Linguistic Geometries for Unsupervised Dimensionality Reduction

Text documents are complex high dimensional objects. To effectively visualize such data it is important to reduce its dimensionality and visualize the low dimensional embedding as a 2-D or 3-D scatter plot. In this paper we explore dimensionality reduction methods that draw upon domain knowledge in order to achieve a better low dimensional embedding and visualization of documents. We consider the use of geometries specified manually by an expert, geometries derived automatically from corpus statistics, and geometries computed from linguistic resources.Comment: 13 pages, 15 figure

Non-Standard Words as Features for Text Categorization

This paper presents categorization of Croatian texts using Non-Standard Words (NSW) as features. Non-Standard Words are: numbers, dates, acronyms, abbreviations, currency, etc. NSWs in Croatian language are determined according to Croatian NSW taxonomy. For the purpose of this research, 390 text documents were collected and formed the SKIPEZ collection with 6 classes: official, literary, informative, popular, educational and scientific. Text categorization experiment was conducted on three different representations of the SKIPEZ collection: in the first representation, the frequencies of NSWs are used as features; in the second representation, the statistic measures of NSWs (variance, coefficient of variation, standard deviation, etc.) are used as features; while the third representation combines the first two feature sets. Naive Bayes, CN2, C4.5, kNN, Classification Trees and Random Forest algorithms were used in text categorization experiments. The best categorization results are achieved using the first feature set (NSW frequencies) with the categorization accuracy of 87%. This suggests that the NSWs should be considered as features in highly inflectional languages, such as Croatian. NSW based features reduce the dimensionality of the feature space without standard lemmatization procedures, and therefore the bag-of-NSWs should be considered for further Croatian texts categorization experiments.Comment: IEEE 37th International Convention on Information and Communication Technology, Electronics and Microelectronics (MIPRO 2014), pp. 1415-1419, 201

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