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A diffusion model of viral evolution predicts mutation fitness and evolutionary trajectories

Research datakeyboard_double_arrow_right Model Under curationPublisher:Zenodo
Authors: Wu, Jinghan; Ding, Xiao; Wu, Aiping;

doi: 10.5281/zenodo.22790015

A diffusion model of viral evolution predicts mutation fitness and evolutionary trajectories

Abstract

- Repository for the Paper A diffusion model of viral evolution predicts mutation fitness and evolutionary trajectories - 1 Code source: https://github.com/wuaipinglab/VES 2 Data source: 2.1 Influenza virus (hemagglutinin protein) file name: aligned_single_processed_HA.a2m collected from GISAID (up to May, 2024) quality control and 100% redundancy removal multiple sequence alignment using MAFFT, selecting the Influenza A virus (A/WSN/1933(H1N1)) strain as the wild type reference sequence a total of 95,560 sequences 2.2 SARS-CoV-2 virus (spike protein) file name: nr_no_X_1273_spike.a2m collected from GISAID (up to June, 2025) quality control and 100% redundancy removal multiple sequence alignment using MAFFT, selecting the hCoV-19/Wuhan/WIV04/2019 (WIV04) strain as the wild type reference sequence a total of 55,246 sequences 3 Model checkpoints: 3.1 VES official implementation file name: FLU_DM_UNet_Attention_128_ch.pth (Influenza virus) file name: COVID_DM_UNet_Attention_4_conv_data_update.pth (SARS-CoV-2 virus)

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