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ZENODO
Dataset . 2024
License: CC BY
Data sources: ZENODO
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
ZENODO
Dataset . 2025
License: CC BY
Data sources: ZENODO
ZENODO
Dataset . 2024
License: CC BY
Data sources: Datacite
ZENODO
Dataset . 2025
License: CC BY
Data sources: Datacite
ZENODO
Dataset . 2025
License: CC BY
Data sources: Datacite
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General Intelligence framework to predict Virus Adaptation based on genome Language model

Authors: Li, Jing; Jiang, Shu-Yang; Wei, Jun-Qing;

General Intelligence framework to predict Virus Adaptation based on genome Language model

Abstract

Current artificial intelligence (AI) solutions for assessing virus phenotypes are mostly limited to fixed tasks, with trained models. We aim to build General Intelligence to predict Virus Adaptation based on Language model (GIVAL), instantly for any input gene or gene segment from any virus. A gene embedder in GIVAL, named virus Bidirectional Encoder Representations from Transformers (vBERT), was pretrained with context-dependently segmented tokens of presently available viruses. Host adaptation of virus input was predicted based on its vBERT embedding, by the input-specified deep learning model, trained with input-specified training data and labels. GIVAL’s vBERT performed well (better than vBERT pretrained on fixed number of amino acids as tokens) on embedding virus genes, at both coarse-grained intact gene and fine-grained gene site levels. GIVAL interpretably predicted the high human adaptation of swine H3N2 and equine H3N8 influenza viruses, and the receptor binding variance of various types of coronaviruses, based on the input of segmented Hemagglutinin (HA) or Spike. GIVAL predicted a significant adaptation shift of the monkeypox viruses since 2022 based on multiple intact viral genes. Summarily, this study provides a general AI solution to assess virus risk, highlights the importance of adaptation shift on transmission risk of multiple viruses. Scripts and data are available on GitHub (https://github.com/Jamalijama/GIVAL) and Zenodo (10.5281/zenodo.14233092).

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average