A graph-embedded deep feedforward network for disease outcome classification and feature selection using gene expression data

Bioinformatics
Yunchuan Kong, Tianwei Yu

Abstract

Gene expression data represents a unique challenge in predictive model building, because of the small number of samples (n) compared with the huge amount of features (p). This 'n≪p' property has hampered application of deep learning techniques for disease outcome classification. Sparse learning by incorporating external gene network information could be a potential solution to this issue. Still, the problem is very challenging because (i) there are tens of thousands of features and only hundreds of training samples, (ii) the scale-free structure of the gene network is unfriendly to the setup of convolutional neural networks. To address these issues and build a robust classification model, we propose the Graph-Embedded Deep Feedforward Networks (GEDFN), to integrate external relational information of features into the deep neural network architecture. The method is able to achieve sparse connection between network layers to prevent overfitting. To validate the method's capability, we conducted both simulation experiments and real data analysis using a breast invasive carcinoma RNA-seq dataset and a kidney renal clear cell carcinoma RNA-seq dataset from The Cancer Genome Atlas. The resulting high classification accuracy and easil...Continue Reading

References

Oct 16, 1999·Science·A L Barabasi, R Albert
Jun 20, 2002·Endocrinology·Tetsuya YamamotoTadashi Matsuda
Jun 28, 2003·Proceedings of the National Academy of Sciences of the United States of America·Therese SorlieDavid Botstein
Nov 14, 2006·Bioinformatics·S Falcon, R Gentleman
Oct 18, 2007·Molecular Systems Biology·Han-Yu ChuangTrey Ideker
Sep 4, 2010·Cancer Biology & Therapy·Gowrishankar Banumathy, Paul Cairns
Sep 23, 2011·The Journal of Biological Chemistry·Nayan J Sarma, Nabeel R Yaseen
Oct 8, 2011·PLoS Computational Biology·Janusz Dutkowski, Trey Ideker
Dec 29, 2011·Frontiers in Bioscience (Landmark Edition)·Debangshu Samanta, Pran K Datta
Jun 16, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Ofer LaviRon Shamir
Sep 25, 2012·Nature·UNKNOWN Cancer Genome Atlas Network
Jun 25, 2013·Nature·UNKNOWN Cancer Genome Atlas Research Network
Jul 5, 2013·Biometrics·Sunkyung KimXiaotong Shen
Aug 7, 2013·Molecular Cancer·Bastian Hoesel, Johannes A Schmid
Oct 26, 2013·Future Oncology·Daniele M Gilkes, Gregg L Semenza
Jan 15, 2014·BMC Bioinformatics·Miron Bartosz Kursa
Mar 19, 2014·Computers in Biology and Medicine·Yen-Chen ChenHung-Wen Chiu
May 27, 2014·Frontiers in Oncology·C Elizabeth Caldon
Nov 8, 2014·The Journal of Medicine and Philosophy·Elselijn Kingma
Jan 30, 2015·Database : the Journal of Biological Databases and Curation·Saikat Chowdhury, Ram Rup Sarkar
Apr 11, 2015·Methods in Molecular Biology·Damian Szklarczyk, Lars Juhl Jensen
May 29, 2015·Nature·Yann LeCunGeoffrey Hinton
Mar 30, 2016·Annals of Oncology : Official Journal of the European Society for Medical Oncology·M R JonesH J Lim
Nov 9, 2016·Archives of Biochemistry and Biophysics·Matthias WolffReinhard Depping
Dec 27, 2016·World Journal of Gastroenterology : WJG·Chi-Wai ChengEric Tse
Feb 22, 2017·Cellular Physiology and Biochemistry : International Journal of Experimental Cellular Physiology, Biochemistry, and Pharmacology·Lifang JinHuaiyu Zhang

❮ Previous
Next ❯

Citations

Jan 11, 2019·Cancers·Kelvin K WongStephen T C Wong
Jul 11, 2019·Journal of Bioinformatics and Computational Biology·Teppei MatsubaraJose C Nacher
Nov 13, 2019·Current Pharmaceutical Design·Shogo NakashimaTatsuya Akutsu
Dec 12, 2019·Frontiers in Genetics·Qiang ZhuTingting He
Dec 21, 2019·BMC Medical Genomics·Léon-Charles TrancheventJagath C Rajapakse
May 5, 2020·Briefings in Bioinformatics·Shuting JinXiangrong Liu
Jul 1, 2020·Briefings in Bioinformatics·Susana Vinga
Feb 11, 2020·Frontiers in Bioengineering and Biotechnology·Yasunari Matsuzaka, Yoshihiro Uesawa
Jul 6, 2020·Computational Biology and Chemistry·Junyi LiYadong Wang
Apr 30, 2021·Frontiers in Genetics·Sijie YangPeiyao Zhao
Aug 8, 2021·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Xuezhu WangYang Chen
Nov 25, 2021·Statistics in Medicine·Zhuxuan JinTianwei Yu
Dec 25, 2021·Analytical and Bioanalytical Chemistry·Chao LiXiaohui Lin

❮ Previous
Next ❯

Related Concepts

Related Feeds

Adenocarcinoma, Clear Cell

Clear Cell Adenocarcinoma is a tumor that arises in the female genital tract and is characterized by cells that appear clear under the microscope. Discover the latest research here.

Breast Invasive Carcinoma (Keystone)

Invasive breast cancers indicate a spread into breast tissues and lymph nodes. Here are the latest discoveries pertaining to breast invasive carcinomas.

Carcinoma, Ductal

Ductal carcinoma is a malignant neoplasm involving the ductal systems of any of a number of organs, such as the mammary glands, pancreas, prostate or lacrimal gland. Discover the latest research on ductal carcinoma here.

Breast Invasive Carcinoma

Invasive breast cancers indicate a spread into breast tissues and lymph nodes. Here are the latest discoveries pertaining to breast invasive carcinomas.

Related Papers

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Heewon ParkSeiya Imoto
Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Yifeng LiWyeth W Wasserman
© 2022 Meta ULC. All rights reserved