Embedding gene sets in low-dimensional space

被引:1
作者
Hoinka, Jan [1 ]
Przytycka, Teresa M. [1 ]
机构
[1] NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bldg 10, Bethesda, MD 20892 USA
基金
美国国家卫生研究院;
关键词
D O I
10.1038/s42256-020-0204-3
中图分类号
TP18 [人工智能理论];
学科分类号
081104 ; 0812 ; 0835 ; 1405 ;
摘要
An important task in system biology is to understand cellular processes through the lens of gene sets and their expression patterns. Machine learning can help, but genes form complex interaction networks, and levarging this information in machine learning applications requires a sophisticated data representation.
引用
收藏
页码:367 / 368
页数:2
相关论文
共 8 条
[1]   A gentle introduction to deep learning for graphs [J].
Bacciu, Davide ;
Errica, Federico ;
Micheli, Alessio ;
Podda, Marco .
NEURAL NETWORKS, 2020, 129 :203-221
[2]   Chapter 5: Network Biology Approach to Complex Diseases [J].
Cho, Dong-Yeon ;
Kim, Yoo-Ah ;
Przytycka, Teresa M. .
PLOS COMPUTATIONAL BIOLOGY, 2012, 8 (12)
[3]   Compact Integration of Multi-Network Topology for Functional Analysis of Genes [J].
Cho, Hyunghoon ;
Berger, Bonnie ;
Peng, Jian .
CELL SYSTEMS, 2016, 3 (06) :540-+
[4]   Network propagation: a universal amplifier of genetic associations [J].
Cowen, Lenore ;
Ideker, Trey ;
Raphael, Benjamin J. ;
Sharan, Roded .
NATURE REVIEWS GENETICS, 2017, 18 (09) :551-562
[5]   To Embed or Not: Network Embedding as a Paradigm in Computational Biology [J].
Nelson, Walter ;
Zitnik, Marinka ;
Wang, Bo ;
Leskovec, Jure ;
Goldenberg, Anna ;
Sharan, Roded .
FRONTIERS IN GENETICS, 2019, 10
[6]  
Tong HH, 2006, IEEE DATA MINING, P613
[7]   Gaussian embedding for large-scale gene set analysis [J].
Wang, Sheng ;
Flynn, Emily R. ;
Altman, Russ B. .
NATURE MACHINE INTELLIGENCE, 2020, 2 (07) :387-395
[8]  
Zhang Si, 2019, Comput Soc Netw, V6, P11, DOI 10.1186/s40649-019-0069-y