25,039 research outputs found
Using Neural Networks for Relation Extraction from Biomedical Literature
Using different sources of information to support automated extracting of
relations between biomedical concepts contributes to the development of our
understanding of biological systems. The primary comprehensive source of these
relations is biomedical literature. Several relation extraction approaches have
been proposed to identify relations between concepts in biomedical literature,
namely, using neural networks algorithms. The use of multichannel architectures
composed of multiple data representations, as in deep neural networks, is
leading to state-of-the-art results. The right combination of data
representations can eventually lead us to even higher evaluation scores in
relation extraction tasks. Thus, biomedical ontologies play a fundamental role
by providing semantic and ancestry information about an entity. The
incorporation of biomedical ontologies has already been proved to enhance
previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1
A text-mining system for extracting metabolic reactions from full-text articles
Background: Increasingly biological text mining research is focusing on the extraction of complex relationships
relevant to the construction and curation of biological networks and pathways. However, one important category of
pathwayâmetabolic pathwaysâhas been largely neglected.
Here we present a relatively simple method for extracting metabolic reaction information from free text that scores
different permutations of assigned entities (enzymes and metabolites) within a given sentence based on the presence
and location of stemmed keywords. This method extends an approach that has proved effective in the context of the
extraction of proteinâprotein interactions.
Results: When evaluated on a set of manually-curated metabolic pathways using standard performance criteria, our
method performs surprisingly well. Precision and recall rates are comparable to those previously achieved for the
well-known protein-protein interaction extraction task.
Conclusions: We conclude that automated metabolic pathway construction is more tractable than has often been
assumed, and that (as in the case of proteinâprotein interaction extraction) relatively simple text-mining approaches can prove surprisingly effective. It is hoped that these results will provide an impetus to further research and act as a useful benchmark for judging the performance of more sophisticated methods that are yet to be developed
The Materials Science Procedural Text Corpus: Annotating Materials Synthesis Procedures with Shallow Semantic Structures
Materials science literature contains millions of materials synthesis
procedures described in unstructured natural language text. Large-scale
analysis of these synthesis procedures would facilitate deeper scientific
understanding of materials synthesis and enable automated synthesis planning.
Such analysis requires extracting structured representations of synthesis
procedures from the raw text as a first step. To facilitate the training and
evaluation of synthesis extraction models, we introduce a dataset of 230
synthesis procedures annotated by domain experts with labeled graphs that
express the semantics of the synthesis sentences. The nodes in this graph are
synthesis operations and their typed arguments, and labeled edges specify
relations between the nodes. We describe this new resource in detail and
highlight some specific challenges to annotating scientific text with shallow
semantic structure. We make the corpus available to the community to promote
further research and development of scientific information extraction systems.Comment: Accepted as a long paper at the Linguistic Annotation Workshop (LAW)
at ACL 201
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