Link Prediction on a Network of Co-occurring MeSH Terms: Towards Literature-based Discovery.

Objectives: Literature-based discovery (LBD) is a text mining methodology for automatically generating research hypotheses from existing knowledge. We mimic the process of LBD as a classification problem on a graph of MeSH terms. We employ unsupervised and supervised link prediction methods for predicting previously unknown connections between biomedical concepts.

Methods: We evaluate the effectiveness of link prediction through a series of experiments using a MeSH network that contains the history of link formation between biomedical concepts. We performed link prediction using proximity measures, such as common neighbor (CN), Jaccard coefficient (JC), Adamic / Adar index (AA) and preferential attachment (PA). Our approach relies on the assumption that similar nodes are more likely to establish a link in the future.

Results: Applying an unsupervised approach, the AA measure achieved the best performance in terms of area under the ROC curve (AUC = 0.76), followed by CN, JC, and PA. In a supervised approach, we evaluate whether proximity measures can be combined to define a model of link formation across all four predictors. We applied various classifiers, including decision trees, k-nearest neighbors, logistic regression, multilayer perceptron, naïve Bayes, and random forests. Random forest classifier accomplishes the best performance (AUC = 0.87).

Conclusions: The link prediction approach proved to be effective for LBD processing. Supervised statistical learning approaches clearly outperform an unsupervised approach to link prediction.