12,639 research outputs found
Introduction to the CoNLL-2003 Shared Task: Language-Independent Named Entity Recognition
We describe the CoNLL-2003 shared task: language-independent named entity
recognition. We give background information on the data sets (English and
German) and the evaluation method, present a general overview of the systems
that have taken part in the task and discuss their performance
Introduction to the CoNLL-2002 Shared Task: Language-Independent Named Entity Recognition
We describe the CoNLL-2002 shared task: language-independent named entity
recognition. We give background information on the data sets and the evaluation
method, present a general overview of the systems that have taken part in the
task and discuss their performance.Comment: 4 page
Evaluation of linear classifiers on articles containing pharmacokinetic evidence of drug-drug interactions
Background. Drug-drug interaction (DDI) is a major cause of morbidity and
mortality. [...] Biomedical literature mining can aid DDI research by
extracting relevant DDI signals from either the published literature or large
clinical databases. However, though drug interaction is an ideal area for
translational research, the inclusion of literature mining methodologies in DDI
workflows is still very preliminary. One area that can benefit from literature
mining is the automatic identification of a large number of potential DDIs,
whose pharmacological mechanisms and clinical significance can then be studied
via in vitro pharmacology and in populo pharmaco-epidemiology. Experiments. We
implemented a set of classifiers for identifying published articles relevant to
experimental pharmacokinetic DDI evidence. These documents are important for
identifying causal mechanisms behind putative drug-drug interactions, an
important step in the extraction of large numbers of potential DDIs. We
evaluate performance of several linear classifiers on PubMed abstracts, under
different feature transformation and dimensionality reduction methods. In
addition, we investigate the performance benefits of including various
publicly-available named entity recognition features, as well as a set of
internally-developed pharmacokinetic dictionaries. Results. We found that
several classifiers performed well in distinguishing relevant and irrelevant
abstracts. We found that the combination of unigram and bigram textual features
gave better performance than unigram features alone, and also that
normalization transforms that adjusted for feature frequency and document
length improved classification. For some classifiers, such as linear
discriminant analysis (LDA), proper dimensionality reduction had a large impact
on performance. Finally, the inclusion of NER features and dictionaries was
found not to help classification.Comment: Pacific Symposium on Biocomputing, 201
Extracting adverse drug reactions and their context using sequence labelling ensembles in TAC2017
Adverse drug reactions (ADRs) are unwanted or harmful effects experienced
after the administration of a certain drug or a combination of drugs,
presenting a challenge for drug development and drug administration. In this
paper, we present a set of taggers for extracting adverse drug reactions and
related entities, including factors, severity, negations, drug class and
animal. The systems used a mix of rule-based, machine learning (CRF) and deep
learning (BLSTM with word2vec embeddings) methodologies in order to annotate
the data. The systems were submitted to adverse drug reaction shared task,
organised during Text Analytics Conference in 2017 by National Institute for
Standards and Technology, archiving F1-scores of 76.00 and 75.61 respectively.Comment: Paper describing submission for TAC ADR shared tas
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