ezGeno: an automatic model selection package for genomic data analysis
Journal
Bioinformatics
Journal Volume
38
Journal Issue
1
Start Page
30
End Page
37
ISSN
1367-4803
1367-4811
Date Issued
2022
Author(s)
Jun-Liang Lin
Tsung-Ting Hsieh
Yi-An Tung
Xuan-Jun Chen
Yu-Chun Hsiao
Tyng-Luh Liu
Abstract
Motivation
To facilitate the process of tailor-making a deep neural network for exploring the dynamics of genomic DNA, we have developed a hands-on package called ezGeno. ezGeno automates the search process of various parameters and network structures and can be applied to any kind of 1D genomic data. Combinations of multiple abovementioned 1D features are also applicable.
Results
For the task of predicting TF binding using genomic sequences as the input, ezGeno can consistently return the best performing set of parameters and network structure, as well as highlight the important segments within the original sequences. For the task of predicting tissue-specific enhancer activity using both sequence and DNase feature data as the input, ezGeno also regularly outperforms the hand-designed models. Furthermore, we demonstrate that ezGeno is superior in efficiency and accuracy compared to the one-layer DeepBind model and AutoKeras, an open-source AutoML package.
Type
journal article