MOTIVATION: Ontologies are widely used in biology for data annotation, integration and analysis. In addition to formally structured axioms, ontologies contain meta-data in the form of annotation axioms which provide valuable pieces of information tha...
Mathematical biosciences and engineering : MBE
Mar 8, 2019
Automatically identifying semantic concepts from medical images provides multimodal insights for clinical research. To study the effectiveness of concept detection on large scale medical images, we reconstructed over 230,000 medical image-concepts pa...
Database : the journal of biological databases and curation
Jan 1, 2019
We investigate the application of deep learning to biocuration tasks that involve classification of text associated with biomedical evidence in primary research articles. We developed a large-scale corpus of molecular papers derived from PubMed and P...
Scientists striving for impact in their fields and to develop their own careers must publish papers that represent new and important science, typically in a peer-reviewed journal. The number of scientific articles published has doubled every nine yea...
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Jan 1, 2019
Biomedical association studies are increasingly done using clinical concepts, and in particular diagnostic codes from clinical data repositories as phenotypes. Clinical concepts can be represented in a meaningful, vector space using word embedding mo...
Journal of experimental psychology. General
Jan 1, 2019
Whereas numerous findings support a distinction between episodic and semantic memory, it is now widely acknowledged that these two forms of memory interact during both encoding and retrieval. The precise nature of this interaction, however, remains p...
Journal of the American Medical Informatics Association : JAMIA
Oct 1, 2018
OBJECTIVE: The aim of this work is to leverage relational information extracted from biomedical literature using a novel synthesis of unsupervised pretraining, representational composition, and supervised machine learning for drug safety monitoring.
How to read Uyghur text from biomedical graphic images is a challenge problem due to the complex layout and cursive writing of Uyghur. In this paper, we propose a system that extracts text from Uyghur biomedical images, and matches the text in a spec...
MOTIVATION: Biological knowledge is widely represented in the form of ontology-based annotations: ontologies describe the phenomena assumed to exist within a domain, and the annotations associate a (kind of) biological entity with a set of phenomena ...
Journal of the American Medical Informatics Association : JAMIA
Jun 1, 2018
OBJECTIVE: Distributional semantics algorithms, which learn vector space representations of words and phrases from large corpora, identify related terms based on contextual usage patterns. We hypothesize that distributional semantics can speed up lex...
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