Related papers: PWM2Vec: An Efficient Embedding Approach for Viral…
Human migration and mobility drives major societal phenomena including epidemics, economies, innovation, and the diffusion of ideas. Although human mobility and migration have been heavily constrained by geographic distance throughout the…
Motivation: With the aim to amplify and make sense of interactions of virus-human proteins in the case of SARS-CoV-2, we performed a structural analysis of the network of protein interactions obtained from the integration of three sources:…
The COVID-19 (coronavirus) is an ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virus was first identified in mid-December 2019 in the Hubei province of Wuhan, China and by now has spread…
The SARS-CoV-2 pandemic has created a global race for a cure. One approach focuses on designing a novel variant of the human angiotensin-converting enzyme 2 (ACE2) that binds more tightly to the SARS-CoV-2 spike protein and diverts it from…
Background: In organisms' genomes, promoters are short DNA sequences on the upstream of structural genes, with the function of controlling genes' transcription. Promoters can be roughly divided into two classes: constitutive promoters and…
The emergence of new variants of SARS-CoV-2 is a major concern given their potential impact on the transmissibility and pathogenicity of the virus as well as the efficacy of therapeutic interventions. Here, we predict the mutability of all…
This study investigates the current landscape and future directions of protein foundation model research. While recent advancements have transformed protein science and engineering, the field lacks a comprehensive benchmark for fair…
Population analyses of functional connectivity have provided a rich understanding of how brain function differs across time, individual, and cognitive task. An important but challenging task in such population analyses is the identification…
The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions of people with coronavirus disease 2019 (COVID-19). While this viral species was unknown prior to January…
Word embedding is a useful approach to capture co-occurrence structures in large text corpora. However, in addition to the text data itself, we often have additional covariates associated with individual corpus documents---e.g. the…
SARS-CoV2, which causes coronavirus disease (COVID-19) is continuing to spread globally and has become a pandemic. People have lost their lives due to the virus and the lack of counter measures in place. Given the increasing caseload and…
The capability of accurate prediction of protein functions and properties is essential in the biotechnology industry, e.g. drug development and artificial protein synthesis, etc. The main challenges of protein function prediction are the…
Respiratory complications due to coronavirus disease COVID-19 have claimed tens of thousands of lives in 2020. Many cases of COVID-19 escalate from Severe Acute Respiratory Syndrome (SARS-CoV-2) to viral pneumonia to acute respiratory…
Support Vector Machine (SVM) is a robust machine learning algorithm with broad applications in classification, regression, and outlier detection. SVM requires tuning the regularization parameter (RP) which controls the model capacity and…
Infectious disease spread is a multi-scale process composed of within-host (biological) and between-host (social) drivers and disentangling them from each other is a central challenge in epidemiology. Here, we introduce VIBES, a multi-scale…
Matrix factorization is at the heart of many machine learning algorithms, for example, dimensionality reduction (e.g. kernel PCA) or recommender systems relying on collaborative filtering. Understanding a singular value decomposition (SVD)…
Representation learning methods that transform encoded data (e.g., diagnosis and drug codes) into continuous vector spaces (i.e., vector embeddings) are critical for the application of deep learning in healthcare. Initial work in this area…
We study pattern matching problems on two major representations of uncertain sequences used in molecular biology: weighted sequences (also known as position weight matrices, PWM) and profiles (i.e., scoring matrices). In the simple version,…
The ultimate target of proteomics identification is to identify and quantify the protein in the organism. Mass spectrometry (MS) based on label-free protein quantitation has mainly focused on analysis of peptide spectral counts and ion peak…
Protein language models (pLMs) have shown strong potential for zero-shot prediction of missense variant effects, yet systematic benchmarking on viral proteins remains limited, a critical gap given the need for proactive tools that can…