A Linear Classifier Based on Entity Recognition Tools and a Statistical Approach to Method Extraction in the Protein-Protein Interaction Literature

We participated, in the Article Classification and the Interaction Method subtasks (ACT and IMT, respectively) of the Protein-Protein Interaction task of the BioCreative III Challenge. For the ACT, we pursued an extensive testing of available Named Entity Recognition and dictionary tools, and used the most promising ones to extend our Variable Trigonometric Threshold linear classifier. For the IMT, we experimented with a primarily statistical approach, as opposed to employing a deeper natural language processing strategy. Finally, we also studied the benefits of integrating the method extraction approach that we have used for the IMT into the ACT pipeline. For the ACT, our linear article classifier leads to a ranking and classification performance significantly higher than all the reported submissions. For the IMT, our results are comparable to those of other systems, which took very different approaches. For the ACT, we show that the use of named entity recognition tools leads to a substantial improvement in the ranking and classification of articles relevant to protein-protein interaction. Thus, we show that our substantially expanded linear classifier is a very competitive classifier in this domain. Moreover, this classifier produces interpretable surfaces that can be understood as "rules" for human understanding of the classification. In terms of the IMT task, in contrast to other participants, our approach focused on identifying sentences that are likely to bear evidence for the application of a PPI detection method, rather than on classifying a document as relevant to a method. As BioCreative III did not perform an evaluation of the evidence provided by the system, we have conducted a separate assessment; the evaluators agree that our tool is indeed effective in detecting relevant evidence for PPI detection methods.Comment: BMC Bioinformatics. In Pres

The Expressive Power of Word Embeddings

We seek to better understand the difference in quality of the several publicly released embeddings. We propose several tasks that help to distinguish the characteristics of different embeddings. Our evaluation of sentiment polarity and synonym/antonym relations shows that embeddings are able to capture surprisingly nuanced semantics even in the absence of sentence structure. Moreover, benchmarking the embeddings shows great variance in quality and characteristics of the semantics captured by the tested embeddings. Finally, we show the impact of varying the number of dimensions and the resolution of each dimension on the effective useful features captured by the embedding space. Our contributions highlight the importance of embeddings for NLP tasks and the effect of their quality on the final results.Comment: submitted to ICML 2013, Deep Learning for Audio, Speech and Language Processing Workshop. 8 pages, 8 figure

SemEval 2017 Task 10: ScienceIE - Extracting Keyphrases and Relations from Scientific Publications

We describe the SemEval task of extracting keyphrases and relations between them from scientific documents, which is crucial for understanding which publications describe which processes, tasks and materials. Although this was a new task, we had a total of 26 submissions across 3 evaluation scenarios. We expect the task and the findings reported in this paper to be relevant for researchers working on understanding scientific content, as well as the broader knowledge base population and information extraction communities

Methodologies for the Automatic Location of Academic and Educational Texts on the Internet

Traditionally online databases of web resources have been compiled by a human editor, or though the submissions of authors or interested parties. Considerable resources are needed to maintain a constant level of input and relevance in the face of increasing material quantity and quality, and much of what is in databases is of an ephemeral nature. These pressures dictate that many databases stagnate after an initial period of enthusiastic data entry. The solution to this problem would seem to be the automatic harvesting of resources, however, this process necessitates the automatic classification of resources as ‘appropriate’ to a given database, a problem only solved by complex text content analysis. This paper outlines the component methodologies necessary to construct such an automated harvesting system, including a number of novel approaches. In particular this paper looks at the specific problems of automatically identifying academic research work and Higher Education pedagogic materials. Where appropriate, experimental data is presented from searches in the field of Geography as well as the Earth and Environmental Sciences. In addition, appropriate software is reviewed where it exists, and future directions are outlined

Methodologies for the Automatic Location of Academic and Educational Texts on the Internet

Traditionally online databases of web resources have been compiled by a human editor, or though the submissions of authors or interested parties. Considerable resources are needed to maintain a constant level of input and relevance in the face of increasing material quantity and quality, and much of what is in databases is of an ephemeral nature. These pressures dictate that many databases stagnate after an initial period of enthusiastic data entry. The solution to this problem would seem to be the automatic harvesting of resources, however, this process necessitates the automatic classification of resources as ‘appropriate’ to a given database, a problem only solved by complex text content analysis. This paper outlines the component methodologies necessary to construct such an automated harvesting system, including a number of novel approaches. In particular this paper looks at the specific problems of automatically identifying academic research work and Higher Education pedagogic materials. Where appropriate, experimental data is presented from searches in the field of Geography as well as the Earth and Environmental Sciences. In addition, appropriate software is reviewed where it exists, and future directions are outlined