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A Multi-scale Convolutional Neural Network for Phenotyping High Content Cellular Images

Godinez Navarro, William Jose and Hossain, Imtiaz and Lazic, Stanley and Davies, John and Zhang, Xian (2017) A Multi-scale Convolutional Neural Network for Phenotyping High Content Cellular Images. Bioinformatics. ISSN 1367-4811; 1367-4803

Abstract

Identifying phenotypes based on high-content cellular images is challenging. Conventional
image analysis pipelines for phenotype identification comprise multiple independent steps, with each step requiring method customization and adjustment of multiple parameters. Here we present an approach based on a multi-scale convolutional neural network (M-CNN) that classifies, in a single cohesive step, cellular images into phenotypes by using directly and solely the images’ pixel intensity values. The only parameters in the approach are the weights of the neural network, which are automatically optimized based on training images. The approach requires no a priori knowledge or manual customization, and is applicable to single- or multi-channel images displaying single or multiple cells. We evaluated the classification performance of the approach on eight diverse benchmark datasets. The approach yielded overall a higher classification accuracy compared to state-of-the-art results, including those of other deep CNN architectures. In addition to using the network to simply obtain a yes-or-no prediction for a given phenotype, we use the probability outputs calculated by the network to quantitatively describe the phenotypes. Our study shows that these probability values correlate with chemical treatment concentrations. This finding validates further our approach and enables chemical treatment potency estimation via convolutional neural networks.

Item Type: Article
Date Deposited: 01 Feb 2017 00:45
Last Modified: 01 Feb 2017 00:45
URI: https://oak.novartis.com/id/eprint/29655

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