Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China.
School of Artificial Intelligence, Jilin University, Changchun, China.
Interdiscip Sci. 2022 Jun;14(2):409-420. doi: 10.1007/s12539-021-00497-6. Epub 2022 Feb 22.
Long non-coding RNAs play a crucial role in many life processes of cell, such as genetic markers, RNA splicing, signaling, and protein regulation. Considering that identifying lncRNA's localization in the cell through experimental methods is complicated, hard to reproduce, and expensive, we propose a novel method named IDDLncLoc in this paper, which adopts an ensemble model to solve the problem of the subcellular localization. In the proposal model, dinucleotide-based auto-cross covariance features, k-mer nucleotide composition features, and composition, transition, and distribution features are introduced to encode a raw RNA sequence to vector. To screen out reliable features, feature selection through binomial distribution, and recursive feature elimination is employed. Furthermore, strategies of oversampling in mini-batch, random sampling, and stacking ensemble strategies are customized to overcome the problem of data imbalance on the benchmark dataset. Finally, compared with the latest methods, IDDLncLoc achieves an accuracy of 94.96% on the benchmark dataset, which is 2.59% higher than the best method, and the results further demonstrate IDDLncLoc is excellent on the subcellular localization of lncRNA. Besides, a user-friendly web server is available at http://lncloc.club .
长非编码 RNA 在细胞的许多生命过程中发挥着关键作用，例如遗传标记、RNA 剪接、信号转导和蛋白质调节。鉴于通过实验方法识别 lncRNA 在细胞中的定位复杂、难以重现且昂贵，我们在本文中提出了一种名为 IDDLncLoc 的新方法，该方法采用集成模型来解决亚细胞定位问题。在该提议模型中，采用二核苷酸自交叉协方差特征、k-mer 核苷酸组成特征以及组成、转换和分布特征将原始 RNA 序列编码为向量。为了筛选出可靠的特征，采用二项式分布和递归特征消除进行特征选择。此外，针对基准数据集的数据不平衡问题，定制了在 mini-batch 中进行过采样、随机抽样和堆叠集成策略。最后，与最新方法相比，IDDLncLoc 在基准数据集上的准确率达到 94.96%，比最佳方法高出 2.59%，结果进一步证明了 IDDLncLoc 在 lncRNA 的亚细胞定位方面表现出色。此外，还提供了一个用户友好的网络服务器，网址为 http://lncloc.club。
