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Deep Learning and Random Forest-Based Augmentation of sRNA Expression Profiles

  • Jelena Fiosina
  • Maksims FiosinsEmail author
  • Stefan Bonn
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11490)

Abstract

The lack of well-structured annotations in a growing amount of RNA expression data complicates data interoperability and reusability. Commonly used text mining methods extract annotations from existing unstructured data descriptions and often provide inaccurate output that requires manual curation. Automatic data-based augmentation (generation of annotations on the base of expression data) can considerably improve the annotation quality and has not been well-studied. We formulate an automatic augmentation of small RNA-seq expression data as a classification problem and investigate deep learning (DL) and random forest (RF) approaches to solve it. We generate tissue and sex annotations from small RNA-seq expression data for tissues and cell lines of homo sapiens. We validate our approach on 4243 annotated small RNA-seq samples from the Small RNA Expression Atlas (SEA) database. The average prediction accuracy for tissue groups is 98% (DL), for tissues - 96.5% (DL), and for sex - 77% (DL). The “one dataset out” average accuracy for tissue group prediction is 83% (DL) and 59% (RF). On average, DL provides better results as compared to RF, and considerably improves classification performance for ‘unseen’ datasets.

Keywords

Augmentation Deep learning Random forest Ontology Small RNA Expression counts Contamination 

Notes

Acknowledgements

The research was supported by the German Federal Ministry of Education and Research (BMBF), project Integrative Data Semantics for Neurodegenerative research (031L0029); by German Research Foundation (DFG), project Quantitative Synaptology (SFB 1286 Z2) and by Volkswagen Foundation.

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Jelena Fiosina
    • 1
  • Maksims Fiosins
    • 2
    • 3
    • 4
    Email author
  • Stefan Bonn
    • 2
    • 3
  1. 1.Clausthal University of TechnologyClausthal-ZellerfeldGermany
  2. 2.German Center for Neurodegenerative DiseasesTübingenGermany
  3. 3.Institute for Medical Systems Biology, Center for Molecular NeurobiologyUniversity Medical Center Hamburg-EppendorfHamburgGermany
  4. 4.Genevention GmbHGöttingenGermany

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