Design of a generic, open platform for machine learning-assisted indexing and clustering of articles in PubMed, a biomedical bibliographic database

Many investigators have carried out text mining of the biomedical literature for a variety of purposes, ranging from the assignment of indexing terms to the disambiguation of author names. A common approach is to define positive and negative training examples, extract features from article metadata, and use machine learning algorithms. At present, each research group tackles each problem from scratch, in isolation of other projects, which causes redundancy and a great waste of effort. Here, we propose and describe the design of a generic platform for biomedical text mining, which can serve as a shared resource for machine learning projects and as a public repository for their outputs. We initially focus on a specific goal, namely, classifying articles according to publication type and emphasize how feature sets can be made more powerful and robust through the use of multiple, heterogeneous similarity measures as input to machine learning models. We then discuss how the generic platform can be extended to include a wide variety of other machine learning-based goals and projects and can be used as a public platform for disseminating the results of natural language processing (NLP) tools to end-users as well.