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2022, Nature Reviews Genetics. DOI: 10.1038/s41576-022-00532-2
Obtaining genetics insights from deep learning via explainable artificial intelligence
Gherman Novakovsky , Nick Dexter , Maxwell W. Libbrecht , Wyeth W. Wasserman , Sara Mostafavi
Abstract:
Artificial intelligence (AI) models based on deep learning now represent the state of the art for making functional predictions in genomics research. However, the underlying basis on which predictive models make such predictions is often unknown. For genomics researchers, this missing explanatory information would frequently be of greater value than the predictions themselves, as it can enable new insights into genetic processes. We review progress in the emerging area of explainable AI (xAI), a field with the potential to empower life science researchers to gain mechanistic insights into complex deep learning models. We discuss and categorize approaches for model interpretation, including an intuitive understanding of how each approach works and their underlying assumptions and limitations in the context of typical high-throughput biological datasets.
2022-10-31 15:22:00
#paper Obtaining genetics insights from deep learning via explainable artificial intelligence, Nature Reviews Genetics https://doi.org/10.1038/ s41576-022-00532-2 基于深度学习的人工智能模型在基因组功能预测中发挥重要作用,被认为是当下表现最好的模型(state of the art)。但是由于深度学习模型的复杂性, 它们往往被认为是黑箱模型,其预测效果/机制往往很难被解释,但是基因组的研究中很多时候作用机制(过程)比预测效果(结果)更有价值。这篇review paper总结了近年来新兴的可解释性机器学习(xAI)技术在基因组领域的研究进展,展望了该技术在揭示生物机理方面的潜能。这篇文章主要以regulatory genomics 作为例子, 总结归纳了4种解释机器学习模型的技术:基于模型的解释(检查隐含层的神经元活动,注意力机制),影响的数学传播(前向传播/后向传播), 特征相互作用的鉴别,和基于先验知识的透明模型,以及这几种技术在高通量测序技术中的潜在假设和相应的局限性。
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