Efficient framework for predicting MiRNA-disease associations based on improved hybrid collaborative filtering

Background Accumulating studies indicates that microRNAs (miRNAs) play vital roles in the process of development and progression of many human complex diseases. However, traditional biochemical experimental methods for identifying disease-related miRNAs cost large amount of time, manpower, material and financial resources. Methods In this study, we developed a framework named hybrid collaborative filtering for miRNA-disease association prediction (HCFMDA) by integrating heterogeneous data, e.g., miRNA functional similarity, disease semantic similarity, known miRNA-disease association networks, and Gaussian kernel similarity of miRNAs and diseases. To capture the intrinsic interaction patterns embedded in the sparse association matrix, we prioritized the predictive score by fusing three types of information: similar disease associations, similar miRNA associations, and similar disease-miRNA associations. Meanwhile, singular value decomposition was adopted to reduce the impact of noise and accelerate predictive speed. Results We then validated HCFMDA with leave-one-out cross-validation (LOOCV) and two types of case studies. In the LOOCV, we achieved 0.8379 of AUC (area under the curve). To evaluate the performance of HCFMDA on real diseases, we further implemented the first type of case validation over three important human diseases: Colon Neoplasms, Esophageal Neoplasms and Prostate Neoplasms. As a result, 44, 46 and 44 out of the top 50 predicted disease-related miRNAs were confirmed by experimental evidence. Moreover, the second type of case validation on Breast Neoplasms indicates that HCFMDA could also be applied to predict potential miRNAs towards those diseases without any known associated miRNA. Conclusions The satisfactory prediction performance demonstrates that our model could serve as a reliable tool to guide the following research for identifying candidate miRNAs associated with human diseases.

Research on Hybrid Collaborative Filtering Recommendation Algorithm Based on the Time Effect and Sentiment Analysis

In this study, we focus on the problem of information expiration when using the traditional collaborative filtering algorithm and propose a new collaborative filtering algorithm by integrating the time factor (ITWCF). This algorithm considers information influence attenuation over time, introduces an information retention period based on the information half-value period, and proposes a time-weighted function, which is applied to the nearest neighbor selection and score prediction to assign different time weights to the scores. In addition, to further improve the quality of the nearest neighbor selection and alleviate the problem of data sparsity, a method of calculating users’ sentiment tendency by analysis of user review features is proposed to mine users’ attitudes about the reviewed items, which expands the score matrix. The time factor and sentiment tendency are then integrated into the K-means clustering algorithm to select the nearest neighbor. A hybrid collaborative filtering model (TWCHR) based on the improved K-means clustering algorithm is then proposed, by combining item-based and user-based collaborative filtering. Finally, the experimental results show that the proposed algorithm can address the time effect and sentiment analysis in recommendations and improve the predictive performance of the model.