Classifying document types to enhance search and recommendations in digital libraries

In this paper, we address the problem of classifying documents available from the global network of (open access) repositories according to their type. We show that the metadata provided by repositories enabling us to distinguish research papers, thesis and slides are missing in over 60% of cases. While these metadata describing document types are useful in a variety of scenarios ranging from research analytics to improving search and recommender (SR) systems, this problem has not yet been sufficiently addressed in the context of the repositories infrastructure. We have developed a new approach for classifying document types using supervised machine learning based exclusively on text specific features. We achieve 0.96 F1-score using the random forest and Adaboost classifiers, which are the best performing models on our data. By analysing the SR system logs of the CORE [1] digital library aggregator, we show that users are an order of magnitude more likely to click on research papers and thesis than on slides. This suggests that using document types as a feature for ranking/filtering SR results in digital libraries has the potential to improve user experience.Comment: 12 pages, 21st International Conference on Theory and Practise of Digital Libraries (TPDL), 2017, Thessaloniki, Greec

Clustering More than Two Million Biomedical Publications: Comparing the Accuracies of Nine Text-Based Similarity Approaches

We investigate the accuracy of different similarity approaches for clustering over two million biomedical documents. Clustering large sets of text documents is important for a variety of information needs and applications such as collection management and navigation, summary and analysis. The few comparisons of clustering results from different similarity approaches have focused on small literature sets and have given conflicting results. Our study was designed to seek a robust answer to the question of which similarity approach would generate the most coherent clusters of a biomedical literature set of over two million documents.We used a corpus of 2.15 million recent (2004-2008) records from MEDLINE, and generated nine different document-document similarity matrices from information extracted from their bibliographic records, including titles, abstracts and subject headings. The nine approaches were comprised of five different analytical techniques with two data sources. The five analytical techniques are cosine similarity using term frequency-inverse document frequency vectors (tf-idf cosine), latent semantic analysis (LSA), topic modeling, and two Poisson-based language models--BM25 and PMRA (PubMed Related Articles). The two data sources were a) MeSH subject headings, and b) words from titles and abstracts. Each similarity matrix was filtered to keep the top-n highest similarities per document and then clustered using a combination of graph layout and average-link clustering. Cluster results from the nine similarity approaches were compared using (1) within-cluster textual coherence based on the Jensen-Shannon divergence, and (2) two concentration measures based on grant-to-article linkages indexed in MEDLINE.PubMed's own related article approach (PMRA) generated the most coherent and most concentrated cluster solution of the nine text-based similarity approaches tested, followed closely by the BM25 approach using titles and abstracts. Approaches using only MeSH subject headings were not competitive with those based on titles and abstracts

Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio

A Comparison of Citation Metrics to Machine Learning Filters for the Identification of High Quality MEDLINE Documents

OBJECTIVE: The present study explores the discriminatory performance of existing and novel gold-standard-specific machine learning (GSS-ML) focused filter models (i.e., models built specifically for a retrieval task and a gold standard against which they are evaluated) and compares their performance to citation count and impact factors, and non-specific machine learning (NS-ML) models (i.e., models built for a different task and/or different gold standard). DESIGN: Three gold standard corpora were constructed using the SSOAB bibliography, the ACPJ-cited treatment articles, and the ACPJ-cited etiology articles. Citation counts and impact factors were obtained for each article. Support vector machine models were used to classify the articles using combinations of content, impact factors, and citation counts as predictors. MEASUREMENTS: Discriminatory performance was estimated using the area under the receiver operating characteristic curve and n-fold cross-validation. RESULTS: For all three gold standards and tasks, GSS-ML filters outperformed citation count, impact factors, and NS-ML filters. Combinations of content with impact factor or citation count produced no or negligible improvements to the GSS machine learning filters. CONCLUSIONS: These experiments provide evidence that when building information retrieval filters focused on a retrieval task and corresponding gold standard, the filter models have to be built specifically for this task and gold standard. Under those conditions, machine learning filters outperform standard citation metrics. Furthermore, citation counts and impact factors add marginal value to discriminatory performance. Previous research that claimed better performance of citation metrics than machine learning in one of the corpora examined here is attributed to using machine learning filters built for a different gold standard and task