27,919 research outputs found
EliXR-TIME: A Temporal Knowledge Representation for Clinical Research Eligibility Criteria.
Effective clinical text processing requires accurate extraction and representation of temporal expressions. Multiple temporal information extraction models were developed but a similar need for extracting temporal expressions in eligibility criteria (e.g., for eligibility determination) remains. We identified the temporal knowledge representation requirements of eligibility criteria by reviewing 100 temporal criteria. We developed EliXR-TIME, a frame-based representation designed to support semantic annotation for temporal expressions in eligibility criteria by reusing applicable classes from well-known clinical temporal knowledge representations. We used EliXR-TIME to analyze a training set of 50 new temporal eligibility criteria. We evaluated EliXR-TIME using an additional random sample of 20 eligibility criteria with temporal expressions that have no overlap with the training data, yielding 92.7% (76 / 82) inter-coder agreement on sentence chunking and 72% (72 / 100) agreement on semantic annotation. We conclude that this knowledge representation can facilitate semantic annotation of the temporal expressions in eligibility criteria
Extracting Biomolecular Interactions Using Semantic Parsing of Biomedical Text
We advance the state of the art in biomolecular interaction extraction with
three contributions: (i) We show that deep, Abstract Meaning Representations
(AMR) significantly improve the accuracy of a biomolecular interaction
extraction system when compared to a baseline that relies solely on surface-
and syntax-based features; (ii) In contrast with previous approaches that infer
relations on a sentence-by-sentence basis, we expand our framework to enable
consistent predictions over sets of sentences (documents); (iii) We further
modify and expand a graph kernel learning framework to enable concurrent
exploitation of automatically induced AMR (semantic) and dependency structure
(syntactic) representations. Our experiments show that our approach yields
interaction extraction systems that are more robust in environments where there
is a significant mismatch between training and test conditions.Comment: Appearing in Proceedings of the Thirtieth AAAI Conference on
Artificial Intelligence (AAAI-16
Kernelized Hashcode Representations for Relation Extraction
Kernel methods have produced state-of-the-art results for a number of NLP
tasks such as relation extraction, but suffer from poor scalability due to the
high cost of computing kernel similarities between natural language structures.
A recently proposed technique, kernelized locality-sensitive hashing (KLSH),
can significantly reduce the computational cost, but is only applicable to
classifiers operating on kNN graphs. Here we propose to use random subspaces of
KLSH codes for efficiently constructing an explicit representation of NLP
structures suitable for general classification methods. Further, we propose an
approach for optimizing the KLSH model for classification problems by
maximizing an approximation of mutual information between the KLSH codes
(feature vectors) and the class labels. We evaluate the proposed approach on
biomedical relation extraction datasets, and observe significant and robust
improvements in accuracy w.r.t. state-of-the-art classifiers, along with
drastic (orders-of-magnitude) speedup compared to conventional kernel methods.Comment: To appear in the proceedings of conference, AAAI-1
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