Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Summary

Existing algorithms generate one solution for a biomarker detection dataset. This protocol demonstrates the existence of multiple similarly effective solutions and presents a user-friendly software to help biomedical researchers investigate their datasets for the proposed challenge. Computer scientists may also provide this feature in their biomarker detection algorithms.

Abstract

Biomarker detection is one of the more important biomedical questions for high-throughput 'omics' researchers, and almost all existing biomarker detection algorithms generate one biomarker subset with the optimized performance measurement for a given dataset. However, a recent study demonstrated the existence of multiple biomarker subsets with similarly effective or even identical classification performances. This protocol presents a simple and straightforward methodology for detecting biomarker subsets with binary classification performances, better than a user-defined cutoff. The protocol consists of data preparation and loading, baseline information summarization, parameter tuning, biomarker screening, result visualization and interpretation, biomarker gene annotations, and result and visualization exportation at publication quality. The proposed biomarker screening strategy is intuitive and demonstrates a general rule for developing biomarker detection algorithms. A user-friendly graphical user interface (GUI) was developed using the programming language Python, allowing biomedical researchers to have direct access to their results. The source code and manual of kSolutionVis can be downloaded from http://www.healthinformaticslab.org/supp/resources.php.

Introduction

Binary classification, one of the most commonly investigated and challenging data mining problems in the biomedical area, is used to build a classification model trained on two groups of samples with the most accurate discrimination power^{1,2,3,4,5,6,7}. However, the big data generated in the biomedical field has the inherent "large p small n" paradigm, with the number of features usually much larger than the number of samples

Protocol

NOTE: The following protocol describes the details of the informatics analytic procedure and pseudo-codes of the major modules. The automatic analysis system was developed using Python version 3.6.0 and the Python modules pandas, abc, numpy, scipy, sklearn, sys, PyQt5, sys, mRMR, math and matplotlib. The materials used in this study are listed in the Table of Materials.

1. Prepare the Data Matrix and Class Labels

1. Prepare the data matrix file as a TAB- or comma-delimited matrix file, as illustrated in Figure 1A.
   NOTE: Each row has all the values of a feature, and the first item ....

Results

The goal of this workflow (Figure 6) is to detect multiple biomarker subsets with similar efficiencies for a binary classification dataset. The whole process is illustrated by two example datasets ALL1 and ALL2 extracted from a recently-published biomarker detection study^12,48. A user may install kSolutionVis by following the instructions in the supplementary materials.

Discussion

This study presents an easy-to-follow multi-solution biomarker detection and characterization protocol for a user-specified binary classification dataset. The software puts an emphasis on user-friendliness and flexible import/export interfaces for various file formats, allowing a biomedical researcher to investigate their dataset easily using the GUI of the software. This study also highlights the necessity of generating more than one solution with similarly effective modeling performances, previously ignored by many exi.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Hardware
laptop	Lenovo	X1 carbon	Any computer works. Recommended minimum configuration: 1GB extra hard disk space, 1 GB memory, 2.0MHz CPU
Name	Company	Catalog Number	Comments
Software
Python 3.0	WingWare	Wing Personal	Any python programming and running environments support Python version 3.0 or above