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Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…
Source code representations are key in applying machine learning techniques for processing and analyzing programs. A popular approach in representing source code is neural source code embeddings that represents programs with…
Word embeddings are often used in natural language processing as a means to quantify relationships between words. More generally, these same word embedding techniques can be used to quantify relationships between features. In this paper, we…
A molecular and cellular understanding of how SARS-CoV-2 variably infects and causes severe COVID-19 remains a bottleneck in developing interventions to end the pandemic. We sought to use deep learning to study the biology of SARS-CoV-2…
The widespread of Coronavirus has led to a worldwide pandemic with a high mortality rate. Currently, the knowledge accumulated from different studies about this virus is very limited. Leveraging a wide-range of biological knowledge, such as…
The new type of coronavirus disease (COVID-19), which started in Wuhan, China in December 2019, continues to spread rapidly affecting the whole world. It is essential to have a highly sensitive diagnostic screening tool to detect the…
Predicting the binding of viral peptides to the major histocompatibility complex with machine learning can potentially extend the computational immunology toolkit for vaccine development, and serve as a key component in the fight against a…
Enveloped viruses enter host cells either through endocytosis, or by direct fusion of the viral membrane envelope and the membrane of the host cell. However, some viruses, such as HIV-1, HSV-1, and Epstein-Barr can enter a cell through…
Current methods for viral discovery target evolutionarily conserved proteins that accurately identify virus families but remain unable to distinguish the zoonotic potential of newly discovered viruses. Here, we apply an attention-enhanced…
Because the infection by Severe Acute Respiratory Syndrome Coronavirus 2 (COVID-19) causes the pneumonia-like effect in the lungs, the examination of chest x-rays can help to diagnose the diseases. For automatic analysis of images, they are…
Coronavirus Disease 2019 (COVID-19) has spread aggressively across the world causing an existential health crisis. Thus, having a system that automatically detects COVID-19 in tomography (CT) images can assist in quantifying the severity of…
The issue of COVID-19, increasing with a massive mortality rate. This led to the WHO declaring it as a pandemic. In this situation, it is crucial to perform efficient and fast diagnosis. The reverse transcript polymerase chain reaction…
Self-supervised pre-training methods have brought remarkable breakthroughs in the understanding of text, image, and speech. Recent developments in genomics has also adopted these pre-training methods for genome understanding. However, they…
Coronavirus disease (Covid-19) has been the main agenda of the whole world since it came in sight in December 2019. It has already caused thousands of causalities and infected several millions worldwide. Any technological tool that can be…
The packaging of genetic material within a protein shell, called the capsid, marks a pivotal step in the life cycle of numerous single-stranded RNA viruses. Understanding how hundreds, or even thousands, of proteins assemble around the…
The rapid and global spread of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), underscored the urgent need for fast, reliable, and adaptable diagnostic tools capable of…
We propose an attention-based method that aggregates local image features to a subject-level representation for predicting disease severity. In contrast to classical deep learning that requires a fixed dimensional input, our method operates…
Due to SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) being a novel virus, there are currently no known effective antiviral drugs capable of slowing its progress. To accelerate the discovery of potential drug candidates,…
The massive amount of genomic data appearing for SARS-CoV-2 since the beginning of the COVID-19 pandemic has challenged traditional methods for studying its dynamics. As a result, new methods such as Pangolin, which can scale to the…
Respiratory symptoms can be a caused by different underlying conditions, and are often caused by viral infections, such as Influenza-like illnesses or other emerging viruses like the Coronavirus. These respiratory viruses, often, have…