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Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network

PLoS Computational Biology 2021年第9期17卷 e1009345-e1009345页

作者： Zhao, Zhengqiao Woloszynek, Stephen Agbavor, Felix Mell, Joshua Chang Sokhansanj, Bahrad A. Rosen, Gail L. Ecological and Evolutionary Signal-Processing and Informatics Laboratory Department of Electrical and Computer Engineering College of Engineering Drexel University PhiladelphiaPA United States Beth Israel Deaconess Medical Center BostonMA United States Harvard Medical School BostonMA United States School of Biomedical Engineering Science and Health Systems Drexel University PhiladelphiaPA United States College of Medicine Drexel University PhiladelphiaPA United States

Recurrent neural networks with memory and attention mechanisms are widely used in natural language processing because they can capture short and long term sequential information for diverse tasks. We propose an integrated deep learning model for microbial DNA sequence data, which exploits convolutional neural networks, recurrent neural networks, and attention mechanisms to predict taxonomic classifications and sample-associated attributes, such as the relationship between the microbiome and host phenotype, on the read/ sequence level. In this paper, we develop this novel deep learning approach and evaluate its application to amplicon sequences. We apply our approach to short DNA reads and full sequences of 16S ribosomal RNA (rRNA) marker genes, which identify the heterogeneity of a microbial community sample. We demonstrate that our implementation of a novel attention- based deep network architecture, Read2Pheno, achieves read-level phenotypic prediction. Training Read2Pheno models will encode sequences (reads) into dense, meaningful representations: learned embedded vectors output from the intermediate layer of the network model, which can provide biological insight when visualized. The attention layer of Read2Pheno models can also automatically identify nucleotide regions in reads/sequences which are particularly informative for classification. As such, this novel approach can avoid pre/post-processing and manual interpretation required with conventional approaches to microbiome sequence classification. We further show, as proof-of-concept, that aggregating read-level information can robustly predict microbial community properties, host phenotype, and taxonomic classification, with performance at least comparable to conventional approaches. An implementation of the attention-based deep learning network is available at https://***/EESI/sequence_attention (a python package) and https://***/ EESI/seq2att (a command line tool). Copyright: © 2021 Zhao et

关键词： Classification (of information)

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Correction: Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing

引用

BMC genomics 2023年第1期24卷 388页

作者： Elena V Demidova Ilya G Serebriiskii Ramilia Vlasenkova Simon Kelow Mark D Andrake Tiffiney R Hartman Tatiana Kent James Virtucio Gail L Rosen Richard T Pomerantz Roland L Dunbrack Erica A Golemis Michael J Hall David Y T Chen Mary B Daly Sanjeevani Arora Cancer Prevention and Control Program Fox Chase Cancer Center 333 Cottman Avenue Philadelphia PA 19111 USA. Kazan Federal University Kazan 420008 Russia. Program in Cancer Signaling and Microenvironment Fox Chase Cancer Center Philadelphia PA 19111 USA. Department of Biochemistry and Molecular Biophysics University of Pennsylvania Philadelphia PA 19104 USA. Arcadia University Glenside PA USA. Department of Biochemistry & Molecular Biology Sidney Kimmel Cancer Center Thomas Jeferson University Philadelphia PA 19107 USA. Ecological and Evolutionary Signal-Processing and Informatics Laboratory Department of Electrical and Computer Engineering College of Engineering Drexel University Philadelphia PA 19104 USA. Department of Cancer and Cellular Biology Lewis Katz School of Medicine Philadelphia PA 19140 USA. Department of Clinical Genetics Fox Chase Cancer Center 333 Cottman Avenue Philadelphia PA 19111 USA. Department of Surgical Oncology Fox Chase Cancer Center Philadelphia PA 19111 USA. Cancer Prevention and Control Program Fox Chase Cancer Center 333 Cottman Avenue Philadelphia PA 19111 USA. Mary.Daly@fccc.edu. Department of Clinical Genetics Fox Chase Cancer Center 333 Cottman Avenue Philadelphia PA 19111 USA. Mary.Daly@fccc.edu. Cancer Prevention and Control Program Fox Chase Cancer Center 333 Cottman Avenue Philadelphia PA 19111 USA. Sanjeevani.Arora@fccc.edu. Department of Radiation Oncology Fox Chase Cancer Center Philadelphia PA 19111 USA. Sanjeevani.Arora@fccc.edu.

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