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Hua Xu, Ph.D. - Publications

Affiliations: 
Columbia University, New York, NY 
Area:
natural language processing, sublanguage
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71 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Dong X, Li J, Soysal E, Bian J, DuVall SL, Hanchrow E, Liu H, Lynch KE, Matheny M, Natarajan K, Ohno-Machado L, Pakhomov S, Reeves RM, Sitapati AM, Abhyankar S, ... ... Xu H, et al. COVID-19 TestNorm - A tool to normalize COVID-19 testing names to LOINC codes. Journal of the American Medical Informatics Association : Jamia. PMID 32569358 DOI: 10.1093/Jamia/Ocaa145  0.307
2019 Xu J, Li Z, Wei Q, Wu Y, Xiang Y, Lee HJ, Zhang Y, Wu S, Xu H. Applying a deep learning-based sequence labeling approach to detect attributes of medical concepts in clinical text. Bmc Medical Informatics and Decision Making. 19: 236. PMID 31801529 DOI: 10.1186/S12911-019-0937-2  0.307
2019 Wu S, Roberts K, Datta S, Du J, Ji Z, Si Y, Soni S, Wang Q, Wei Q, Xiang Y, Zhao B, Xu H. Deep learning in clinical natural language processing: a methodical review. Journal of the American Medical Informatics Association : Jamia. PMID 31794016 DOI: 10.1093/Jamia/Ocz200  0.324
2019 Wei Q, Zhang Y, Amith M, Lin R, Lapeyrolerie J, Tao C, Xu H. Recognizing software names in biomedical literature using machine learning. Health Informatics Journal. 1460458219869490. PMID 31566474 DOI: 10.1177/1460458219869490  0.303
2019 Shi X, Yi Y, Xiong Y, Tang B, Chen Q, Wang X, Ji Z, Zhang Y, Xu H. Extracting entities with attributes in clinical text via joint deep learning. Journal of the American Medical Informatics Association : Jamia. PMID 31550346 DOI: 10.1093/Jamia/Ocz158  0.33
2019 Soysal E, Warner JL, Wang J, Jiang M, Harvey K, Jain SK, Dong X, Song HY, Siddhanamatha H, Wang L, Dai Q, Chen Q, Du X, Tao C, Yang P, ... ... Xu H, et al. Developing Customizable Cancer Information Extraction Modules for Pathology Reports Using CLAMP. Studies in Health Technology and Informatics. 264: 1041-1045. PMID 31438083 DOI: 10.3233/Shti190383  0.324
2019 Si Y, Wang J, Xu H, Roberts K. Enhancing clinical concept extraction with contextual embeddings. Journal of the American Medical Informatics Association : Jamia. PMID 31265066 DOI: 10.1093/Jamia/Ocz096  0.324
2019 Wei Q, Ji Z, Li Z, Du J, Wang J, Xu J, Xiang Y, Tiryaki F, Wu S, Zhang Y, Tao C, Xu H. A study of deep learning approaches for medication and adverse drug event extraction from clinical text. Journal of the American Medical Informatics Association : Jamia. PMID 31135882 DOI: 10.1093/Jamia/Ocz063  0.324
2019 Xiong Y, Wang Z, Jiang D, Wang X, Chen Q, Xu H, Yan J, Tang B. A fine-grained Chinese word segmentation and part-of-speech tagging corpus for clinical text. Bmc Medical Informatics and Decision Making. 19: 66. PMID 30961602 DOI: 10.1186/S12911-019-0770-7  0.313
2019 Xiang Y, Xu J, Si Y, Li Z, Rasmy L, Zhou Y, Tiryaki F, Li F, Zhang Y, Wu Y, Jiang X, Zheng WJ, Zhi D, Tao C, Xu H. Time-sensitive clinical concept embeddings learned from large electronic health records. Bmc Medical Informatics and Decision Making. 19: 58. PMID 30961579 DOI: 10.1186/S12911-019-0766-3  0.314
2019 Zhang Y, Tiryaki F, Jiang M, Xu H. Parsing clinical text using the state-of-the-art deep learning based parsers: a systematic comparison. Bmc Medical Informatics and Decision Making. 19: 77. PMID 30943955 DOI: 10.1186/S12911-019-0783-2  0.331
2019 Liu Z, Wang X, Chen Q, Tang B, Xu H. Temporal indexing of medical entity in Chinese clinical notes. Bmc Medical Informatics and Decision Making. 19: 17. PMID 30700331 DOI: 10.1186/S12911-019-0735-X  0.316
2019 Li Z, Yang Z, Shen C, Xu J, Zhang Y, Xu H. Integrating shortest dependency path and sentence sequence into a deep learning framework for relation extraction in clinical text. Bmc Medical Informatics and Decision Making. 19: 22. PMID 30700301 DOI: 10.1186/S12911-019-0736-9  0.344
2018 Lee HJ, Zhang Y, Jiang M, Xu J, Tao C, Xu H. Identifying direct temporal relations between time and events from clinical notes. Bmc Medical Informatics and Decision Making. 18: 49. PMID 30066643 DOI: 10.1186/S12911-018-0627-5  0.31
2018 Wang L, Zhang Y, Jiang M, Wang J, Dong J, Liu Y, Tao C, Jiang G, Zhou Y, Xu H. Toward a normalized clinical drug knowledge base in China-applying the RxNorm model to Chinese clinical drugs. Journal of the American Medical Informatics Association : Jamia. PMID 29635469 DOI: 10.1093/Jamia/Ocy020  0.327
2018 Wang Y, Zheng K, Xu H, Mei Q. Interactive medical word sense disambiguation through informed learning. Journal of the American Medical Informatics Association : Jamia. PMID 29584896 DOI: 10.1093/Jamia/Ocy013  0.312
2017 Amith M, Manion FJ, Harris MR, Zhang Y, Xu H, Tao C. Expressing Biomedical Ontologies in Natural Language for Expert Evaluation. Studies in Health Technology and Informatics. 245: 838-842. PMID 29295217 DOI: 10.3233/978-1-61499-830-3-838  0.314
2017 Soysal E, Wang J, Jiang M, Wu Y, Pakhomov S, Liu H, Xu H. CLAMP - a toolkit for efficiently building customized clinical natural language processing pipelines. Journal of the American Medical Informatics Association : Jamia. PMID 29186491 DOI: 10.1093/Jamia/Ocx132  0.339
2017 Redman JS, Natarajan Y, Hou JK, Wang J, Hanif M, Feng H, Kramer JR, Desiderio R, Xu H, El-Serag HB, Kanwal F. Accurate Identification of Fatty Liver Disease in Data Warehouse Utilizing Natural Language Processing. Digestive Diseases and Sciences. PMID 28861720 DOI: 10.1007/S10620-017-4721-9  0.31
2017 Liu Z, Yang M, Wang X, Chen Q, Tang B, Wang Z, Xu H. Entity recognition from clinical texts via recurrent neural network. Bmc Medical Informatics and Decision Making. 17: 67. PMID 28699566 DOI: 10.1186/S12911-017-0468-7  0.34
2017 Tao C, Gong Y, Xu H, Zhao Z. Introduction: the International Conference on Intelligent Biology and Medicine (ICIBM) 2016: special focus on medical informatics and big data. Bmc Medical Informatics and Decision Making. 17: 77. PMID 28699553 DOI: 10.1186/S12911-017-0462-0  0.32
2017 Amith M, Song HY, Zhang Y, Xu H, Tao C. Lightweight predicate extraction for patient-level cancer information and ontology development. Bmc Medical Informatics and Decision Making. 17: 73. PMID 28699547 DOI: 10.1186/S12911-017-0465-X  0.319
2017 Chen Y, Lask TA, Mei Q, Chen Q, Moon S, Wang J, Nguyen K, Dawodu T, Cohen T, Denny JC, Xu H. An active learning-enabled annotation system for clinical named entity recognition. Bmc Medical Informatics and Decision Making. 17: 82. PMID 28699546 DOI: 10.1186/S12911-017-0466-9  0.309
2017 Lee HJ, Wu Y, Zhang Y, Xu J, Xu H, Roberts K. A hybrid approach to automatic de-identification of psychiatric notes. Journal of Biomedical Informatics. PMID 28602904 DOI: 10.1016/J.Jbi.2017.06.006  0.336
2016 Zhang Y, Wu HY, Xu J, Wang J, Soysal E, Li L, Xu H. Leveraging syntactic and semantic graph kernels to extract pharmacokinetic drug drug interactions from biomedical literature. Bmc Systems Biology. 10: 67. PMID 27585838 DOI: 10.1186/S12918-016-0311-2  0.337
2016 Wu Y, Denny JC, Rosenbloom ST, Miller RA, Giuse DA, Wang L, Blanquicett C, Soysal E, Xu J, Xu H. A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD). Journal of the American Medical Informatics Association : Jamia. PMID 27539197 DOI: 10.1093/Jamia/Ocw109  0.361
2016 Fathiamini S, Johnson AM, Zeng J, Araya A, Holla V, Bailey AM, Litzenburger BC, Sanchez NS, Khotskaya Y, Xu H, Meric-Bernstam F, Bernstam EV, Cohen T. Automated identification of molecular effects of drugs (AIMED). Journal of the American Medical Informatics Association : Jamia. PMID 27107438 DOI: 10.1093/Jamia/Ocw030  0.327
2016 Zhang Y, Xu J, Chen H, Wang J, Wu Y, Prakasam M, Xu H. Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning. Database : the Journal of Biological Databases and Curation. 2016. PMID 27087307 DOI: 10.1093/Database/Baw049  0.368
2015 Chen Y, Lasko TA, Mei Q, Denny JC, Xu H. A study of active learning methods for named entity recognition in clinical text. Journal of Biomedical Informatics. PMID 26385377 DOI: 10.1016/J.Jbi.2015.09.010  0.338
2015 Wu Y, Jiang M, Lei J, Xu H. Named Entity Recognition in Chinese Clinical Text Using Deep Neural Network. Studies in Health Technology and Informatics. 216: 624-8. PMID 26262126 DOI: 10.3233/978-1-61499-564-7-624  0.349
2015 Zheng K, Vydiswaran VG, Liu Y, Wang Y, Stubbs A, Uzuner O, Gururaj AE, Bayer S, Aberdeen J, Rumshisky A, Pakhomov S, Liu H, Xu H. Ease of adoption of clinical natural language processing software: An evaluation of five systems. Journal of Biomedical Informatics. PMID 26210361 DOI: 10.1016/J.Jbi.2015.07.008  0.315
2015 Wu Y, Denny JC, Rosenbloom ST, Miller RA, Giuse DA, Song M, Xu H. A Preliminary Study of Clinical Abbreviation Disambiguation in Real Time. Applied Clinical Informatics. 6: 364-74. PMID 26171081 DOI: 10.4338/Aci-2014-10-Ra-0088  0.325
2015 Zhang Y, Tang B, Jiang M, Wang J, Xu H. Domain adaptation for semantic role labeling of clinical text. Journal of the American Medical Informatics Association : Jamia. PMID 26063745 DOI: 10.1093/Jamia/Ocu048  0.346
2015 Jiang M, Huang Y, Fan JW, Tang B, Denny J, Xu H. Parsing clinical text: how good are the state-of-the-art parsers? Bmc Medical Informatics and Decision Making. 15: S2. PMID 26045009 DOI: 10.1186/1472-6947-15-S1-S2  0.562
2015 Tang B, Feng Y, Wang X, Wu Y, Zhang Y, Jiang M, Wang J, Xu H. A comparison of conditional random fields and structured support vector machines for chemical entity recognition in biomedical literature. Journal of Cheminformatics. 7: S8. PMID 25810779 DOI: 10.1186/1758-2946-7-S1-S8  0.317
2015 Krallinger M, Rabal O, Leitner F, Vazquez M, Salgado D, Lu Z, Leaman R, Lu Y, Ji D, Lowe DM, Sayle RA, Batista-Navarro RT, Rak R, Huber T, Rocktäschel T, ... ... Xu H, et al. The CHEMDNER corpus of chemicals and drugs and its annotation principles. Journal of Cheminformatics. 7: S2. PMID 25810773 DOI: 10.1186/1758-2946-7-S1-S2  0.333
2015 Xu H, Aldrich MC, Chen Q, Liu H, Peterson NB, Dai Q, Levy M, Shah A, Han X, Ruan X, Jiang M, Li Y, Julien JS, Warner J, Friedman C, et al. Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality. Journal of the American Medical Informatics Association : Jamia. 22: 179-91. PMID 25053577 DOI: 10.1136/Amiajnl-2014-002649  0.495
2014 Shang N, Xu H, Rindflesch TC, Cohen T. Identifying plausible adverse drug reactions using knowledge extracted from the literature. Journal of Biomedical Informatics. 52: 293-310. PMID 25046831 DOI: 10.1016/J.Jbi.2014.07.011  0.337
2014 Tang B, Cao H, Wang X, Chen Q, Xu H. Evaluating word representation features in biomedical named entity recognition tasks. Biomed Research International. 2014: 240403. PMID 24729964 DOI: 10.1155/2014/240403  0.314
2014 Lei J, Tang B, Lu X, Gao K, Jiang M, Xu H. A comprehensive study of named entity recognition in Chinese clinical text. Journal of the American Medical Informatics Association : Jamia. 21: 808-14. PMID 24347408 DOI: 10.1136/Amiajnl-2013-002381  0.355
2014 Doan S, Lin KW, Conway M, Ohno-Machado L, Hsieh A, Feupe SF, Garland A, Ross MK, Jiang X, Farzaneh S, Walker R, Alipanah N, Zhang J, Xu H, Kim HE. Phendisco: Phenotype discovery system for the database of genotypes and phenotypes Journal of the American Medical Informatics Association. 21: 31-36. PMID 23989082 DOI: 10.1136/Amiajnl-2013-001882  0.314
2013 Fan JW, Yang EW, Jiang M, Prasad R, Loomis RM, Zisook DS, Denny JC, Xu H, Huang Y. Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences. Journal of the American Medical Informatics Association : Jamia. 20: 1168-77. PMID 23907286 DOI: 10.1136/Amiajnl-2013-001810  0.581
2013 Tang B, Wu Y, Jiang M, Chen Y, Denny JC, Xu H. A hybrid system for temporal information extraction from clinical text Journal of the American Medical Informatics Association. 20: 828-835. PMID 23571849 DOI: 10.1136/Amiajnl-2013-001635  0.32
2013 Tang B, Cao H, Wu Y, Jiang M, Xu H. Recognizing clinical entities in hospital discharge summaries using Structural Support Vector Machines with word representation features Bmc Medical Informatics and Decision Making. 13. PMID 23566040 DOI: 10.1186/1472-6947-13-S1-S1  0.332
2013 McCoy AB, Wright A, Eysenbach G, Malin BA, Patterson ES, Xu H, Sittig DF. State of the Art in Clinical Informatics: Evidence and Examples Yearbook of Medical Informatics. 22: 13-19. DOI: 10.1055/S-0038-1638827  0.326
2012 Xu H, Stetson PD, Friedman C. Combining corpus-derived sense profiles with estimated frequency information to disambiguate clinical abbreviations. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 2012: 1004-13. PMID 23304376  0.544
2012 Jiang M, Denny JC, Tang B, Cao H, Xu H. Extracting semantic lexicons from discharge summaries using machine learning and the C-Value method Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 2012: 409-416. PMID 23304311  0.308
2012 Xu H, Wu Y, Elhadad N, Stetson PD, Friedman C. A new clustering method for detecting rare senses of abbreviations in clinical notes. Journal of Biomedical Informatics. 45: 1075-83. PMID 22742938 DOI: 10.1016/J.Jbi.2012.06.003  0.536
2012 Doan S, Collier N, Xu H, Pham HD, Tu MP. Recognition of medication information from discharge summaries using ensembles of classifiers. Bmc Medical Informatics and Decision Making. 12: 36. PMID 22564405 DOI: 10.1186/1472-6947-12-36  0.364
2012 Roden DM, Xu H, Denny JC, Wilke RA. Electronic medical records as a tool in clinical pharmacology: Opportunities and challenges Clinical Pharmacology and Therapeutics. 91: 1083-1086. PMID 22534870 DOI: 10.1038/Clpt.2012.42  0.312
2012 Liu M, Matheny ME, Hu Y, Xu H. Data mining methodologies for pharmacovigilance Acm Sigkdd Explorations Newsletter. 14: 35-42. DOI: 10.1145/2408736.2408742  0.31
2011 Xu H, AbdelRahman S, Lu Y, Denny JC, Doan S. Applying semantic-based probabilistic context-free grammar to medical language processing - A preliminary study on parsing medication sentences Journal of Biomedical Informatics. 44: 1068-1075. PMID 21856440 DOI: 10.1016/J.Jbi.2011.08.009  0.317
2011 Xu H, Jiang M, Oetjens M, Bowton EA, Ramirez AH, Jeff JM, Basford MA, Pulley JM, Cowan JD, Wang X, Ritchie MD, Masys DR, Roden DM, Crawford DC, Denny JC. Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin. Journal of the American Medical Informatics Association : Jamia. 18: 387-91. PMID 21672908 DOI: 10.1136/Amiajnl-2011-000208  0.34
2011 Jiang M, Chen Y, Liu M, Rosenbloom ST, Mani S, Denny JC, Xu H. A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. Journal of the American Medical Informatics Association : Jamia. 18: 601-6. PMID 21508414 DOI: 10.1136/Amiajnl-2011-000163  0.336
2011 Wilke RA, Xu H, Denny JC, Roden DM, Krauss RM, McCarty CA, Davis RL, Skaar T, Lamba J, Savova G. The emerging role of electronic medical records in pharmacogenomics. Clinical Pharmacology and Therapeutics. 89: 379-86. PMID 21248726 DOI: 10.1038/Clpt.2010.260  0.303
2011 Rosenbloom ST, Denny JC, Xu H, Lorenzi N, Stead WW, Johnson KB. Data from clinical notes: A perspective on the tension between structure and flexible documentation Journal of the American Medical Informatics Association. 18: 181-186. PMID 21233086 DOI: 10.1136/Jamia.2010.007237  0.322
2011 Xu H, AbdelRahman S, Jiang M, Fan JW, Huang Y. An initial study of full parsing of clinical text using the Stanford Parser 2011 Ieee International Conference On Bioinformatics and Biomedicine Workshops, Bibmw 2011. 607-614. DOI: 10.1109/BIBMW.2011.6112438  0.466
2010 Doan S, Bastarache L, Klimkowski S, Denny JC, Xu H. Integrating existing natural language processing tools for medication extraction from discharge summaries. Journal of the American Medical Informatics Association : Jamia. 17: 528-31. PMID 20819857 DOI: 10.1136/Jamia.2010.003855  0.332
2010 Xu H, Stenner SP, Doan S, Johnson KB, Waitman LR, Denny JC. MedEx: A medication information extraction system for clinical narratives Journal of the American Medical Informatics Association. 17: 19-24. PMID 20064797 DOI: 10.1197/Jamia.M3378  0.339
2009 Xu H, Stetson PD, Friedman C. Methods for building sense inventories of abbreviations in clinical notes. Journal of the American Medical Informatics Association : Jamia. 16: 103-8. PMID 18952935 DOI: 10.1197/Jamia.M2927  0.531
2008 Xu H, Stetson PD, Friedman C. Methods for building sense inventories of abbreviations in clinical notes. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 819. PMID 18999007  0.465
2008 Chen ES, Hripcsak G, Xu H, Markatou M, Friedman C. Automated acquisition of disease drug knowledge from biomedical and clinical documents: an initial study. Journal of the American Medical Informatics Association : Jamia. 15: 87-98. PMID 17947625 DOI: 10.1197/Jamia.M2401  0.537
2007 Xu H, Stetson PD, Friedman C. A study of abbreviations in clinical notes. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 821-5. PMID 18693951  0.573
2007 Fan JW, Xu H, Friedman C. Using distributional analysis to semantically classify UMLS concepts. Studies in Health Technology and Informatics. 129: 519-23. PMID 17911771  0.632
2007 Fan JW, Xu H, Friedman C. Using contextual and lexical features to restructure and validate the classification of biomedical concepts. Bmc Bioinformatics. 8: 264. PMID 17650333 DOI: 10.1186/1471-2105-8-264  0.639
2007 Xu H, Fan JW, Hripcsak G, Mendonça EA, Markatou M, Friedman C. Gene symbol disambiguation using knowledge-based profiles. Bioinformatics (Oxford, England). 23: 1015-22. PMID 17314123 DOI: 10.1093/Bioinformatics/Btm056  0.62
2007 Tulipano PK, 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. Journal of Biomedical Informatics. 40: 270-81. PMID 17084109 DOI: 10.1016/J.Jbi.2006.08.002  0.641
2006 Xu H, Krupke D, Blake J, Friedman C. A natural language processing (NLP) tool to assist in the curation of the laboratory Mouse Tumor Biology Database. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 1150. PMID 17238769  0.512
2006 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. 7: 334. PMID 16822321 DOI: 10.1186/1471-2105-7-334  0.568
2004 Xu H, Anderson K, Grann VR, Friedman C. Facilitating cancer research using natural language processing of pathology reports. Studies in Health Technology and Informatics. 107: 565-72. PMID 15360876 DOI: 10.3233/978-1-60750-949-3-565  0.557
2003 Xu H, Friedman C. Facilitating research in pathology using natural language processing. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 1057. PMID 14728560  0.53
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