1. CircNet: an encoder–decoder-based convolution neural network (CNN) for circular RNA identification
- Author
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Muhammad Nabeel Asim, Marco Stricker, Sheraz Ahmed, and Andreas Dengel
- Subjects
Whole genome sequencing ,0209 industrial biotechnology ,Computer science ,business.industry ,Deep learning ,Feature vector ,RNA ,Pattern recognition ,02 engineering and technology ,Convolutional neural network ,Identification (information) ,ComputingMethodologies_PATTERNRECOGNITION ,020901 industrial engineering & automation ,Discriminative model ,Artificial Intelligence ,Circular RNA ,Margin (machine learning) ,RNA Sequence ,0202 electrical engineering, electronic engineering, information engineering ,020201 artificial intelligence & image processing ,Artificial intelligence ,business ,Software - Abstract
Discrimination of circular RNA from long non-coding RNA is important to understand its role in different biological processes, disease prediction and cure. Identifying circular RNA through manual laboratories work is expensive, time-consuming and prone to errors. Development of computational methodologies for identification of circular RNA is an active area of research. State-of-the-art circular RNA identification methodologies make use of handcrafted features, which not only increase the feature space, but also extract irrelevant and redundant features. The paper in hand proposes an end-to-end deep learning-based framework named as CircNet, which does not require any handcrafted features. It takes raw RNA sequence as an input and utilises encoder–decoder based convolutional operations to learn lower-dimensional latent representation. This latent representation is further passed to another convolutional architecture to extract discriminative features followed by a classification layer. We performed extensive experimentation to highlight different regions of genome sequence that preserve the most important information for identifying circular RNAs. CircNet significantly outperforms state-of-the-art approaches with a considerable margin 10.29% in terms F1 measure.
- Published
- 2021
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