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Attention-Based Deep Multiple-Instance Learning for Classifying Circular RNA and Other Long Non-Coding RNA

Circular RNA (circRNA) is a distinguishable circular formed long non-coding RNA (lncRNA), which has specific roles in transcriptional regulation, multiple biological processes. The identification of circRNA from other lncRNA is necessary for relevant research. In this study, we designed attention-ba...

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Detalles Bibliográficos
Autores principales: Liu, Yunhe, Fu, Qiqing, Peng, Xueqing, Zhu, Chaoyu, Liu, Gang, Liu, Lei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8701965/
https://www.ncbi.nlm.nih.gov/pubmed/34946967
http://dx.doi.org/10.3390/genes12122018
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author Liu, Yunhe
Fu, Qiqing
Peng, Xueqing
Zhu, Chaoyu
Liu, Gang
Liu, Lei
author_facet Liu, Yunhe
Fu, Qiqing
Peng, Xueqing
Zhu, Chaoyu
Liu, Gang
Liu, Lei
author_sort Liu, Yunhe
collection PubMed
description Circular RNA (circRNA) is a distinguishable circular formed long non-coding RNA (lncRNA), which has specific roles in transcriptional regulation, multiple biological processes. The identification of circRNA from other lncRNA is necessary for relevant research. In this study, we designed attention-based multi-instance learning (MIL) network architecture fed with a raw sequence, to learn the sparse features of RNA sequences and to accomplish the circRNAs identification task. The model outperformed the state-of-art models. Moreover, following the validation of the attention mechanism effectiveness by the handwritten digit dataset, the key sequence loci underlying circRNA’s recognition were obtained based on the corresponding attention score. Then, motif enrichment analysis identified some of the key motifs for circRNA formation. In conclusion, we designed deep learning network architecture suitable for learning gene sequences with sparse features and implemented it for the circRNA identification task, and the model has strong representation capability in the indication of some key loci.
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spelling pubmed-87019652021-12-24 Attention-Based Deep Multiple-Instance Learning for Classifying Circular RNA and Other Long Non-Coding RNA Liu, Yunhe Fu, Qiqing Peng, Xueqing Zhu, Chaoyu Liu, Gang Liu, Lei Genes (Basel) Article Circular RNA (circRNA) is a distinguishable circular formed long non-coding RNA (lncRNA), which has specific roles in transcriptional regulation, multiple biological processes. The identification of circRNA from other lncRNA is necessary for relevant research. In this study, we designed attention-based multi-instance learning (MIL) network architecture fed with a raw sequence, to learn the sparse features of RNA sequences and to accomplish the circRNAs identification task. The model outperformed the state-of-art models. Moreover, following the validation of the attention mechanism effectiveness by the handwritten digit dataset, the key sequence loci underlying circRNA’s recognition were obtained based on the corresponding attention score. Then, motif enrichment analysis identified some of the key motifs for circRNA formation. In conclusion, we designed deep learning network architecture suitable for learning gene sequences with sparse features and implemented it for the circRNA identification task, and the model has strong representation capability in the indication of some key loci. MDPI 2021-12-19 /pmc/articles/PMC8701965/ /pubmed/34946967 http://dx.doi.org/10.3390/genes12122018 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Liu, Yunhe
Fu, Qiqing
Peng, Xueqing
Zhu, Chaoyu
Liu, Gang
Liu, Lei
Attention-Based Deep Multiple-Instance Learning for Classifying Circular RNA and Other Long Non-Coding RNA
title Attention-Based Deep Multiple-Instance Learning for Classifying Circular RNA and Other Long Non-Coding RNA
title_full Attention-Based Deep Multiple-Instance Learning for Classifying Circular RNA and Other Long Non-Coding RNA
title_fullStr Attention-Based Deep Multiple-Instance Learning for Classifying Circular RNA and Other Long Non-Coding RNA
title_full_unstemmed Attention-Based Deep Multiple-Instance Learning for Classifying Circular RNA and Other Long Non-Coding RNA
title_short Attention-Based Deep Multiple-Instance Learning for Classifying Circular RNA and Other Long Non-Coding RNA
title_sort attention-based deep multiple-instance learning for classifying circular rna and other long non-coding rna
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8701965/
https://www.ncbi.nlm.nih.gov/pubmed/34946967
http://dx.doi.org/10.3390/genes12122018
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