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A Similarity Searching System for Biological Phenotype Images Using Deep Convolutional Encoder-decoder Architecture

[ Vol. 14 , Issue. 7 ]

Author(s):

Bizhi Wu, Hangxiao Zhang, Limei Lin, Huiyuan Wang, Yubang Gao, Liangzhen Zhao, Yi-Ping Phoebe Chen*, Riqing Chen* and Lianfeng Gu*   Pages 628 - 639 ( 12 )

Abstract:


Background: The BLAST (Basic Local Alignment Search Tool) algorithm has been widely used for sequence similarity searching. Analogously, the public phenotype images must be efficiently retrieved using biological images as queries and identify the phenotype with high similarity. Due to the accumulation of genotype-phenotype-mapping data, a system of searching for similar phenotypes is not available due to the bottleneck of image processing.

Objective: In this study, we focus on the identification of similar query phenotypic images by searching the biological phenotype database, including information about loss-of-function and gain-of-function.

Methods: We propose a deep convolutional autoencoder architecture to segment the biological phenotypic images and develop a phenotype retrieval system to enable a better understanding of genotype–phenotype correlation.

Results: This study shows how deep convolutional autoencoder architecture can be trained on images from biological phenotypes to achieve state-of-the-art performance in a phenotypic images retrieval system.

Conclusion: Taken together, the phenotype analysis system can provide further information on the correlation between genotype and phenotype. Additionally, it is obvious that the neural network model of image segmentation and the phenotype retrieval system is equally suitable for any species, which has enough phenotype images to train the neural network.

Keywords:

Biological phenotype similarity searching, convolutional encoder-decoder architecture, segmentation of biological images, phenotypic image retrieval system, histogram, benchmark dataset.

Affiliation:

The College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, The College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, The College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, The College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002

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