MeSHHeading2vec: A new method for representing MeSH headings as feature vectors based on graph embedding algorithm

Abstract

Motivation: Effectively representing the MeSH headings (terms) such as disease and drug as discriminative vectors could greatly improve the performance of downstream computational prediction models. However, these terms are often abstract and difficult to quantify. Results: In this paper, we converted the MeSH tree structure into a relationship network and applied several graph embedding algorithms on it to represent these terms. Specifically, the relationship network consisting of nodes (MeSH headings) and edges (relationships) which can be constructed by the rule of tree num. Then, five graph embedding algorithms including DeepWalk (DW), LINE, SDNE, LAP and HOPE were implemented on the relationship network to represent MeSH headings as vectors. In order to evaluate the performance of the proposed method, we carried out the node classification and relationship prediction tasks. The experimental results show that the MeSH headings characterized by graph embedding algorithms can not only be treated as an independent carrier for representation, but also can be utilized as additional information to enhance the distinguishable ability of vectors. Thus, it can act as input and continue to play a significant role in any disease-, drug-, microbe-and etc.-related computational models. Besides, our method holds great hope to inspire relevant researchers to study the representation of terms in this network perspective. Contact: zhuhongyou@ms.xjb.ac.cn