Local Leave-one-out Cross Validation Research Articles

DRMDA: deep representations-based miRNA-disease association prediction.

Recently, microRNAs (miRNAs) are confirmed to be important molecules within many crucial biological processes and therefore related to various complex human diseases. However, previous methods of predicting miRNA–disease associations have their own deficiencies. Under this circumstance, we developed a prediction method called deep representations‐based miRNA–disease association (DRMDA) prediction. The original miRNA–disease association data were extracted from HDMM database. Meanwhile, stacked auto‐encoder, greedy layer‐wise unsupervised pre‐training algorithm and support vector machine were implemented to predict potential associations. We compared DRMDA with five previous classical prediction models (HGIMDA, RLSMDA, HDMP, WBSMDA and RWRMDA) in global leave‐one‐out cross‐validation (LOOCV), local LOOCV and fivefold cross‐validation, respectively. The AUCs achieved by DRMDA were 0.9177, 08339 and 0.9156 ± 0.0006 in the three tests above, respectively. In further case studies, we predicted the top 50 potential miRNAs for colon neoplasms, lymphoma and prostate neoplasms, and 88%, 90% and 86% of the predicted miRNA can be verified by experimental evidence, respectively. In conclusion, DRMDA is a promising prediction method which could identify potential and novel miRNA–disease associations.

DPFMDA: Distributed and privatized framework for miRNA-Disease association prediction

In this paper, we developed a novel distributed and privatized framework for miRNA-disease association prediction (DPFMDA) to predict potential miRNA-disease associations. DPFMDA assumes that diseases and miRNAs can be represented as feature matrices. Through independent factorization, collaborative analysis and matrix re-factorization, feature matrices are estimated and potential associations in miRNA-disease association matrix are predicted. The proposed computational model is tested and verified by leave-one-out cross validation (LOOCV). The AUCs of global and local LOOCV are 0.8859 and 0.8267 respectively, which outperform the state-of-the-art computational models. DPFMDA is further evaluated with case studies of four important human complex diseases. We test Esophageal Neoplasms and Prostate Neoplasms using DPFMDA in the HMDD v2.0 database. For Breast Neoplasms, we use the HMDD v2.0 database which removes all the known miRNAs-disease associations on Breast Neoplasms. For Hepatocellular Carcinoma, HMDD v1.0 database is used as the input of DPFMDA and predicted results are verified with HMDD v2.0, dbDEMC and miR2Disease databases. The results show that 90% (Esophageal Neoplasms), 88% (Prostate Neoplasms), 98% (Breast Neoplasms) and 86% (Hepatocellular Carcinoma) of top 50 predicted miRNA-disease associations are confirmed by recent experimental studies respectively. It is anticipated that DPFMDA would be an effective and extensible method for potential miRNA-disease association prediction.

MCMDA: Matrix completion for MiRNA-disease association prediction.

Nowadays, researchers have realized that microRNAs (miRNAs) are playing a significant role in many important biological processes and they are closely connected with various complex human diseases. However, since there are too many possible miRNA-disease associations to analyze, it remains difficult to predict the potential miRNAs related to human diseases without a systematic and effective method. In this study, we developed a Matrix Completion for MiRNA-Disease Association prediction model (MCMDA) based on the known miRNA-disease associations in HMDD database. MCMDA model utilized the matrix completion algorithm to update the adjacency matrix of known miRNA-disease associations and furthermore predict the potential associations. To evaluate the performance of MCMDA, we performed leave-one-out cross validation (LOOCV) and 5-fold cross validation to compare MCMDA with three previous classical computational models (RLSMDA, HDMP, and WBSMDA). As a result, MCMDA achieved AUCs of 0.8749 in global LOOCV, 0.7718 in local LOOCV and average AUC of 0.8767+/−0.0011 in 5-fold cross validation. Moreover, the prediction results associated with colon neoplasms, kidney neoplasms, lymphoma and prostate neoplasms were verified. As a consequence, 84%, 86%, 78% and 90% of the top 50 potential miRNAs for these four diseases were respectively confirmed by recent experimental discoveries. Therefore, MCMDA model is superior to the previous models in that it improves the prediction performance although it only depends on the known miRNA-disease associations.

Risk-based adaptive metric learning for nearest neighbour classification

The performance of k-nearest neighbour classification highly depends on the appropriateness of distance metric designation. Optimal performance can be obtained when the distance metric is matched to the characteristics of data. Existing works on distance-metric learning typically learn a global linear transform from training samples, and the effectiveness is limited to data, which are well-separated by linear decision boundaries. To address this problem, we propose a locally adaptive weighted distance-metric learning method to deal with the non-linearity of the data. The metric are learned based on local leave-one-out cross-validation (LOOCV) risks in each dimension, so that the local variations in feature component discriminability are taken into account. Experiments on both public datasets and hyper-spectral imagery classification demonstrate that the classification accuracy of the proposed method shows about 2–10% improvements over other competitive methods.