期刊
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
卷 178, 期 -, 页码 275-287出版社
ELSEVIER IRELAND LTD
DOI: 10.1016/j.cmpb.2019.07.009
关键词
Human protein atlas; Multi-label classification; Deep learning; Convolutional neural network
类别
资金
- National Nature Science Foundation of China [NSFC 61673163]
- Chang-Zhu-Tan National Indigenous Innovation Demonstration Zone Project [2017XK2102]
- Hunan Key Laboratory of Intelligent Robot Technology in Electronic Manufacturing [IRT2018003]
Background and objectives: The multi-label Human Protein Atlas (HPA) classification can yield a better understanding of human diseases and help doctors to enhance the automatic analysis of biomedical images. The existing automatic protein recognition methods have been limited to single pattern. Therefore, an automatic multi-label human protein atlas recognition system with satisfactory performance should be conducted. This work aims to build an automatic recognition system for multi-label human protein atlas classification based on deep learning. Methods: In this work, an automatic feature extraction and multi-label classification framework is proposed. Specifically, an asymmetric and multi-scale convolutional neural network is designed for HPA classification. Furthermore, this work introduces a combined loss that consists of the binary cross-entropy and F1-score losses to improve identification performance. Results: Rigorous experiments are conducted to estimate the proposed system. In particular, unlike the current automatic identification systems, which focus on a limited number of patterns, the proposed method is capable of classifying mixed patterns of proteins in microscope images and can handle the subcellular multi-label protein classification task including 28 subcellular localization patterns. The proposed framework based on deep convolutional neural network outperformed the existing approaches with a F1-score of 0.823, which illustrates the robustness and effectiveness of the proposed system. Conclusion: This study proposed a high-performance recognition system for protein atlas classification based on deep learning, and it achieved an automatic multi-label human protein atlas identification framework with superior performance than previous studies. (C) 2019 Elsevier B.V. All rights reserved.
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