LDNFSGB: prediction of long non-coding rna and disease association using network feature similarity

LDNFSGB: prediction of long non-coding rna and disease association using network feature similarity and gradient boosting

LDNFSGB:利用网络特征相似度和梯度增强预测长链非编码RNA和疾病相关性

Background:

A large number of experimental studies show that the mutation and regulation of long non-coding RNAs (lncRNAs) are associated with various human diseases. Accurate prediction of lncRNA-disease associations can provide a new perspective for the diagnosis and treatment of diseases. The main function of many lncRNAs is still unclear and using traditional experiments to detect lncRNA-disease associations is time-consuming. Results: In this paper, we develop a novel and effective method for the prediction of lncRNA-disease associations using network feature similarity and gradient boosting (LDNFSGB). In LDNFSGB, we first construct a comprehensive feature vector to effectively extract the global and local information of lncRNAs and diseases through considering the disease semantic similarity (DISSS), the lncRNA function similarity (LNCFS), the lncRNA Gaussian interaction profile kernel similarity (LNCGS), the disease Gaussian interaction profile kernel similarity (DISGS), and the lncRNA-disease interaction (LNCDIS). Particularly, two methods are used to calculate the DISSS (LNCFS) for considering the local and global information of disease semantics (lncRNA functions) respectively. An autoencoder is then used to reduce the dimensionality of the feature vector to obtain the optimal feature parameter from the original feature set. Furthermore, we employ the gradient boosting algorithm to obtain the lncRNA-disease association prediction. Conclusions: In this study, hold-out, leave-one-out cross-validation, and ten-fold cross-validation methods are implemented on three publicly available datasets to evaluate the performance of LDNFSGB. Extensive experiments show that LDNFSGB dramatically outperforms other state-of-the-art methods. The case studies on six diseases, including cancers and non-cancers, further demonstrate the effectiveness of our method in real-world applications.

背景:

大量实验研究表明，长链非编码rna (long non-coding RNAs, lncRNAs)的突变和调控与人类多种疾病有关。
准确预测lncrna -疾病相关性可以为疾病的诊断和治疗提供新的视角。
许多lncrna的主要功能尚不清楚，使用传统实验来检测lncrna与疾病的相关性耗时较长。
结果:在本文中，我们开发了一种新的和有效的方法来预测lncrna -疾病关联使用网络特征相似度和梯度增强(LDNFSGB)。
在LDNFSGB,我们首先构建一个全面的有效特征向量提取lncRNAs和疾病的全球和本地信息通过语义相似性(侮辱),考虑到疾病lncRNA函数相似(LNCFS) lncRNA高斯交互配置内核相似(LNCGS),疾病高斯交互配置内核相似(DISGS)和lncRNA-disease交互(LNCDIS)。
其中，考虑疾病语义(lncRNA函数)局部信息和全局信息的DISSS (LNCFS)分别采用了两种方法进行计算。
然后使用自编码器对特征向量进行降维，得到原始特征集的最优特征参数。然后使用梯度增强算法得到lncRNA-disease关联预测。
结论:在本研究中，在三个公开的数据集上执行了保留验证、单留交叉验证和十倍交叉验证方法，以评估LDNFSGB的性能。
大量的实验表明，LDNFSGB显著优于其他最先进的方法。
对包括癌症和非癌症在内的六种疾病的案例研究，进一步证明了我们的方法在实际应用中的有效性。