The interaction of miRNA and lncRNA is known to be important for gene regulations. However, the number of known lncRNA-miRNA interactions is still very limited and there are limited computational tools available for predicting new ones. Considering that lncRNAs and miRNAs share internal patterns in the partnership between each other, the underlying lncRNA-miRNA interactions could be predicted by utilizing the known ones, which could be considered as a semi-supervised learning problem. It is shown that the attributes of lncRNA and miRNA have a close relationship with the interaction between each other. Effective use of side information could be helpful for improving the performance especially when the training samples are limited. In view of this, we proposed an end-to-end prediction model called GCLMI (Graph Convolution for novel lncRNA-miRNA Interactions) by combining the techniques of graph convolution and auto-encoder. Without any preprocessing process on the feature information, our method can incorporate raw data of node attributes with the topology of the interaction network. Based on a real dataset collected from a public database, the results of experiments conducted on k-fold cross validations illustrate the robustness and effectiveness of the prediction performance of the proposed prediction model. We prove the graph convolution layer as designed in the proposed model able to effectively integrate the input data by filtering the graph with node features. The proposed model is anticipated to yield highly potential lncRNA-miRNA interactions in the scenario that different types of numerical features describing lncRNA or miRNA are provided by users, serving as a useful computational tool.
In classical sparse representation based classification (SRC) and weighted SRC (WSRC) algorithms, the test samples are sparely represented by all training samples. They emphasize the sparsity of the coding coefficients but without considering the local structure of the input data. Although the more training samples, the better the sparse representation, it is time consuming to find a global sparse representation for the test sample on the large-scale database. To overcome the shortcoming, aiming at the difficult problem of plant leaf recognition on the large-scale database, a two-stage local similarity based classification learning (LSCL) method is proposed by combining local mean-based classification (LMC) method and local WSRC (LWSRC). In the first stage, LMC is applied to coarsely classifying the test sample. k nearest neighbors of the test sample, as a neighbor subset, is selected from each training class, then the local geometric center of each class is calculated. S candidate neighbor subsets of the test sample are determined with the first S smallest distances between the test sample and each local geometric center. In the second stage, LWSRC is proposed to approximately represent the test sample through a linear weighted sum of all k×S samples of the S candidate neighbor subsets. The rationale of the proposed method is as follows: (1) the first stage aims to eliminate the training samples that are ''far'' from the test sample and assume that these samples have no effects on the ultimate classification decision, then select the candidate neighbor subsets of the test sample. Thus the classification problem becomes simple with fewer subsets; (2) the second stage pays more attention to those training samples of the candidate neighbor subsets in weighted representing the test sample. This is helpful to accurately represent the test sample. Experimental results on the leaf image database demonstrate that the proposed method not only has a high accuracy and low time cost, but also can be clearly interpreted.
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