Chi-square-based scoring function for categorization of MEDLINE citations

Objectives: Text categorization has been used in biomedical informatics for identifying documents containing relevant topics of interest. We developed a simple method that uses a chi-square-based scoring function to determine the likelihood of MEDLINE citations containing genetic relevant topic. Methods: Our procedure requires construction of a genetic and a nongenetic domain document corpus. We used MeSH descriptors assigned to MEDLINE citations for this categorization task. We compared frequencies of MeSH descriptors between two corpora applying chi-square test. A MeSH descriptor was considered to be a positive indicator if its relative observed frequency in the genetic domain corpus was greater than its relative observed frequency in the nongenetic domain corpus. The output of the proposed method is a list of scores for all the citations, with the highest score given to those citations containing MeSH descriptors typical for the genetic domain. Results: Validation was done on a set of 734 manually annotated MEDLINE citations. It achieved predictive accuracy of 0.87 with 0.69 recall and 0.64 precision. We evaluated the method by comparing it to three machine learning algorithms (support vector machines, decision trees, na\"ive Bayes). Although the differences were not statistically significantly different, results showed that our chi-square scoring performs as good as compared machine learning algorithms. Conclusions: We suggest that the chi-square scoring is an effective solution to help categorize MEDLINE citations. The algorithm is implemented in the BITOLA literature-based discovery support system as a preprocessor for gene symbol disambiguation process.Comment: 34 pages, 2 figure

Coherent Keyphrase Extraction via Web Mining

Keyphrases are useful for a variety of purposes, including summarizing, indexing, labeling, categorizing, clustering, highlighting, browsing, and searching. The task of automatic keyphrase extraction is to select keyphrases from within the text of a given document. Automatic keyphrase extraction makes it feasible to generate keyphrases for the huge number of documents that do not have manually assigned keyphrases. A limitation of previous keyphrase extraction algorithms is that the selected keyphrases are occasionally incoherent. That is, the majority of the output keyphrases may fit together well, but there may be a minority that appear to be outliers, with no clear semantic relation to the majority or to each other. This paper presents enhancements to the Kea keyphrase extraction algorithm that are designed to increase the coherence of the extracted keyphrases. The approach is to use the degree of statistical association among candidate keyphrases as evidence that they may be semantically related. The statistical association is measured using web mining. Experiments demonstrate that the enhancements improve the quality of the extracted keyphrases. Furthermore, the enhancements are not domain-specific: the algorithm generalizes well when it is trained on one domain (computer science documents) and tested on another (physics documents).Comment: 6 pages, related work available at http://purl.org/peter.turney

Towards the Automatic Classification of Documents in User-generated Classifications

There is a huge amount of information scattered on the World Wide Web. As the information flow occurs at a high speed in the WWW, there is a need to organize it in the right manner so that a user can access it very easily. Previously the organization of information was generally done manually, by matching the document contents to some pre-defined categories. There are two approaches for this text-based categorization: manual and automatic. In the manual approach, a human expert performs the classification task, and in the second case supervised classifiers are used to automatically classify resources. In a supervised classification, manual interaction is required to create some training data before the automatic classification task takes place. In our new approach, we intend to propose automatic classification of documents through semantic keywords and building the formulas generation by these keywords. Thus we can reduce this human participation by combining the knowledge of a given classification and the knowledge extracted from the data. The main focus of this PhD thesis, supervised by Prof. Fausto Giunchiglia, is the automatic classification of documents into user-generated classifications. The key benefits foreseen from this automatic document classification is not only related to search engines, but also to many other fields like, document organization, text filtering, semantic index managing