Related papers: VARIANT: Web Server for Decoding and Analyzing Vir…
Sequence diversity is one of the major challenges in the design of diagnostic, prophylactic and therapeutic interventions against viruses. DiMA is a novel tool that is big data-ready and designed to facilitate the dissection of sequence…
Neural networks are widely adopted to solve complex and challenging tasks. Especially in high-stakes decision-making, understanding their reasoning process is crucial, yet proves challenging for modern deep networks. Feature visualization…
Viral infections are causing significant morbidity and mortality worldwide. Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying mechanism of viral infection…
Genomic prediction of drug resistance in Mycobacterium tuberculosis is often hindered by complex epistatic interactions and variable sequencing quality. We present the Interpretable Variant-Aware Multi-Path Network (VAMP-Net), a novel…
Genomic surveillance of infectious diseases allows monitoring circulating and emerging variants and quantifying their epidemic potential. However, due to the high costs associated with genomic sequencing, only a limited number of samples…
Integrative analysis of disparate data blocks measured on a common set of experimental subjects is a major challenge in modern data analysis. This data structure naturally motivates the simultaneous exploration of the joint and individual…
In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. Most methods for viral diversity estimation…
Generative models able to synthesize layouts of different kinds (e.g. documents, user interfaces or furniture arrangements) are a useful tool to aid design processes and as a first step in the generation of synthetic data, among other…
After the completion of human genome sequence was anounced, it is evident that interpretation of DNA sequences is an immediate task to work on. For understanding their signals, improvement of present sequence analysis tools and developing…
Branch-specific substitution models are popular for detecting evolutionary change-points, such as shifts in selective pressure. However, applying such models typically requires prior knowledge of change-point locations on the phylogeny or…
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…
Our work introduces SAVeD (Semantically Aware Version Detection), a contrastive learning-based framework for identifying versions of structured datasets without relying on metadata, labels, or integration-based assumptions. SAVeD addresses…
The variant graph is a new, hybrid algorithm that combines the strengths of established global grain graph and local neighbor level voting approaches, while alleviating their shortcomings, to reconstruct parent grains from orientation maps…
Autonomous driving systems remain critically vulnerable to the long-tail of rare, out-of-distribution semantic anomalies. While VLMs have emerged as promising tools for perception, their application in anomaly detection remains largely…
Web browsing is the main Internet Service and every customer wants the minimum web page loading times. To satisfy this perpetual need, web browsers offer new processing engines and increased functionalities. Web developers make use of new…
Deep neural networks tend to make overconfident predictions and often require additional detectors for misclassifications, particularly for safety-critical applications. Existing detection methods usually only focus on adversarial attacks…
Despite the rapid advancements of electrocardiogram (ECG) signal diagnosis and analysis methods through deep learning, two major hurdles still limit their clinical adoption: the lack of versatility in processing ECG signals with diverse…
Standard models assign disease progression to discrete categories or stages based on well-characterized clinical markers. However, such a system is potentially at odds with our understanding of the underlying biology, which in highly…
Due to the high mutation rate of the virus, the COVID-19 pandemic evolved rapidly. Certain variants of the virus, such as Delta and Omicron, emerged with altered viral properties leading to severe transmission and death rates. These…
When investigating a malicious file, searching for related files is a common task that malware analysts must perform. Given that production malware corpora may contain over a billion files and consume petabytes of storage, many feature…