BackgroundThis article provides an overview of the first BioASQ challenge, a competition on large-scale biomedical semantic indexing and question answering (QA), which took place between March and September 2013. BioASQ assesses the ability of systems to semantically index very large numbers of biomedical scientific articles, and to return concise and user-understandable answers to given natural language questions by combining information from biomedical articles and ontologies.ResultsThe 2013 BioASQ competition comprised two tasks, Task 1a and Task 1b. In Task 1a participants were asked to automatically annotate new PubMed documents with MeSH headings. Twelve teams participated in Task 1a, with a total of 46 system runs submitted, and one of the teams performing consistently better than the MTI indexer used by NLM to suggest MeSH headings to curators. Task 1b used benchmark datasets containing 29 development and 282 test English questions, along with gold standard (reference) answers, prepared by a team of biomedical experts from around Europe and participants had to automatically produce answers. Three teams participated in Task 1b, with 11 system runs. The BioASQ infrastructure, including benchmark datasets, evaluation mechanisms, and the results of the participants and baseline methods, is publicly available.ConclusionsA publicly available evaluation infrastructure for biomedical semantic indexing and QA has been developed, which includes benchmark datasets, and can be used to evaluate systems that: assign MeSH headings to published articles or to English questions; retrieve relevant RDF triples from ontologies, relevant articles and snippets from PubMed Central; produce “exact” and paragraph-sized “ideal” answers (summaries). The results of the systems that participated in the 2013 BioASQ competition are promising. In Task 1a one of the systems performed consistently better from the NLM’s MTI indexer. In Task 1b the systems received high scores in the manual evaluation of the “ideal” answers; hence, they produced high quality summaries as answers. Overall, BioASQ helped obtain a unified view of how techniques from text classification, semantic indexing, document and passage retrieval, question answering, and text summarization can be combined to allow biomedical experts to obtain concise, user-understandable answers to questions reflecting their real information needs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0564-6) contains supplementary material, which is available to authorized users.

Probabilistic topic models are generative models that describe the content of documents by discovering the latent topics underlying them. However, the structure of the textual input, and for instance the grouping of words in coherent text spans such as sentences, contains much information which is generally lost with these models. In this paper, we propose sentenceLDA, an extension of LDA whose goal is to overcome this limitation by incorporating the structure of the text in the generative and inference processes. We illustrate the advantages of sentenceLDA by comparing it with LDA using both intrinsic (perplexity) and extrinsic (text classification) evaluation tasks on different text collections.

This paper describes the participation of the team "TwiSE" in the SemEval 2016 challenge.Specifically, we participated in Task 4, namely "Sentiment Analysis in Twitter" for which we implemented sentiment classification systems for subtasks A, B, C and D. Our approach consists of two steps. In the first step, we generate and validate diverse feature sets for twitter sentiment evaluation, inspired by the work of participants of previous editions of such challenges. In the second step, we focus on the optimization of the evaluation measures of the different subtasks. To this end, we examine different learning strategies by validating them on the data provided by the task organisers. For our final submissions we used an ensemble learning approach (stacked generalization) for Subtask A and single linear models for the rest of the subtasks. In the official leaderboard we were ranked 9/35, 8/19, 1/11 and 2/14 for subtasks A, B, C and D respectively. The code can be found at https://github.com/ balikasg/SemEval2016-Twitter_ Sentiment_Evaluation.

This article provides an overview of BIOASQ, a new competition on biomedical semantic indexing and question answering (QA). BIOASQ aims to push towards systems that will allow biomedical workers to express their information needs in natural language and that will return concise and user-understandable answers by combining information from multiple sources of different kinds, including biomedical articles, databases, and ontologies. BIOASQ encourages participants to adopt semantic indexing as a means to combine multiple information sources and to facilitate the matching of questions to answers. It also adopts a broad semantic indexing and QA architecture that subsumes current relevant approaches, even though no current system instantiates all of its components. Hence, the architecture can also be seen as our view of how relevant work from fields such as information retrieval, hierarchical classification, question answering, ontologies, and linked data can be combined, extended, and applied to biomedical question answering. BIOASQ will develop publicly available benchmarks and it will adopt and possibly refine existing evaluation measures. The evaluation infrastructure of the competition will remain publicly available beyond the end of BIOASQ.

Traditional sentiment analysis approaches tackle problems like ternary (3-category) and finegrained (5-category) classification by learning the tasks separately. We argue that such classification tasks are correlated and we propose a multitask approach based on a recurrent neural network that benefits by jointly learning them. Our study demonstrates the potential of multitask models on this type of problems and improves the state-of-the-art results in the fine-grained sentiment classification problem.