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Browsing by Subject "Negation"
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Item Advanced natural language processing and temporal mining for clinical discovery(2015-08-17) Mehrabi, Saeed; Jones, Josette F.; Palakal, Mathew J.; Chien, Stanley Yung-Ping; Liu, Xiaowen; Schmidt, C. MaxThere has been vast and growing amount of healthcare data especially with the rapid adoption of electronic health records (EHRs) as a result of the HITECH act of 2009. It is estimated that around 80% of the clinical information resides in the unstructured narrative of an EHR. Recently, natural language processing (NLP) techniques have offered opportunities to extract information from unstructured clinical texts needed for various clinical applications. A popular method for enabling secondary uses of EHRs is information or concept extraction, a subtask of NLP that seeks to locate and classify elements within text based on the context. Extraction of clinical concepts without considering the context has many complications, including inaccurate diagnosis of patients and contamination of study cohorts. Identifying the negation status and whether a clinical concept belongs to patients or his family members are two of the challenges faced in context detection. A negation algorithm called Dependency Parser Negation (DEEPEN) has been developed in this research study by taking into account the dependency relationship between negation words and concepts within a sentence using the Stanford Dependency Parser. The study results demonstrate that DEEPEN, can reduce the number of incorrect negation assignment for patients with positive findings, and therefore improve the identification of patients with the target clinical findings in EHRs. Additionally, an NLP system consisting of section segmentation and relation discovery was developed to identify patients' family history. To assess the generalizability of the negation and family history algorithm, data from a different clinical institution was used in both algorithm evaluations.Item DEEPEN: A negation detection system for clinical text incorporating dependency relation into NegEx(Elsevier, 2015-04) Mehrabi, Saeed; Krishnan, Krishnan; Sohn, Sunghwan; Roch, Alexandra M; Schmidt, Heidi; Kesterson, Joe; Beesley, Chris; Dexter, Paul; Schmidt, C. Max; Liu, Hongfang; Palakal, Mathew; Surgery, School of MedicineIn Electronic Health Records (EHRs), much of valuable information regarding patients’ conditions is embedded in free text format. Natural language processing (NLP) techniques have been developed to extract clinical information from free text. One challenge faced in clinical NLP is that the meaning of clinical entities is heavily affected by modifiers such as negation. A negation detection algorithm, NegEx, applies a simplistic approach that has been shown to be powerful in clinical NLP. However, due to the failure to consider the contextual relationship between words within a sentence, NegEx fails to correctly capture the negation status of concepts in complex sentences. Incorrect negation assignment could cause inaccurate diagnosis of patients’ condition or contaminated study cohorts. We developed a negation algorithm called DEEPEN to decrease NegEx’s false positives by taking into account the dependency relationship between negation words and concepts within a sentence using Stanford dependency parser. The system was developed and tested using EHR data from Indiana University (IU) and it was further evaluated on Mayo Clinic dataset to assess its generalizability. The evaluation results demonstrate DEEPEN, which incorporates dependency parsing into NegEx, can reduce the number of incorrect negation assignment for patients with positive findings, and therefore improve the identification of patients with the target clinical findings in EHRs.