A high-performance SNP panel developed by machine-learning approaches for characterizing genetic differences of Southern and Northern Han Chinese,Korean, and Japanese individuals

Population stratification analyses targeting genetically closely related East Asians have revealed that distinguishable differentiation exists between Han Chinese, Korean, and Japanese individuals, as well as between southern (S-) and northern (N-) Han Chinese. Previous studies offer a number of choices for ancestry informative single nucleotide polymorphisms (AISNPs) to discriminate East-Asian populations. In this study, we collected and examined the efficiency of 1185 AISNPs using frequency and genotype data from various publicly available databases. With the aim to perform fine-scale classification of S-Han, N-Han, Korean, and Japanese subjects, machine-learning methods (Softmax and Random Forest) were used to screen a panel of highly informative AISNPs and to develop a superior classification model. Stepwise classification was implemented to increase and balance the discrimination in the process of AISNP selection, first discriminating Han, Korean, and Japanese individuals, and then characterizing stratification between S-Han and N-Han. The final 272-AISNP panel is an alternative optimization of various previous works, which promises reliable and >90% accuracy in classification of the four East-Asian groups. This AISNP panel and the machine-learning model could be a useful and superior choice in medical genome-wide association studies and in forensic investigations for unknown suspect identity.     

残差网络分层融合的高光谱地物分类

高光谱图像具有较高的空间分辨率,蕴含着丰富的空间光谱信息,近年来被广泛用于城市地物分类中。在高光谱图像分类过程中,空间光谱特征的提取直接影响着分类精度;传统的高光谱图像特征提取方法只利用了4或8邻域的像素进行简单卷积处理,因而丢失了大量的复杂、有效信息;卷积神经网络（CNN）虽然可以自动提取空间光谱特征,在保留图像空间信息的同时,简化网络模型,但是,随着网络深度增加,网络分类产生退化现象,而且网络间缺乏相关信息的互补性,从而影响分类精度。该工作引入CNN自动提取空间光谱特征,并且针对CNN深度增加所导致的退化问题,设计了面向地物分类的高光谱特征融合残差网络。首先,为了降低高光谱图像的光谱冗余度,利用PCA提取主要光谱波段;然后,为了逐级提取光谱图像的空间光谱特征,定义了卷积核为16,32,64的低、中、高3层残差网络模块,并利用64个1×1的卷积核对3层特征输出进行卷积,完成维度匹配与特征图融合;接着,对融合后的特征图进行全局平均池化(GAP)生成用于分类的特征向量;最后,引入具有可调节机制的Large-Margin Softmax损失函数,监督模型完成训练过程,实现高光谱图像分类。实验采用Indian Pines,University of Pavia和Salinas地区的高光谱图像来验证方法有效性,设置批次训练的样本集为100,网络训练的初始学习率为0.1,当损失函数稳定后学习率降低为0.001,动量为0.9,权重延迟为0.000 1,最大训练迭代次数为2×104,当3个数据集的样本块像素分别设置为25×25,23×23,27×27,网络深度分别为28,32和28时,3个数据集的分类准确率最高,其平均总体准确率（OA）为98.75%、平均准确率（AA）的评价值为98.1%,平均Kappa系数为0.98。实验结果表明,基于残差网络的分类方法能够自动学习更丰富的空间光谱特征,残差网络层数的增加和不同网络层融合可以提高高光谱分类精度;Large-Margin Softmax实现了类内紧凑和类间分离,可以进一步提高高光谱图像分类精度。