Related papers: VirusT5: Harnessing Large Language Models to Predi…

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…

The large-scale evolution of the SARS-CoV-2 virus has been marked by rapid turnover of genetic clades. New variants show intrinsic changes, notably increased transmissibility, as well as antigenic changes that reduce the cross-immunity…

In recent years, with the rapid development of deep learning technology, large language models (LLMs) such as BERT and GPT have achieved breakthrough results in natural language processing tasks. Machine translation (MT), as one of the core…

Applying a ML approach to the temporal variability of the Spike protein sequence enables us to identify, classify and track emerging virus variants. Our analysis is unbiased, in the sense that it does not require any prior knowledge of the…

SARS-CoV-2, like any other virus, continues to mutate as it spreads, according to an evolutionary process. Unlike any other virus, the number of currently available sequences of SARS-CoV-2 in public databases such as GISAID is already…

In the rapidly evolving landscape of genomics, deep learning has emerged as a useful tool for tackling complex computational challenges. This review focuses on the transformative role of Large Language Models (LLMs), which are mostly based…

Novel deep learning architectures are increasingly being applied to biological data, including genetic sequences. These models, referred to as genomic language models (gLMs), have demonstrated impressive predictive and generative…

The widespread availability of large amounts of genomic data on the SARS-CoV-2 virus, as a result of the COVID-19 pandemic, has created an opportunity for researchers to analyze the disease at a level of detail unlike any virus before it.…

Code metamorphism refers to a computer programming exercise wherein the program modifies its own code (partial or entire) consistently and automatically while retaining its core functionality. This technique is often used for online…

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…

Predicting the future evolutionary trajectory of SARS-CoV-2 remains a critical challenge, particularly due to the pivotal role of spike protein mutations. It is therefore essential to develop evolutionary models capable of continuously…

Large language models (LLMs) demonstrate remarkable ability in cross-lingual tasks. Understanding how LLMs acquire this ability is crucial for their interpretability. To quantify the cross-lingual ability of LLMs accurately, we propose a…

Change detection is a fundamental task in computer vision that processes a bi-temporal image pair to differentiate between semantically altered and unaltered regions. Large language models (LLMs) have been utilized in various domains for…

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused an ongoing pandemic infecting 219 million people as of 10/19/21, with a 3.6% mortality rate. Natural selection can generate favorable mutations with improved fitness…

The large transformer-based language models demonstrate excellent performance in natural language processing. By considering the transferability of the knowledge gained by these models in one domain to other related domains, and the…

Large Language Models (LLMs) are revolutionizing bioinformatics, enabling advanced analysis of DNA, RNA, proteins, and single-cell data. This survey provides a systematic review of recent advancements, focusing on genomic sequence modeling,…

The mechanism of SARS-CoV-2 evolution and transmission is elusive and its understanding, a prerequisite to forecast emerging variants, is of paramount importance. SARS-CoV-2 evolution is driven by the mechanisms at molecular and organism…

This paper pursues the insight that large language models (LLMs) trained to generate code can vastly improve the effectiveness of mutation operators applied to programs in genetic programming (GP). Because such LLMs benefit from training…

Large Language Models (LLMs) have recently advanced many applications on software engineering tasks, particularly the potential for code generation. Among contemporary challenges, code generated by LLMs often suffers from inaccuracies and…

A pipeline to evaluate the evolution of viral dynamics based on a new model-driven approach has been developed in the present study. The proposed methods exploit real data and the multiscale structure of the infection dynamics to provide…