Related papers: ViralVectors: Compact and Scalable Alignment-free …
The typical process for classifying and submitting a newly sequenced virus to the NCBI database involves two steps. First, a BLAST search is performed to determine likely family candidates. That is followed by checking the candidate…
Structure-based Deep Fusion models were recently shown to outperform several physics- and machine learning-based protein-ligand binding affinity prediction methods. As part of a multi-institutional COVID-19 pandemic response, over 500…
Genomic surveillance of SARS-CoV-2 has been instrumental in tracking the spread and evolution of the virus during the pandemic. The availability of SARS-CoV-2 molecular sequences isolated from infected individuals, coupled with phylodynamic…
Background: Global viral threats underscore the need for effective genomic surveillance, but high costs and uneven resource distribution hamper its implementation. Targeting surveillance to international travelers in major travel hubs may…
Support vector machines (SVM) and other kernel techniques represent a family of powerful statistical classification methods with high accuracy and broad applicability. Because they use all or a significant portion of the training data,…
Gradient-based sampling algorithms have demonstrated their effectiveness in text generation, especially in the context of controlled text generation. However, there exists a lack of theoretically grounded and principled approaches for this…
Understanding the viral dynamics and immunizing antibodies of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for devising better therapeutic and prevention strategies for COVID-19. Here, we present a Bayesian…
The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) threatens global medical systems and economies, and rules our daily living life. Controlling the outbreak of SARS-CoV-2 has become one of the most important…
Vector graphics are widely used in digital art and highly favored by designers due to their scalability and layer-wise properties. However, the process of creating and editing vector graphics requires creativity and design expertise, making…
The SARS-CoV-2 spike (S) protein facilitates viral infection, and has been the focus of many structure determination efforts. Its flexible loop regions are known to be involved in protein binding and may adopt multiple conformations. This…
Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed…
We introduce semi-supervised data classification algorithms based on total variation (TV), Reproducing Kernel Hilbert Space (RKHS), support vector machine (SVM), Cheeger cut, labeled and unlabeled data points. We design binary and…
In this work, we propose MEDICO, a Multi-viEw Deep generative model for molecule generation, structural optimization, and the SARS-CoV-2 Inhibitor disCOvery. To the best of our knowledge, MEDICO is the first-of-this-kind graph generative…
We introduce Synthetic Visual Genome 2 (SVG2), a large-scale panoptic video scene graph dataset. SVG2 contains over 636K videos with 6.6M objects, 52.0M attributes, and 6.7M relations, providing an order-of-magnitude increase in scale and…
Motivation: PCR is more economical and quicker than Next Generation Sequencing for detecting target organisms, with primer design being a critical step. In epidemiology with rapidly mutating viruses, designing effective primers is…
The genetic evolution of SARS-CoV-2 has caused recurring epidemic waves, understanding its global dispersal patterns is critical for effective surveillance. We developed the Site-based mutation dynamics - Equal Power Sampling (S-EPS)…
During a virus's evolution,various regions of the genome are subjected to distinct levels of functional constraints.Combined with factors like codon bias and DNA repair efficiency,these constraints contribute to unique mutation patterns…
Cosmological shock waves are essential to understanding the formation of cosmological structures. To study them, scientists run computationally expensive high-resolution 3D hydrodynamic simulations. Interpreting the simulation results is…
More infectious virus variants can arise from rapid mutations in their proteins, creating new infection waves. These variants can evade one's immune system and infect vaccinated individuals, lowering vaccine efficacy. Hence, to improve…
Two-stage object detectors generate object proposals and classify them to detect objects in images. These proposals often do not contain the objects perfectly but overlap with them in many possible ways, exhibiting great variability in the…