Evaluation of linear classifiers on articles containing pharmacokinetic evidence of drug-drug interactions

Artemy Kolchinsky1,2, Anália Lourenço3, Lang Li4 and Luis M. Rocha1,2,*

1School of Informatics, Indiana University, Bloomington IN, USA
2FLAD Computational Biology Collaboratorium, Instituto Gulbenkian de Ciencia, Portugal
3IBB/CEB, University of Minho, Campus Gualtar, Braga, Portugal
4Department of Medical and Molecular Genetics, Indiana Univeristy School of Medicine, USA

Citation: A. Kolchinsky, A. Lourenço, L. Li, L.M. Rocha [2013]. "Evaluation of linear classifiers on articles containing pharmacokinetic evidence of drug-drug interactions". Pacific Symposium on Biocomputing 18:409-420.

Due to mathematical notation and graphics, the full text is available in pdf. The pre-print is also available.


Background. Drug-drug interaction (DDI) is a major cause of morbidity and mortality. DDI research includes the study of different aspects of drug interactions, from in vitro pharmacology, which deals with drug interaction mechanisms, to pharmaco-epidemiology, which investigates the effects of DDI on drug efficacy and adverse drug reactions. Biomedical literature mining can aid both kinds of approaches by extracting relevant DDI signals from either the published literature or large clinical databases. However, though drug interaction is an ideal area for translational research, the inclusion of literature mining methodologies in DDI workflows is still very preliminary. One area that can benefit from literature mining is the automatic identification of a large number of potential DDIs, whose pharmacological mechanisms and clinical significance can then be studied via in vitro pharmacology and in populo pharmaco-epidemiology.

Experiments. We implemented a set of classifiers for identifying published articles relevant to experimental pharmacokinetic DDI evidence. These documents are important for identifying causal mechanisms behind putative drug-drug interactions, an important step in the extraction of large numbers of potential DDIs. We evaluate performance of several linear classifiers on PubMed abstracts, under different feature transformation and dimensionality reduction methods. In addition, we investigate the performance benefits of including various publicly-available named entity recognition features, as well as a set of internally-developed pharmacokinetic dictionaries.

Results. We found that several classifiers performed well in distinguishing relevant and irrelevant abstracts. We found that the combination of unigram and bigram textual features gave better performance than unigram features alone, and also that normalization transforms that adjusted for feature frequency and document length improved classification. For some classifiers, such as linear discriminant analysis (LDA), proper dimensionality reduction had a large impact on performance. Finally, the inclusion of NER features and dictionaries was found not to help classification.

Keywords:Drug-drug interaction, literature mining, text mining, text classification, machine learning, pharmacokinetics, translational science

For more information contact Luis Rocha at rocha@indiana.edu. Check the Web Design Credits, for due credit.
Last Modified:October 22, 2012