通过深度学习鉴定12种癌症

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https://www.nature.com/articles/s41598-019-53989-3

背景：

由大量研究表明，癌症是由于基因突变导致的，但是癌症具体的发病原理并没有研究清楚，只知道与一些基因有关，但这些基因与癌症并没有呈现出绝对的相关性。这是因为基因表达是一个完整复杂的网络调控过程。而基于多个隐藏层和非线性变换的深度学习完美适用于端对端模型的建立。所以我们提出基因组深度学习的方法来研究基因组变异与癌症之间的关系，这是一种新的癌症鉴定方法，为疾病诊断提供新的方向，同时也提供了一种预测性状的新方法。 原始分析数据来源于公共数据库。千人基因组（http://www.internationalgenome.org/）数据1991份原始WES测序数据，癌症数据库（TCGA，https://cancergenome.nih.gov/）6083 变异vcf文件。利用深度学习建模，模型输入为点突变，输出为是否患有癌症或者癌症种类（训练数据中涉及到的12种分类）。同时通过反向传播算法和梯度下降算法优化神经网络中的参数，用指数衰减法优化学习率，用L2正则化减少过拟合，用滑动平均模型提高模型的健壮性。

Abstract：

Cancer is a major cause of death worldwide, and an early diagnosis is required for a favorable prognosis.
Histological examination is the gold standard for cancer identification; however, large amount of interobserver variability exists in histological diagnosis. Numerous studies have shown cancer genesis is
accompanied by an accumulation of harmful mutations, potentiating the identification of cancer based
on genomic information. We have proposed a method, GDL (genome deep learning), to study the
relationship between genomic variations and traits based on deep neural networks. We analyzed 6,083
samples’ WES (Whole Exon Sequencing) mutations files from 12 cancer types obtained from the TCGA
(The Cancer Genome Atlas) and 1,991 healthy samples’ WES data from the 1000 Genomes project. We
constructed 12 specific models to distinguish between certain type of cancer and healthy tissues, a totalspecific model that can identify healthy and cancer tissues, and a mixture model to distinguish between all
12 types of cancer based on GDL. We demonstrate that the accuracy of specific, mixture and total specific
model are 97.47%, 70.08% and 94.70% for cancer identification. We developed an efficient method for the
identification of cancer based on genomic information that offers a new direction for disease diagnosis.