An Approach to Reducing Annotation Costs for BioNLP

There is a broad range of BioNLP tasks for which active learning (AL) can significantly reduce annotation costs and a specific AL algorithm we have developed is particularly effective in reducing annotation costs for these tasks. We have previously developed an AL algorithm called ClosestInitPA that works best with tasks that have the following characteristics: redundancy in training material, burdensome annotation costs, Support Vector Machines (SVMs) work well for the task, and imbalanced datasets (i.e. when set up as a binary classification problem, one class is substantially rarer than the other). Many BioNLP tasks have these characteristics and thus our AL algorithm is a natural approach to apply to BioNLP tasks

Biomedical event extraction from abstracts and full papers using search-based structured prediction.

BACKGROUND: Biomedical event extraction has attracted substantial attention as it can assist researchers in understanding the plethora of interactions among genes that are described in publications in molecular biology. While most recent work has focused on abstracts, the BioNLP 2011 shared task evaluated the submitted systems on both abstracts and full papers. In this article, we describe our submission to the shared task which decomposes event extraction into a set of classification tasks that can be learned either independently or jointly using the search-based structured prediction framework. Our intention is to explore how these two learning paradigms compare in the context of the shared task. RESULTS: We report that models learned using search-based structured prediction exceed the accuracy of independently learned classifiers by 8.3 points in F-score, with the gains being more pronounced on the more complex Regulation events (13.23 points). Furthermore, we show how the trade-off between recall and precision can be adjusted in both learning paradigms and that search-based structured prediction achieves better recall at all precision points. Finally, we report on experiments with a simple domain-adaptation method, resulting in the second-best performance achieved by a single system. CONCLUSIONS: We demonstrate that joint inference using the search-based structured prediction framework can achieve better performance than independently learned classifiers, thus demonstrating the potential of this learning paradigm for event extraction and other similarly complex information-extraction tasks.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Boosting Drug Named Entity Recognition using an Aggregate Classifier

AbstractObjectiveDrug named entity recognition (NER) is a critical step for complex biomedical NLP tasks such as the extraction of pharmacogenomic, pharmacodynamic and pharmacokinetic parameters. Large quantities of high quality training data are almost always a prerequisite for employing supervised machine-learning techniques to achieve high classification performance. However, the human labour needed to produce and maintain such resources is a significant limitation. In this study, we improve the performance of drug NER without relying exclusively on manual annotations.MethodsWe perform drug NER using either a small gold-standard corpus (120 abstracts) or no corpus at all. In our approach, we develop a voting system to combine a number of heterogeneous models, based on dictionary knowledge, gold-standard corpora and silver annotations, to enhance performance. To improve recall, we employed genetic programming to evolve 11 regular-expression patterns that capture common drug suffixes and used them as an extra means for recognition.MaterialsOur approach uses a dictionary of drug names, i.e. DrugBank, a small manually annotated corpus, i.e. the pharmacokinetic corpus, and a part of the UKPMC database, as raw biomedical text. Gold-standard and silver annotated data are used to train maximum entropy and multinomial logistic regression classifiers.ResultsAggregating drug NER methods, based on gold-standard annotations, dictionary knowledge and patterns, improved the performance on models trained on gold-standard annotations, only, achieving a maximum F-score of 95%. In addition, combining models trained on silver annotations, dictionary knowledge and patterns are shown to achieve comparable performance to models trained exclusively on gold-standard data. The main reason appears to be the morphological similarities shared among drug names.ConclusionWe conclude that gold-standard data are not a hard requirement for drug NER. Combining heterogeneous models build on dictionary knowledge can achieve similar or comparable classification performance with that of the best performing model trained on gold-standard annotations