Journal ArticleDOI
Evaluation of deep learning in non-coding RNA classification
TLDR
This study reviews the progress of ncRNA type classification, specifically lncRNA, lincRNA, circular RNA and small nc RNA, and presents a comprehensive comparison of six deep learning based classification methods published in the past two years, and takes a close look at six state-of-the-art deep learning non-coding RNA classifiers.Abstract:
Non-coding (nc) RNA plays a vital role in biological processes and has been associated with diseases such as cancer. Classification of ncRNAs is necessary for understanding the underlying mechanisms of the diseases and to design effective treatments. Recently, deep learning has been employed for ncRNA identification and classification and has shown promising results. In this study, we review the progress of ncRNA type classification, specifically lncRNA, lincRNA, circular RNA and small ncRNA, and present a comprehensive comparison of six deep learning based classification methods published in the past two years. We identify research gaps and challenges of ncRNA types, such as the classification of subclasses of lncRNA, transcript length and compositional variation, dependency on database searches and the high false positive rate of existing approaches. We suggest future directions for cross-species performance deviation, deep learning model selection and sequence intrinsic features. Many functions of RNA strands that do not code for proteins are still to be deciphered. Methods to classify different groups of non-coding RNA increasingly use deep learning, but the landscape is diverse and methods need to be categorized and benchmarked to move forward. The authors take a close look at six state-of-the-art deep learning non-coding RNA classifiers and compare their performance and architecture.read more
Citations
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Journal ArticleDOI
Competing Endogenous RNA Networks as Biomarkers in Neurodegenerative Diseases.
Leticia Moreno-García,Tresa López-Royo,Ana C. Calvo,Janne M. Toivonen,Miriam de la Torre,Laura Moreno-Martínez,Nora Molina,Paula Aparicio,Pilar Zaragoza,Raquel Manzano,Rosario Osta +10 more
TL;DR: Although numerous studies have been carried out, further research is needed to validate these complex interactions between RNAs and the alterations in RNA editing that could provide specific ceRNET profiles for neurodegenerative disorders, paving the way to a better understanding of these diseases.
Journal ArticleDOI
Boosting Tree-Assisted Multitask Deep Learning for Small Scientific Datasets.
TL;DR: It is found that the proposed BTAMDL models outperform the current state-of-the-art methods in various applications involving small datasets, including toxicity, partition coefficient, solubility and solvation.
Journal ArticleDOI
The roles of non-coding RNAs in vascular calcification and opportunities as therapeutic targets.
TL;DR: NcRNAs can modulate VC by acting as promoters or inhibitors and may be useful in the clinical diagnosis and treatment of VC and the therapeutic implications of these nc RNAs are discussed.
Journal ArticleDOI
Machine learning meets omics: applications and perspectives.
TL;DR: A comprehensive survey and discussion on what happened, is happening and will happen when machine learning meets omics is presented in this article, where artificial intelligence can be applied to omics studies and review recent advancements at the interface between machine learning and the ever-widest range of omics including genomics, transcriptomics, proteomics, metabolomics, radiomics, as well as those at the single-cell resolution.
Journal ArticleDOI
Noncoding RNAs in Glioblastoma: Emerging Biological Concepts and Potential Therapeutic Implications.
TL;DR: In this article, the authors present an overview of the biogenesis of the different classes of ncRNAs, discuss their biological roles, as well as their relevance to gliomagenesis.
References
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Posted Content
DeepLab: Semantic Image Segmentation with Deep Convolutional Nets, Atrous Convolution, and Fully Connected CRFs
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GENCODE: The reference human genome annotation for The ENCODE Project
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