GeneRAIN: multifaceted representation of genes via deep learning of gene expression networks

IF 10.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Zheng Su, Mingyan Fang, Andrei Smolnikov, Marcel E. Dinger, Emily C. Oates, Fatemeh Vafaee
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引用次数: 0

Abstract

We develop GeneRAIN, a suite of Transformer-based models that learn gene expression relationships from 410 K human bulk RNA-seq samples. Featuring a novel Binning-By-Gene normalization technique, our models capture diverse biological information beyond expression. We introduce GeneRAIN-vec, a multifaceted vectorized gene representation that outperforms those from existing models. We demonstrate knowledge transfer from protein-coding genes to Make 62.5 million biological attribute predictions for 13,030 long noncoding RNAs. This work advances Transformer and self-supervised deep learning applications to expression data, enhancing biological exploration.
GeneRAIN:通过基因表达网络的深度学习实现基因的多面表示
我们开发了GeneRAIN,这是一套基于transformer的模型,可以从410 K人类大量RNA-seq样本中学习基因表达关系。我们的模型采用了一种新颖的基因归一化技术,可以捕获各种无法表达的生物信息。我们引入了GeneRAIN-vec,这是一种多层面的矢量化基因表示,优于现有模型。我们展示了从蛋白质编码基因到对13030个长链非编码rna进行6250万个生物属性预测的知识转移。这项工作推进了Transformer和自监督深度学习在表达数据中的应用,增强了生物探索。
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来源期刊
Genome Biology
Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
21.00
自引率
3.30%
发文量
241
审稿时长
2 months
期刊介绍: Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.
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