Deep learning model with L1 penalty for predicting breast cancer metastasis using gene expression data

Author:

Kim JaeyoonORCID,Lee MinhyeokORCID,Seok JunheeORCID

Abstract

Abstract Breast cancer has the highest incidence and death rate among women; moreover, its metastasis to other organs increases the mortality rate. Since several studies have reported gene expression and cancer prognosis to be related, the study of breast cancer metastasis using gene expression is crucial. To this end, a novel deep neural network architecture, deep learning-based cancer metastasis estimator (DeepCME), is proposed in this paper for predicting breast cancer metastasis. However, the problem of overfitting occurs frequently while training deep learning models using gene expression data because they contain a large number of genes and the sample size is rather small. To address overfitting, several regularization methods are implemented, such as L1 penalty, batch normalization, and dropout. To demonstrate the superior performance of our model, area under curve (AUC) scores are evaluated and then compared with five baseline models: logistic regression, support vector classifier (SVC), random forest, decision tree, and k-nearest neighbor. Considering results, DeepCME demonstrates the highest average AUC scores in most cross-validation cases, and the average AUC score of DeepCME is 0.754, which is approximately 12.9% higher than SVC, the second-best model. In addition, the 30 most significant genes related to breast cancer metastasis are identified based on DeepCME results and some are discussed in further detail considering the reports from some previous medical studies. Considering the high expense involved in measuring the expression of a single gene, the ability to develop the cost-effective and time-efficient tests using only a few key genes is valuable. Based on this study, we expect DeepCME to be utilized clinically for predicting breast cancer metastasis and be applied to other types of cancer as well after further research.

Funder

National Research Foundation of Korea

Publisher

IOP Publishing

Subject

Artificial Intelligence,Human-Computer Interaction,Software

Cited by 2 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3