Predicting Disease-related Associations by Heterogeneous Network Embedding

SRG-vote: Predicting miRNA-gene relationships via embedding and LSTM ensemble

AbstractTargeted therapy for one for a set of genes has made it possible to apply precision medicine for different patients due to the existence of tumor heterogeneity. However, how to regulate those genes are still problematic. One of the natural regulators of genes is microRNAs. Thus, a better understanding of the miRNA-gene interaction mechanism might contribute to future diagnosis, prevention, and cancer therapy. The interactions between microRNA and genes play an essential role in molecular genetics. The in-vivo experiments validating the relationships between them are time-consuming, money-costly, and labor-intensive. With the development of high-throughput technology, we dealt with tons of biological data. However, extracting features from tremendous raw data and making a mathematical model is still a challenging topic. Machine learning and deep learning algorithms have become powerful tools in dealing with biological data. Inspired by this, in this paper, we propose a model that combines features/embedding extraction methods, deep learning algorithms, and a voting system. We leverage doc2vec to generate sequential embedding from molecular sequences. The role2vec, GCN, and GMM for geometrical embedding were generated from the complex network from similarity and pair-wise datasets. For the deep learning algorithms, we leveraged LSTM and Bi-LSTM according to different embedding and features. Finally, we adopted a voting system to balance results from different data sources. The results have shown that our voting system could achieve a higher AUC than the existing benchmark. The case studies demonstrate that our model could reveal potential relationships between miRNAs and genes. The source code, features, and predictive results can be downloaded at https://github.com/Xshelton/SRG-vote.

SG-LSTM-FRAME: a computational frame using sequence and geometrical information via LSTM to predict miRNA-gene associations

MOTIVATION

MircroRNAs (miRNAs) regulate target genes and are responsible for lethal diseases such as cancers. Accurately recognizing and identifying miRNA and gene pairs could be helpful in deciphering the mechanism by which miRNA affects and regulates the development of cancers. Embedding methods and deep learning methods have shown their excellent performance in traditional classification tasks in many scenarios. But not so many attempts have adapted and merged these two methods into miRNA-gene relationship prediction. Hence, we proposed a novel computational framework. We first generated representational features for miRNAs and genes using both sequence and geometrical information and then leveraged a deep learning method for the associations' prediction.

RESULTS

We used long short-term memory (LSTM) to predict potential relationships and proved that our method outperformed other state-of-the-art methods. Results showed that our framework SG-LSTM got an area under curve of 0.94 and was superior to other methods. In the case study, we predicted the top 10 miRNA-gene relationships and recommended the top 10 potential genes for hsa-miR-335-5p for SG-LSTM-core. We also tested our model using a larger dataset, from which 14 668 698 miRNA-gene pairs were predicted. The top 10 unknown pairs were also listed.

AVAILABILITY

Our work can be download in https://github.com/Xshelton/SG_LSTM.

CONTACT

luojiawei@hnu.edu.cn.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Briefings in Bioinformatics online.

Constructing a knowledge-based heterogeneous information graph for medical health status classification

Applying Pearson correlation and semantic relations in building a heterogeneous information graph (HIG) to develop a classification model has achieved a notable performance in improving the accuracy of predicting the status of health risks. In this study, the approach that was used, integrated knowledge of the medical domain as well as taking advantage of applying Pearson correlation and semantic relations in building a classification model for diagnosis. The research mined knowledge which was extracted from titles and abstracts of MEDLINE to discover how to assess the links between objects relating to medical concepts. A knowledge-base HIG model then was developed for the prediction of a patient's health status. The results of the experiment showed that the knowledge-base model was superior to the baseline model and has demonstrated that the knowledge-base could help improve the performance of the classification model. The contribution of this study has been to provide a framework for applying a knowledge-base in the classification model which helps these models achieve the best performance of predictions. This study has also contributed a model to medical practice to help practitioners become more confident in making final decisions in diagnosing illness. Moreover, this study affirmed that biomedical literature could assist in building a classification model. This contribution will be advantageous for future researchers in mining the knowledge-base to develop different kinds of classification models.