# DeepPIG: deep neural network architecture with pairwise connected layers and stochastic gates using knockoff frameworks for feature selection

## TL;DR

DeepPIG is a new deep learning model that improves feature selection in machine learning, especially when feature signals are weak.

## Contribution

DeepPIG introduces a novel deep neural network architecture with pairwise connected layers and stochastic gates for robust feature selection.

## Key findings

- DeepPIG outperformed baseline and recent models in synthetic data without violating the FDR level.
- It showed superior classification performance in real-world cancer prognosis and microbiome datasets.
- The model is effective even when feature signals are weak.

## Abstract

Selecting relevant feature subsets is essential for machine learning applications. Among the feature selection techniques, the knockoff filter procedure proposes a unique framework that minimizes false discovery rates (FDR). However, employing a deep neural network architecture for a knockoff filter framework requires higher detection power. Using the knockoff filter framework, we present a Deep neural network with PaIrwise connected layers integrated with stochastic Gates (DeepPIG) for the feature selection model. DeepPIG exhibited better detection power in synthetic data than the baseline and recent models such as Deep feature selection using Paired-Input Nonlinear Knockoffs (DeepPINK), Stochastic Gates (STG), and SHapley Additive exPlanations (SHAP) while not violating the preselected FDR level, especially when the signal of the features were weak. The selected features determined by DeepPIG demonstrated superior classification performance compared with the baseline model in real-world data analyses, including the prediction of certain cancer prognosis and classification tasks using microbiome and single-cell datasets. In conclusion, DeepPIG is a robust feature selection approach even when the signals of features are weak. Source code is available at https://github.com/DMCB-GIST/DeepPIG.