23,834 research outputs found
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
Multi-Target Prediction: A Unifying View on Problems and Methods
Multi-target prediction (MTP) is concerned with the simultaneous prediction
of multiple target variables of diverse type. Due to its enormous application
potential, it has developed into an active and rapidly expanding research field
that combines several subfields of machine learning, including multivariate
regression, multi-label classification, multi-task learning, dyadic prediction,
zero-shot learning, network inference, and matrix completion. In this paper, we
present a unifying view on MTP problems and methods. First, we formally discuss
commonalities and differences between existing MTP problems. To this end, we
introduce a general framework that covers the above subfields as special cases.
As a second contribution, we provide a structured overview of MTP methods. This
is accomplished by identifying a number of key properties, which distinguish
such methods and determine their suitability for different types of problems.
Finally, we also discuss a few challenges for future research
Constructing Datasets for Multi-hop Reading Comprehension Across Documents
Most Reading Comprehension methods limit themselves to queries which can be
answered using a single sentence, paragraph, or document. Enabling models to
combine disjoint pieces of textual evidence would extend the scope of machine
comprehension methods, but currently there exist no resources to train and test
this capability. We propose a novel task to encourage the development of models
for text understanding across multiple documents and to investigate the limits
of existing methods. In our task, a model learns to seek and combine evidence -
effectively performing multi-hop (alias multi-step) inference. We devise a
methodology to produce datasets for this task, given a collection of
query-answer pairs and thematically linked documents. Two datasets from
different domains are induced, and we identify potential pitfalls and devise
circumvention strategies. We evaluate two previously proposed competitive
models and find that one can integrate information across documents. However,
both models struggle to select relevant information, as providing documents
guaranteed to be relevant greatly improves their performance. While the models
outperform several strong baselines, their best accuracy reaches 42.9% compared
to human performance at 74.0% - leaving ample room for improvement.Comment: This paper directly corresponds to the TACL version
(https://transacl.org/ojs/index.php/tacl/article/view/1325) apart from minor
changes in wording, additional footnotes, and appendice
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