建立跨领域的生物AI模型评估标准,推动可靠虚拟细胞研究
Benchmarking and Evaluation of AI Models in Biology: Outcomes and Recommendations from the CZI Virtual Cells Workshop
- 汇聚多组学专家共建统一评估框架
- 提出数据异质性、可复现性等核心挑战
- 适合生物信息学与AI交叉研究者参考
人工智能在生物学中潜力巨大,但缺乏跨领域标准化基准制约了可靠模型的构建。本文基于克里格·泽克曼研究所(CZI)虚拟细胞研讨会成果,汇集成像、转录组、蛋白质组和基因组领域机器学习与计算生物学专家,识别出数据异质性、噪声、可复现性难题、偏见以及公开资源碎片化等主要技术与系统性瓶颈。研究提出一套建议,旨在构建高效比较不同任务与数据模态下生物系统机器学习模型的基准框架。通过推动高质量数据整理、标准化工具链、全面评估指标及开放协作平台,助力发展稳健的虚拟细胞基准体系。这些基准对确保研究严谨性、可复现性和生物学相关性至关重要,将最终推动整合模型发展,促进新发现、治疗洞察和对细胞系统的深入理解。
原文摘要 · Abstract (English)
Artificial intelligence holds immense promise for transforming biology, yet a lack of standardized, cross domain, benchmarks undermines our ability to build robust, trustworthy models. Here, we present insights from a recent workshop that convened machine learning and computational biology experts across imaging, transcriptomics, proteomics, and genomics to tackle this gap. We identify major technical and systemic bottlenecks such as data heterogeneity and noise, reproducibility challenges, biases, and the fragmented ecosystem of publicly available resources and propose a set of recommendations for building benchmarking frameworks that can efficiently compare ML models of biological systems across tasks and data modalities. By promoting high quality data curation, standardized tooling, comprehensive evaluation metrics, and open, collaborative platforms, we aim to accelerate the development of robust benchmarks for AI driven Virtual Cells. These benchmarks are crucial for ensuring rigor, reproducibility, and biological relevance, and will ultimately advance the field toward integrated models that drive new discoveries, therapeutic insights, and a deeper understanding of cellular systems.
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