25,092 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
Collaborative Layer-wise Discriminative Learning in Deep Neural Networks
Intermediate features at different layers of a deep neural network are known
to be discriminative for visual patterns of different complexities. However,
most existing works ignore such cross-layer heterogeneities when classifying
samples of different complexities. For example, if a training sample has
already been correctly classified at a specific layer with high confidence, we
argue that it is unnecessary to enforce rest layers to classify this sample
correctly and a better strategy is to encourage those layers to focus on other
samples.
In this paper, we propose a layer-wise discriminative learning method to
enhance the discriminative capability of a deep network by allowing its layers
to work collaboratively for classification. Towards this target, we introduce
multiple classifiers on top of multiple layers. Each classifier not only tries
to correctly classify the features from its input layer, but also coordinates
with other classifiers to jointly maximize the final classification
performance. Guided by the other companion classifiers, each classifier learns
to concentrate on certain training examples and boosts the overall performance.
Allowing for end-to-end training, our method can be conveniently embedded into
state-of-the-art deep networks. Experiments with multiple popular deep
networks, including Network in Network, GoogLeNet and VGGNet, on scale-various
object classification benchmarks, including CIFAR100, MNIST and ImageNet, and
scene classification benchmarks, including MIT67, SUN397 and Places205,
demonstrate the effectiveness of our method. In addition, we also analyze the
relationship between the proposed method and classical conditional random
fields models.Comment: To appear in ECCV 2016. Maybe subject to minor changes before
camera-ready versio
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VarSight: prioritizing clinically reported variants with binary classification algorithms.
BackgroundWhen applying genomic medicine to a rare disease patient, the primary goal is to identify one or more genomic variants that may explain the patient's phenotypes. Typically, this is done through annotation, filtering, and then prioritization of variants for manual curation. However, prioritization of variants in rare disease patients remains a challenging task due to the high degree of variability in phenotype presentation and molecular source of disease. Thus, methods that can identify and/or prioritize variants to be clinically reported in the presence of such variability are of critical importance.MethodsWe tested the application of classification algorithms that ingest variant annotations along with phenotype information for predicting whether a variant will ultimately be clinically reported and returned to a patient. To test the classifiers, we performed a retrospective study on variants that were clinically reported to 237 patients in the Undiagnosed Diseases Network.ResultsWe treated the classifiers as variant prioritization systems and compared them to four variant prioritization algorithms and two single-measure controls. We showed that the trained classifiers outperformed all other tested methods with the best classifiers ranking 72% of all reported variants and 94% of reported pathogenic variants in the top 20.ConclusionsWe demonstrated how freely available binary classification algorithms can be used to prioritize variants even in the presence of real-world variability. Furthermore, these classifiers outperformed all other tested methods, suggesting that they may be well suited for working with real rare disease patient datasets
User Intent Prediction in Information-seeking Conversations
Conversational assistants are being progressively adopted by the general
population. However, they are not capable of handling complicated
information-seeking tasks that involve multiple turns of information exchange.
Due to the limited communication bandwidth in conversational search, it is
important for conversational assistants to accurately detect and predict user
intent in information-seeking conversations. In this paper, we investigate two
aspects of user intent prediction in an information-seeking setting. First, we
extract features based on the content, structural, and sentiment
characteristics of a given utterance, and use classic machine learning methods
to perform user intent prediction. We then conduct an in-depth feature
importance analysis to identify key features in this prediction task. We find
that structural features contribute most to the prediction performance. Given
this finding, we construct neural classifiers to incorporate context
information and achieve better performance without feature engineering. Our
findings can provide insights into the important factors and effective methods
of user intent prediction in information-seeking conversations.Comment: Accepted to CHIIR 201
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