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arXiv 1906.02241q-bio.NCcs.LGeess.SP
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用于体外多电极阵列记录分类的深度学习框架

A Deep Learning Framework for Classification of in vitro Multi-Electrode Array Recordings

University of California, Santa Barbara(加利福尼亚大学圣巴巴拉分校);Neuroscience Research Institute(神经科学研究所)

Yun Zhao, Elmer Guzman, Morgane Audouard, Zhuowei Cheng, PaulK. Hansma, Kenneth S. Kosik, Linda Petzold

摘要:

多电极阵列(MEA)被广泛用于记录神经元的活动,可用于基因缺陷和药物效应的诊断。在本文中,我们解决的问题,在体外MEA记录的小鼠和人类神经元培养物从不同的基因型,没有简单的方法来直接利用原始序列作为输入训练的端到端的分类模型进行分类。虽然手工仔细提取一些特征可以部分解决问题,但这种方法存在明显的缺点,例如难以推广。我们提出了一个深度学习框架来应对这一挑战。我们的方法正确地分类了从两种不同基因型制备的神经元培养数据-小鼠敲除δ-连环蛋白基因和威廉姆斯综合征的人类诱导多能干细胞衍生神经元。通过将长记录分成短切片进行训练,并在测试期间应用共识预测,与基于特征的逻辑回归相比,我们的深度学习方法将预测准确率提高了16.69%。我们在小鼠MEA记录数据的一个子集中使用共识预测进一步实现了95.91%的准确度,这些数据都是在体外6天记录的。随着高密度MEA记录变得越来越广泛,这种方法可以推广到携带不同突变的神经元的分类和药物反应的分类。

英文摘要:

Multi-Electrode Arrays (MEAs) have been widely used to record neuronal activities, which could be used in the diagnosis of gene defects and drug effects. In this paper, we address the problem of classifying in vitro MEA recordings of mouse and human neuronal cultures from different genotypes, where there is no easy way to directly utilize raw sequences as inputs to train an end-to-end classification model. While carefully extracting some features by hand could partially solve the problem, this approach suffers from obvious drawbacks such as difficulty of generalizing. We propose a deep learning framework to address this challenge. Our approach correctly classifies neuronal culture data prepared from two different genotypes -- a mouse Knockout of the delta-catenin gene and human induced Pluripotent Stem Cell-derived neurons from Williams syndrome. By splitting the long recordings into short slices for training, and applying Consensus Prediction during testing, our deep learning approach improves the prediction accuracy by 16.69% compared with feature based Logistic Regression for mouse MEA recordings. We further achieve an accuracy of 95.91% using Consensus Prediction in one subset of mouse MEA recording data, which were all recorded at six days in vitro. As high-density MEA recordings become more widely available, this approach could be generalized for classification of neurons carrying different mutations and classification of drug responses.

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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