Scientists from China published a deep learning framework to predict virus variation drivers that works for influenza, zika, covid and HIV. Notably, the software and the model are developed on the domestic Exa-scale AI compute cluster in the Pengcheng lab. An earlier stage milestone of this work was nominated for the Gordon Bell prize in 2022.
Paper in English:
A unified evolution-driven deep learning framework for virus variation driver prediction
The increasing frequency of emerging viral infections necessitates a rapid human response, highlighting the cost-effectiveness of computational methods. However, existing computational approaches are limited by their input forms or incomplete functionalities, preventing a unified prediction of diverse virus variation drivers and hindering in-depth applications. To address this issue, we propose a unified evolution-driven framework for predicting virus variation drivers, named Evolution-driven Virus Variation Driver prediction (E2VD), which is guided by virus evolutionary traits. With evolution-inspired design, E2VD comprehensively and significantly outperforms state-of-the-art methods across various virus mutational driver prediction tasks. Moreover, E2VD effectively captures the fundamental patterns of virus evolution. It not only distinguishes different types of mutations but also accurately identifies rare beneficial mutations that are critical for viruses to survive, while maintaining generalization capabilities across different lineages of SARS-CoV-2 and different types of viruses. Importantly, with predicted biological drivers, E2VD perceives virus evolutionary trends in which potential high-risk mutation sites are accurately recommended. Overall, E2VD represents a unified, structure-free and interpretable approach for analysing and predicting viral evolutionary fitness, providing an ideal alternative to costly wet-lab measurements to accelerate responses to emerging viral infections.
News in Chinese:
鹏城实验室-北京大学联合团队与广州实验室研究员周鹏团队合作,研究实现了跨病毒类型和跨毒株的通用预测,涵盖新冠、流感、寨卡和艾滋病病毒,展现了AI助力自然科学研究范式革新的巨大潜力。近日,相关成果发表于《自然-机器智能》(Nature Machine Intelligence)。
2024年诺贝尔物理学奖和化学奖双双花落AI领域——物理学奖突出表彰“Science如何应用并改变AI”, 化学奖突出展现“AI如何改变科学和人们的认知”,将AI4S的研究热度推上新高潮——AI4S成为了学界前沿趋势,并正在推动科学研究范式的变革。
研究团队基于进化论和表观遗传学重新审视进化预测难题,从宏观进化角度凝练了病毒进化的两大本质问题,通过“微弱突变放大”和“稀少有益突变挖掘”两个创新设计实现了跨病毒类型和跨毒株的通用预测,涵盖新冠、流感、寨卡和艾滋病病毒,该研究实现了不同尺度的病毒进化预测,展现了自然科学和AI架构的高度融合,为疫苗、药物的快速主动更新以及提高人类对于新发病毒感染的响应速度提供了强大工具,支撑和加速对于物种复杂进化机制的探索。未来可与疫苗和蛋白类药物设计流程相结合,有望提升设计效率和设计可控度。
国产E级智算平台“鹏城云脑Ⅱ”支撑了模型训练及验证,保障了模型的快速部署。研究团队通过多层次联合优化高性能计算策略实现了模型的高效并行训练和微调,有力支撑了该研究的顺利进行和发表,充分展现了国产自主可控AI算力平台的先进性和优越性。
值得一提的是,鹏城实验室研究员高文、田永鸿、陈杰团队一直致力于推动AI4S的发展,团队前期成果曾入围2022年度戈登贝尔特别奖,与世界一流科研团队在世界顶级平台上角逐这一超级计算机领域的国际最高奖项,团队于众多世界级顶尖强队中脱颖而出名列前茅,展现出中国人工智能在计算集群和科研创新领域的全球顶尖水平。