Large-Scale Online Semantic Indexing of Biomedical Articles via an Ensemble of Multi-Label Classification Models

Background: In this paper we present the approaches and methods employed in order to deal with a large scale multi-label semantic indexing task of biomedical papers. This work was mainly implemented within the context of the BioASQ challenge of 2014. Methods: The main contribution of this work is a multi-label ensemble method that incorporates a McNemar statistical significance test in order to validate the combination of the constituent machine learning algorithms. Some secondary contributions include a study on the temporal aspects of the BioASQ corpus (observations apply also to the BioASQ's super-set, the PubMed articles collection) and the proper adaptation of the algorithms used to deal with this challenging classification task. Results: The ensemble method we developed is compared to other approaches in experimental scenarios with subsets of the BioASQ corpus giving positive results. During the BioASQ 2014 challenge we obtained the first place during the first batch and the third in the two following batches. Our success in the BioASQ challenge proved that a fully automated machine-learning approach, which does not implement any heuristics and rule-based approaches, can be highly competitive and outperform other approaches in similar challenging contexts

Incidental or influential? – A decade of using text-mining for citation function classification.

This work looks in depth at several studies that have attempted to automate the process of citation importance classification based on the publications’ full text. We offer a comparison of their individual similarities, strengths and weaknesses. We analyse a range of features that have been previously used in this task. Our experimental results confirm that the number of in-text references are highly predictive of influence. Contrary to the work of Valenzuela et al. (2015), we find abstract similarity one of the most predictive features. Overall, we show that many of the features previously described in literature have been either reported as not particularly predictive, cannot be reproduced based on their existing descriptions or should not be used due to their reliance on external changing evidence. Additionally, we find significant variance in the results provided by the PDF extraction tools used in the pre-processing stages of citation extraction. This has a direct and significant impact on the classification features that rely on this extraction process. Consequently, we discuss challenges and potential improvements in the classification pipeline, provide a critical review of the performance of individual features and address the importance of constructing a large-scale gold-standard reference dataset

A Novel ILP Framework for Summarizing Content with High Lexical Variety

Summarizing content contributed by individuals can be challenging, because people make different lexical choices even when describing the same events. However, there remains a significant need to summarize such content. Examples include the student responses to post-class reflective questions, product reviews, and news articles published by different news agencies related to the same events. High lexical diversity of these documents hinders the system's ability to effectively identify salient content and reduce summary redundancy. In this paper, we overcome this issue by introducing an integer linear programming-based summarization framework. It incorporates a low-rank approximation to the sentence-word co-occurrence matrix to intrinsically group semantically-similar lexical items. We conduct extensive experiments on datasets of student responses, product reviews, and news documents. Our approach compares favorably to a number of extractive baselines as well as a neural abstractive summarization system. The paper finally sheds light on when and why the proposed framework is effective at summarizing content with high lexical variety.Comment: Accepted for publication in the journal of Natural Language Engineering, 201