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

Background. Drug-drug interaction (DDI) is a major cause of morbidity and mortality. [...] Biomedical literature mining can aid DDI research 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.Comment: Pacific Symposium on Biocomputing, 201

Toward Optimal Feature Selection in Naive Bayes for Text Categorization

Automated feature selection is important for text categorization to reduce the feature size and to speed up the learning process of classifiers. In this paper, we present a novel and efficient feature selection framework based on the Information Theory, which aims to rank the features with their discriminative capacity for classification. We first revisit two information measures: Kullback-Leibler divergence and Jeffreys divergence for binary hypothesis testing, and analyze their asymptotic properties relating to type I and type II errors of a Bayesian classifier. We then introduce a new divergence measure, called Jeffreys-Multi-Hypothesis (JMH) divergence, to measure multi-distribution divergence for multi-class classification. Based on the JMH-divergence, we develop two efficient feature selection methods, termed maximum discrimination ($MD$) and $MD-\chi^2$ methods, for text categorization. The promising results of extensive experiments demonstrate the effectiveness of the proposed approaches.Comment: This paper has been submitted to the IEEE Trans. Knowledge and Data Engineering. 14 pages, 5 figure

Local feature weighting in nearest prototype classification

The distance metric is the corner stone of nearest neighbor (NN)-based methods, and therefore, of nearest prototype (NP) algorithms. That is because they classify depending on the similarity of the data. When the data is characterized by a set of features which may contribute to the classification task in different levels, feature weighting or selection is required, sometimes in a local sense. However, local weighting is typically restricted to NN approaches. In this paper, we introduce local feature weighting (LFW) in NP classification. LFW provides each prototype its own weight vector, opposite to typical global weighting methods found in the NP literature, where all the prototypes share the same one. Providing each prototype its own weight vector has a novel effect in the borders of the Voronoi regions generated: They become nonlinear. We have integrated LFW with a previously developed evolutionary nearest prototype classifier (ENPC). The experiments performed both in artificial and real data sets demonstrate that the resulting algorithm that we call LFW in nearest prototype classification (LFW-NPC) avoids overfitting on training data in domains where the features may have different contribution to the classification task in different areas of the feature space. This generalization capability is also reflected in automatically obtaining an accurate and reduced set of prototypes.Publicad