| Research Projects and Interests |
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Natural language processing of clinical notes
-developed a framework to handle clinical abbreviations, including methods to detect clinical abbreviations from corpus, generate sense inventory, and disambiguate senses
-applied NLP technologies to clinical pathology reports to automatically retrieve cancer findings for a clinical tumor registry database
Text mining of biomedical literature
-developed methods to disambiguate gene symbols in biomedical literature
-designed and implemented a NLP-based curation tool for Mouse Genome Informatics (MGI) databas
Data mining
-studied disease-drug relations from corpus of clinical notes and biomedical literature by combining structured and unstructured data
-participated a data mining task on National Inpatient Sample (NIS) database (AMIA 2007, KDDM competition
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1. Chen ES, Hripcsak G, Xu H, Markatou M, Friedman C. Automated Acquisition of Disease-Drug Knowledge from Biomedical and Clinical Documents. (In Press) JAMIA 2008 Jan.
2. Xu H, Stetson P, Friedman C. A Study of Abbreviations in Clinical Notes. (In Press) AMIA Annu Symp Proc. 2007.
3. Xu H, Fan JW, Hripcsak G, Mendonca EA, Markatou M, Friedman C. Gene symbol disambiguation using knowledge-based profiles. Bioinformatics, 2007 23(8):1015-1022.
4. Xu H, Jung-Wei Fan, Friedman C. Combine multiple evidence for gene symbol disambiguation. ACL 2007, BioNLP Workshop, p41-48.
5. Fan JW, Xu H, Friedman C. Using Distributional Analysis to Semantically Classify UMLS Concepts. In Proceedings of Medinfo. 2007, 519-23.
6. Fan JW, Xu H, Friedman C. Classifying biomedical concepts using contextual and lexical features. BMC Bioinformatics. 2007; 8: 264.
7. Karina Tulipano P, Tao Y, Millar WS, Zanzonico P, Kolbert K, Xu H, Yu H, Chen L, Lussier YA, Friedman C. Natural language processing and visualization in the molecular imaging domain. J Biomed Inform. 2007 40:3, 270-281
8. Xu H, Markatou M, Dimova R, Liu H, Friedman C. Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues. BMC Bioinformatics. 2006; 7:334.
9. Xu, H, Anderson, K, Grann, V, Friedman, C. Facilitating Cancer Research using Natural Language Processing of Pathology Reports. In Proceedings of Medinfo. 2004:565-72.
10. Lee HT, Xu H, Nasr SH, Schnermann J, Emala CW. A1 adenosine receptor knock-out mice exhibit increased renal injury following ischemia and reperfusion. Am J Physiol Renal Physiol. 2004 Feb;286(2):F298-306.
11. Lee HT, Xu H, Ota-Setlik A, Emala CW. Oxidant preconditioning protects human proximal tubular cells against lethal oxidant injury via p38 MAPK and heme oxygenase-1. Am J Nephrol. 2003 Sep-Oct; 23(5):324-33.
12. Lee HT, Xu H, Siegel CD, Krichevsky IE. Local Anesthetics Induce Human Renal Cell Apoptosis. Am J Nephrol. 2003 May-Jun; 23(3):129-39.
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