48,894 research outputs found
A Relation Extraction Approach for Clinical Decision Support
In this paper, we investigate how semantic relations between concepts
extracted from medical documents can be employed to improve the retrieval of
medical literature. Semantic relations explicitly represent relatedness between
concepts and carry high informative power that can be leveraged to improve the
effectiveness of retrieval functionalities of clinical decision support
systems. We present preliminary results and show how relations are able to
provide a sizable increase of the precision for several topics, albeit having
no impact on others. We then discuss some future directions to minimize the
impact of negative results while maximizing the impact of good results.Comment: 4 pages, 1 figure, DTMBio-KMH 2018, in conjunction with ACM 27th
Conference on Information and Knowledge Management (CIKM), October 22-26
2018, Lingotto, Turin, Ital
Entity Query Feature Expansion Using Knowledge Base Links
Recent advances in automatic entity linking and knowledge base
construction have resulted in entity annotations for document and
query collections. For example, annotations of entities from large
general purpose knowledge bases, such as Freebase and the Google
Knowledge Graph. Understanding how to leverage these entity
annotations of text to improve ad hoc document retrieval is an open
research area. Query expansion is a commonly used technique to
improve retrieval effectiveness. Most previous query expansion
approaches focus on text, mainly using unigram concepts. In this
paper, we propose a new technique, called entity query feature
expansion (EQFE) which enriches the query with features from
entities and their links to knowledge bases, including structured
attributes and text. We experiment using both explicit query entity
annotations and latent entities. We evaluate our technique on TREC
text collections automatically annotated with knowledge base entity
links, including the Google Freebase Annotations (FACC1) data.
We find that entity-based feature expansion results in significant
improvements in retrieval effectiveness over state-of-the-art text
expansion approaches
Conceptual biology, hypothesis discovery, and text mining: Swanson's legacy
Innovative biomedical librarians and information specialists who want to expand their roles as expert searchers need to know about profound changes in biology and parallel trends in text mining. In recent years, conceptual biology has emerged as a complement to empirical biology. This is partly in response to the availability of massive digital resources such as the network of databases for molecular biologists at the National Center for Biotechnology Information. Developments in text mining and hypothesis discovery systems based on the early work of Swanson, a mathematician and information scientist, are coincident with the emergence of conceptual biology. Very little has been written to introduce biomedical digital librarians to these new trends. In this paper, background for data and text mining, as well as for knowledge discovery in databases (KDD) and in text (KDT) is presented, then a brief review of Swanson's ideas, followed by a discussion of recent approaches to hypothesis discovery and testing. 'Testing' in the context of text mining involves partially automated methods for finding evidence in the literature to support hypothetical relationships. Concluding remarks follow regarding (a) the limits of current strategies for evaluation of hypothesis discovery systems and (b) the role of literature-based discovery in concert with empirical research. Report of an informatics-driven literature review for biomarkers of systemic lupus erythematosus is mentioned. Swanson's vision of the hidden value in the literature of science and, by extension, in biomedical digital databases, is still remarkably generative for information scientists, biologists, and physicians. © 2006Bekhuis; licensee BioMed Central Ltd
MAG: A Multilingual, Knowledge-base Agnostic and Deterministic Entity Linking Approach
Entity linking has recently been the subject of a significant body of
research. Currently, the best performing approaches rely on trained
mono-lingual models. Porting these approaches to other languages is
consequently a difficult endeavor as it requires corresponding training data
and retraining of the models. We address this drawback by presenting a novel
multilingual, knowledge-based agnostic and deterministic approach to entity
linking, dubbed MAG. MAG is based on a combination of context-based retrieval
on structured knowledge bases and graph algorithms. We evaluate MAG on 23 data
sets and in 7 languages. Our results show that the best approach trained on
English datasets (PBOH) achieves a micro F-measure that is up to 4 times worse
on datasets in other languages. MAG, on the other hand, achieves
state-of-the-art performance on English datasets and reaches a micro F-measure
that is up to 0.6 higher than that of PBOH on non-English languages.Comment: Accepted in K-CAP 2017: Knowledge Capture Conferenc
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
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