Annotating Named Entities in Consumer Health Questions
Halil Kilicoglu | Asma Ben Abacha | Yassine Mrabet | Kirk Roberts | Laritza Rodriguez | Sonya Shooshan | Dina Demner-Fushman
Proceedings of the Tenth International Conference on Language Resources and Evaluation (LREC'16)
We describe a corpus of consumer health questions annotated with named entities. The corpus consists of 1548 de-identified questions about diseases and drugs, written in English. We defined 15 broad categories of biomedical named entities for annotation. A pilot annotation phase in which a small portion of the corpus was double-annotated by four annotators was followed by a main phase in which double annotation was carried out by six annotators, and a reconciliation phase in which all annotations were reconciled by an expert. We conducted the annotation in two modes, manual and assisted, to assess the effect of automatic pre-annotation and calculated inter-annotator agreement. We obtained moderate inter-annotator agreement; assisted annotation yielded slightly better agreement and fewer missed annotations than manual annotation. Due to complex nature of biomedical entities, we paid particular attention to nested entities for which we obtained slightly lower inter-annotator agreement, confirming that annotating nested entities is somewhat more challenging. To our knowledge, the corpus is the first of its kind for consumer health text and is publicly available.
A Hybrid Approach to Generation of Missing Abstracts in Biomedical Literature
Suchet Chachra | Asma Ben Abacha | Sonya Shooshan | Laritza Rodriguez | Dina Demner-Fushman
Proceedings of COLING 2016, the 26th International Conference on Computational Linguistics: Technical Papers
Readers usually rely on abstracts to identify relevant medical information from scientific articles. Abstracts are also essential to advanced information retrieval methods. More than 50 thousand scientific publications in PubMed lack author-generated abstracts, and the relevancy judgements for these papers have to be based on their titles alone. In this paper, we propose a hybrid summarization technique that aims to select the most pertinent sentences from articles to generate an extractive summary in lieu of a missing abstract. We combine i) health outcome detection, ii) keyphrase extraction, and iii) textual entailment recognition between sentences. We evaluate our hybrid approach and analyze the improvements of multi-factor summarization over techniques that rely on a single method, using a collection of 295 manually generated reference summaries. The obtained results show that the hybrid approach outperforms the baseline techniques with an improvement of 13% in recall and 4% in F1 score.
Automatic inference of indexing rules for MEDLINE
Aurélie Névéol | Sonya Shooshan | Vincent Claveau
Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
- Asma Ben Abacha 2
- Laritza Rodriguez 2
- Dina Demner-Fushman 2
- Halil Kilicoglu 1
- Yassine M’rabet 1
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