Browsing by Subject "Text-mining"

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    Identify Opiod Use Problem
    (2018-12) Alzeer, Abdullah Hamad; Jones, Josette; Dixon, Brian; Bair, Matthew; Liu, Xiaowen
    The aim of this research is to design a new method to identify the opioid use problems (OUP) among long-term opioid therapy patients in Indiana University Health using text mining and machine learning approaches. First, a systematic review was conducted to investigate the current variables, methods, and opioid problem definitions used in the literature. We identified 75 distinct variables in 9 models that majorly used ICD codes to identify the opioid problem (OUP). The review concluded that using ICD codes alone may not be enough to determine the real size of the opioid problem and more effort is needed to adopt other methods to understand the issue. Next, we developed a text mining approach to identify OUP and compared the results with the current conventional method of identifying OUP using ICD-9 codes. Following the institutional review board and an approval from the Regenstrief Institute, structured and unstructured data of 14,298 IUH patients were collected from the Indiana Network for Patient Care. Our text mining approach identified 127 opioid cases compared to 45 cases identified by ICD codes. We concluded that the text mining approach may be used successfully to identify OUP from patients clinical notes. Moreover, we developed a machine learning approach to identify OUP by analyzing patients’ clinical notes. Our model was able to classify positive OUP from clinical notes with a sensitivity of 88% on unseen data. We concluded that the machine learning approach may be used successfully to identify the opioid use problem from patients’ clinical notes.
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    Leveraging syntactic and semantic graph kernels to extract pharmacokinetic drug drug interactions from biomedical literature
    (BioMed Central, 2016-08-26) Zhang, Yaoyun; Wu, Heng-Yi; Xu, Jun; Wang, Jingqi; Soysal, Ergin; Li, Lang; Xu, Hua; Department of Medicine, IU School of Medicine
    BACKGROUND: Information about drug-drug interactions (DDIs) supported by scientific evidence is crucial for establishing computational knowledge bases for applications like pharmacovigilance. Since new reports of DDIs are rapidly accumulating in the scientific literature, text-mining techniques for automatic DDI extraction are critical. We propose a novel approach for automated pharmacokinetic (PK) DDI detection that incorporates syntactic and semantic information into graph kernels, to address the problem of sparseness associated with syntactic-structural approaches. First, we used a novel all-path graph kernel using shallow semantic representation of sentences. Next, we statistically integrated fine-granular semantic classes into the dependency and shallow semantic graphs. RESULTS: When evaluated on the PK DDI corpus, our approach significantly outperformed the original all-path graph kernel that is based on dependency structure. Our system that combined dependency graph kernel with semantic classes achieved the best F-scores of 81.94 % for in vivo PK DDIs and 69.34 % for in vitro PK DDIs, respectively. Further, combining shallow semantic graph kernel with semantic classes achieved the highest precisions of 84.88 % for in vivo PK DDIs and 74.83 % for in vitro PK DDIs, respectively. CONCLUSIONS: We presented a graph kernel based approach to combine syntactic and semantic information for extracting pharmacokinetic DDIs from Biomedical Literature. Experimental results showed that our proposed approach could extract PK DDIs from literature effectively, which significantly enhanced the performance of the original all-path graph kernel based on dependency structure.