On transformative adaptive activation functions in neural networks for gene expression inference

PLoS One. 2021 Jan 14;16(1):e0243915. doi: 10.1371/journal.pone.0243915. eCollection 2021.

Abstract

Gene expression profiling was made more cost-effective by the NIH LINCS program that profiles only ∼1, 000 selected landmark genes and uses them to reconstruct the whole profile. The D-GEX method employs neural networks to infer the entire profile. However, the original D-GEX can be significantly improved. We propose a novel transformative adaptive activation function that improves the gene expression inference even further and which generalizes several existing adaptive activation functions. Our improved neural network achieves an average mean absolute error of 0.1340, which is a significant improvement over our reimplementation of the original D-GEX, which achieves an average mean absolute error of 0.1637. The proposed transformative adaptive function enables a significantly more accurate reconstruction of the full gene expression profiles with only a small increase in the complexity of the model and its training procedure compared to other methods.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology*
  • Gene Expression Profiling*
  • Gene Regulatory Networks*
  • Humans
  • Neural Networks, Computer*
  • Transcriptome*

Grants and funding

This study was supported by the Czech Science Foundation (GACR - https://gacr.cz/en/) in the form of a grant awarded to JK (20-19162S) and the Research Center for Informatics (https://ec.europa.eu/) in the form of a grant awarded to JK (CZ.02.1.01/0.0/0.0/16_019/0000765). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.