insertions or deletions (indels). This paper presents an enhancement to DeepChem, a…
This study presents a novel approach at the intersection of genomic analysis and artificial intelligence (AI) to predict viral mutations and assess the risks of future pandemics. Through comprehensive genomic analysis, genetic markers…
Variational inference provides approximations to the computationally intractable posterior distribution in Bayesian networks. A prominent medical application of noisy-or Bayesian network is to infer potential diseases given observed…
Pattern detection and string matching are fundamental problems in computer science and the accelerated expansion of bioinformatics and computational biology have made them a core topic for both disciplines. The SARS-CoV-2 pandemic has made…
DNA read mapping is a ubiquitous task in bioinformatics, and many tools have been developed to solve the read mapping problem. However, there are two trends that are changing the landscape of readmapping: First, new sequencing technologies…
It is well known that anti-malware scanners depend on malware signatures to identify malware. However, even minor modifications to malware code structure results in a change in the malware signature thus enabling the variant to evade…
Vision Transformers (ViTs) have emerged as the state-of-the-art architecture in representation learning, leveraging self-attention mechanisms to excel in various tasks. ViTs split images into fixed-size patches, constraining them to a…
SARS-CoV-2 is an upper respiratory system RNA virus that has caused over 3 million deaths and infecting over 150 million worldwide as of May 2021. With thousands of strains sequenced to date, SARS-CoV-2 mutations pose significant challenges…
Online scanners analyze user-submitted files with a large number of security tools and provide access to the analysis results. As the most popular online scanner, VirusTotal (VT) is often used for determining if samples are malicious,…
We propose a Vision-Language Transformer (VLT) framework for referring segmentation to facilitate deep interactions among multi-modal information and enhance the holistic understanding to vision-language features. There are different ways…
Variation graphs, which represent genetic variation within a population, are replacing sequences as reference genomes. Path indexes are one of the most important tools for working with variation graphs. They generalize text indexes to…
The accurate identification of antiviral peptides (AVPs) is crucial for novel drug development. However, existing methods still have limitations in capturing complex sequence dependencies and distinguishing confusing samples with high…