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1.  Towards generating a patient's timeline: Extracting temporal relationships from clinical notes 
Journal of biomedical informatics  2013;46(0):S40-S47.
Clinical records include both coded and free-text fields that interact to reflect complicated patient stories. The information often covers not only the present medical condition and events experienced by the patient, but also refers to relevant events in the past (such as signs, symptoms, tests or treatments). In order to automatically construct a timeline of these events, we first need to extract the temporal relations between pairs of events or time expressions presented in the clinical notes. We designed separate extraction components for different types of temporal relations, utilizing a novel hybrid system that combines machine learning with a graph-based inference mechanism to extract the temporal links. The temporal graph is a directed graph based on parse tree dependencies of the simplified sentences and frequent pattern clues. We generalized the sentences in order to discover patterns that, given the complexities of natural language, might not be directly discoverable in the original sentences. The proposed hybrid system performance reached an F-measure of 0.63, with precision at 0.76 and recall at 0.54 on the 2012 i2b2 Natural Language Processing corpus for the temporal relation (TLink) extraction task, achieving the highest precision and third highest f-measure among participating teams in the TLink track.
PMCID: PMC3974721  PMID: 24212118
Temporal relation extraction; Clinical text mining; Automatic patient timeline; Natural Language Processing; Machine learning; Temporal graph
2.  Unsupervised gene function extraction using semantic vectors 
Finding gene functions discussed in the literature is an important task of information extraction (IE) from biomedical documents. Automated computational methodologies can significantly reduce the need for manual curation and improve quality of other related IE systems. We propose an open-IE method for the BioCreative IV GO shared task (subtask b), focused on finding gene function terms [Gene Ontology (GO) terms] for different genes in an article. The proposed open-IE approach is based on distributional semantic similarity over the GO terms. The method does not require annotated data for training, which makes it highly generalizable. We achieve an F-measure of 0.26 on the test-set in the official submission for BioCreative-GO shared task, the third highest F-measure among the seven participants in the shared task.
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PMCID: PMC4160099  PMID: 25209025
3.  Overview of the gene ontology task at BioCreative IV 
Gene Ontology (GO) annotation is a common task among model organism databases (MODs) for capturing gene function data from journal articles. It is a time-consuming and labor-intensive task, and is thus often considered as one of the bottlenecks in literature curation. There is a growing need for semiautomated or fully automated GO curation techniques that will help database curators to rapidly and accurately identify gene function information in full-length articles. Despite multiple attempts in the past, few studies have proven to be useful with regard to assisting real-world GO curation. The shortage of sentence-level training data and opportunities for interaction between text-mining developers and GO curators has limited the advances in algorithm development and corresponding use in practical circumstances. To this end, we organized a text-mining challenge task for literature-based GO annotation in BioCreative IV. More specifically, we developed two subtasks: (i) to automatically locate text passages that contain GO-relevant information (a text retrieval task) and (ii) to automatically identify relevant GO terms for the genes in a given article (a concept-recognition task). With the support from five MODs, we provided teams with >4000 unique text passages that served as the basis for each GO annotation in our task data. Such evidence text information has long been recognized as critical for text-mining algorithm development but was never made available because of the high cost of curation. In total, seven teams participated in the challenge task. From the team results, we conclude that the state of the art in automatically mining GO terms from literature has improved over the past decade while much progress is still needed for computer-assisted GO curation. Future work should focus on addressing remaining technical challenges for improved performance of automatic GO concept recognition and incorporating practical benefits of text-mining tools into real-world GO annotation.
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PMCID: PMC4142793  PMID: 25157073

Results 1-3 (3)