Hua Xu

Summary

Affiliation: Vanderbilt University
Country: USA

Publications

  1. pmc Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin
    Hua Xu
    Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
    J Am Med Inform Assoc 18:387-91. 2011
  2. pmc Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs
    Mei Liu
    Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, USA
    J Am Med Inform Assoc 19:e28-35. 2012
  3. pmc Recognition of medication information from discharge summaries using ensembles of classifiers
    Son Doan
    National Institute of Informatics, Hitotsubashi, Chiyoda, Tokyo, Japan
    BMC Med Inform Decis Mak 12:36. 2012
  4. pmc A new clustering method for detecting rare senses of abbreviations in clinical notes
    Hua Xu
    Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37203, USA
    J Biomed Inform 45:1075-83. 2012
  5. pmc Applying semantic-based probabilistic context-free grammar to medical language processing--a preliminary study on parsing medication sentences
    Hua Xu
    Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
    J Biomed Inform 44:1068-75. 2011
  6. pmc MedEx: a medication information extraction system for clinical narratives
    Hua Xu
    Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, USA
    J Am Med Inform Assoc 17:19-24. 2010
  7. pmc Methods for building sense inventories of abbreviations in clinical notes
    Hua Xu
    Department of Biomedical Informatics, Columbia University, New York, NY, USA
    J Am Med Inform Assoc 16:103-8. 2009
  8. pmc A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries
    Min Jiang
    Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, USA
    J Am Med Inform Assoc 18:601-6. 2011
  9. pmc A study of transportability of an existing smoking status detection module across institutions
    Mei Liu
    Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN, USA
    AMIA Annu Symp Proc 2012:577-86. 2012
  10. pmc Detecting abbreviations in discharge summaries using machine learning methods
    Yonghui Wu
    Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
    AMIA Annu Symp Proc 2011:1541-9. 2011

Collaborators

Detail Information

Publications39

  1. pmc Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin
    Hua Xu
    Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
    J Am Med Inform Assoc 18:387-91. 2011
    ..This study sought to develop natural-language-processing algorithms to extract drug-dose information from clinical text, and to assess the capabilities of such tools to automate the data-extraction process for pharmacogenetic studies...
  2. pmc Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs
    Mei Liu
    Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, USA
    J Am Med Inform Assoc 19:e28-35. 2012
    ..Accurate prediction of potential ADRs is required in the entire life cycle of a drug, including early stages of drug design, different phases of clinical trials, and post-marketing surveillance...
  3. pmc Recognition of medication information from discharge summaries using ensembles of classifiers
    Son Doan
    National Institute of Informatics, Hitotsubashi, Chiyoda, Tokyo, Japan
    BMC Med Inform Decis Mak 12:36. 2012
    ..Combining classifiers into an ensemble classifier presents both challenges and opportunities to improve performance in such NLP tasks...
  4. pmc A new clustering method for detecting rare senses of abbreviations in clinical notes
    Hua Xu
    Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37203, USA
    J Biomed Inform 45:1075-83. 2012
    ..Further analysis demonstrated that the improvement by the TCRS method was mainly from additionally detected rare senses, thus indicating its usefulness for building more complete sense inventories of clinical abbreviations...
  5. pmc Applying semantic-based probabilistic context-free grammar to medical language processing--a preliminary study on parsing medication sentences
    Hua Xu
    Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
    J Biomed Inform 44:1068-75. 2011
    ..Our evaluation using a 10-fold cross validation showed that the PCFG parser dramatically improved parsing performance when compared to the CFG parser...
  6. pmc MedEx: a medication information extraction system for clinical narratives
    Hua Xu
    Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, USA
    J Am Med Inform Assoc 17:19-24. 2010
    ..5%, 93.9%, and 96.0% respectively. We then applied MedEx unchanged to outpatient clinic visit notes. It performed similarly with F-measures over 90% on a set of 25 clinic visit notes...
  7. pmc Methods for building sense inventories of abbreviations in clinical notes
    Hua Xu
    Department of Biomedical Informatics, Columbia University, New York, NY, USA
    J Am Med Inform Assoc 16:103-8. 2009
    ..To develop methods for building corpus-specific sense inventories of abbreviations occurring in clinical documents...
  8. pmc A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries
    Min Jiang
    Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, USA
    J Am Med Inform Assoc 18:601-6. 2011
    ..This project was part of the 2010 Center of Informatics for Integrating Biology and the Bedside/Veterans Affairs (VA) natural-language-processing challenge...
  9. pmc A study of transportability of an existing smoking status detection module across institutions
    Mei Liu
    Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN, USA
    AMIA Annu Symp Proc 2012:577-86. 2012
    ..Our results showed that the customized module achieved significantly higher F-measures at all levels of classification (i.e., sentence, document, patient) compared to the direct application of the cTAKES module to the Vanderbilt data...
  10. pmc Detecting abbreviations in discharge summaries using machine learning methods
    Yonghui Wu
    Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
    AMIA Annu Symp Proc 2011:1541-9. 2011
    ..8% (precision 98.8% and recall of 91.2%). When a voting scheme was used to combine output from various ML classifiers, the system achieved the highest F-measure of 95.7%...
  11. pmc Extracting timing and status descriptors for colonoscopy testing from electronic medical records
    Joshua C Denny
    Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, USA
    J Am Med Inform Assoc 17:383-8. 2010
    ..Further investigations must validate extension of NLP approaches for other types of CRC screening applications...
  12. pmc Applying active learning to high-throughput phenotyping algorithms for electronic health records data
    Yukun Chen
    Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, Tennessee, USA
    J Am Med Inform Assoc 20:e253-9. 2013
    ..However, they often require large numbers of annotated samples, which are costly and time-consuming to review. We investigated the use of active learning (AL) in ML-based phenotyping algorithms...
  13. pmc Extracting semantic lexicons from discharge summaries using machine learning and the C-Value method
    Min Jiang
    Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, TN, USA
    AMIA Annu Symp Proc 2012:409-16. 2012
    ..04%). We conclude that such corpus-based methods are effective for generating semantic lexicons, which may improve named entity recognition tasks and may aid in augmenting synonymy within existing terminologies...
  14. ncbi request reprint Gene symbol disambiguation using knowledge-based profiles
    Hua Xu
    Department of Biomedical Informatics, Columbia University, New York City, New York, USA
    Bioinformatics 23:1015-22. 2007
    ..Existing knowledge sources, such as Entrez Gene and the MEDLINE database, contain information concerning the characteristics of a particular gene that could be used to disambiguate gene symbols...
  15. pmc Integrating existing natural language processing tools for medication extraction from discharge summaries
    Son Doan
    Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, TN, USA
    J Am Med Inform Assoc 17:528-31. 2010
    ..This task required accurate recognition of medication name, dosage, mode, frequency, duration, and reason for drug administration...
  16. pmc DTome: a web-based tool for drug-target interactome construction
    Jingchun Sun
    Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    BMC Bioinformatics 13:S7. 2012
    ....
  17. pmc Extracting and integrating data from entire electronic health records for detecting colorectal cancer cases
    Hua Xu
    Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, TN, USA
    AMIA Annu Symp Proc 2011:1564-72. 2011
    ..996 for document level concept identification, and 0.93 for patient level case detection...
  18. pmc A comparative study of current Clinical Natural Language Processing systems on handling abbreviations in discharge summaries
    Yonghui Wu
    Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN, USA
    AMIA Annu Symp Proc 2012:997-1003. 2012
    ..This study suggested that accurate identification of clinical abbreviations is a challenging task and that more advanced abbreviation recognition modules might improve existing clinical NLP systems...
  19. pmc Predicting warfarin dosage in European-Americans and African-Americans using DNA samples linked to an electronic health record
    Andrea H Ramirez
    Department of Medicine, Vanderbilt University in Nashville, TN 37232, USA
    Pharmacogenomics 13:407-18. 2012
    ..Electronic health record (EHR) systems linked to biobanks may allow for pharmacogenomic analysis, but they have not yet been used for this purpose...
  20. pmc Development and evaluation of an ensemble resource linking medications to their indications
    Wei Qi Wei
    Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, USA
    J Am Med Inform Assoc 20:954-61. 2013
    ..To create a computable MEDication Indication resource (MEDI) to support primary and secondary use of electronic medical records (EMRs)...
  21. pmc Using contextual and lexical features to restructure and validate the classification of biomedical concepts
    Jung Wei Fan
    Department of Biomedical Informatics, Columbia University Vanderbilt Clinic, 5th Floor, 622 West 168th Street, New York, NY 10032, USA
    BMC Bioinformatics 8:264. 2007
    ..In this paper, we introduce another classification approach based on words of the concept strings and compare it to the contextual syntactic approach...
  22. pmc Modeling drug exposure data in electronic medical records: an application to warfarin
    Mei Liu
    Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, TN, USA
    AMIA Annu Symp Proc 2011:815-23. 2011
    ..We applied the framework to determine patient warfarin exposure at hospital admissions and achieved 87% precision, 79% recall, and an area under the receiver-operator characteristic curve of 0.93...
  23. pmc Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues
    Hua Xu
    Department of Biomedical Informatics, Columbia University, 622 168th St, New York City, New York, USA
    BMC Bioinformatics 7:334. 2006
    ..Thus, there is a need to explicitly address the factors and to systematically quantify their effects on performance...
  24. pmc Applying active learning to supervised word sense disambiguation in MEDLINE
    Yukun Chen
    Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
    J Am Med Inform Assoc 20:1001-6. 2013
    ....
  25. ncbi request reprint Natural language processing and visualization in the molecular imaging domain
    P Karina Tulipano
    Department of Biomedical Informatics, Columbia University, 622 West 168th Street, Vanderbilt Clinic Floor 5, NY 10032, USA
    J Biomed Inform 40:270-81. 2007
    ..74 (95% CI: [.70-.76]) and 0.70 (95% CI [.63-.76]), respectively. We adapt a JAVA viewer known as PGviewer for the simultaneous visualization of images with NLP extracted information...
  26. ncbi request reprint Using distributional analysis to semantically classify UMLS concepts
    Jung Wei Fan
    Department of Biomedical Informatics, Columbia University, USA
    Stud Health Technol Inform 129:519-23. 2007
    ..54 and recall of 0.654 was achieved by the top prediction; precision of 0.64 and recall of 0.769 was achieved by the top 2 predictions. Error analysis revealed problems in the current method, and provided insight into future improvements...
  27. pmc Identifying the status of genetic lesions in cancer clinical trial documents using machine learning
    Yonghui Wu
    Department of Biomedical Informatics, Vanderbilt University, School of Medicine, 2209 Garland Ave, Nashville, TN 37232, USA
    BMC Genomics 13:S21. 2012
    ..To facilitate search and identification of gene-associated clinical trials by potential participants and clinicians, it is important to develop automated methods to identify genetic information from narrative trial documents...
  28. pmc Applying active learning to assertion classification of concepts in clinical text
    Yukun Chen
    Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, TN, USA
    J Biomed Inform 45:265-72. 2012
    ..For example, to achieve an AUC of 0.79, the random sampling method used 32 samples, while our best active learning algorithm required only 12 samples, a reduction of 62.5% in manual annotation effort...
  29. pmc Data from clinical notes: a perspective on the tension between structure and flexible documentation
    S Trent Rosenbloom
    Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
    J Am Med Inform Assoc 18:181-6. 2011
    ..When reusable data are needed from notes, providers can use structured documentation or rely on post-hoc text processing to produce structured data, as appropriate...
  30. pmc Portability of an algorithm to identify rheumatoid arthritis in electronic health records
    Robert J Carroll
    Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
    J Am Med Inform Assoc 19:e162-9. 2012
    ..This study evaluated the portability of a published phenotype algorithm to identify rheumatoid arthritis (RA) patients from EHR records at three institutions with different EHR systems...
  31. pmc Genomics in 2012: challenges and opportunities in the next generation sequencing era
    Zhongming Zhao
    Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    BMC Genomics 13:S1. 2012
    ..It included six sessions, a tutorial - Introduction to Proteome Informatics, a workshop - Next Generation Sequencing, and a poster session. The selected papers in this Supplement issue represent the genomic focus in ICIBM 2012...
  32. pmc Combining corpus-derived sense profiles with estimated frequency information to disambiguate clinical abbreviations
    Hua Xu
    Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN, USA
    AMIA Annu Symp Proc 2012:1004-13. 2012
    ..875 on the same test set, indicating that integrating sense frequency information with local context is effective for clinical abbreviation disambiguation...
  33. pmc The use of a DNA biobank linked to electronic medical records to characterize pharmacogenomic predictors of tacrolimus dose requirement in kidney transplant recipients
    Kelly A Birdwell
    Division of Nephrology, Vanderbilt University Medical Center, Nashville, Tennesse, USA
    Pharmacogenet Genomics 22:32-42. 2012
    ..The importance of other drug absorption, distribution, metabolism, and elimination (ADME) gene variants has not been well characterized...
  34. pmc Development of a natural language processing system to identify timing and status of colonoscopy testing in electronic medical records
    Joshua C Denny
    Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
    AMIA Annu Symp Proc 2009:141. 2009
    ..The system detected completed colonoscopies with recall and precision of 0.93 and 0.92. The system was superior to a query of colonoscopy billing codes to determine screening status...
  35. doi request reprint Network-assisted investigation of antipsychotic drugs and their targets
    Jingchun Sun
    Department of Biomedical Informatics, Vanderbilt University School of Medicine, 2525 West End Avenue, Suite 600, Nashville, TN 37203, USA
    Chem Biodivers 9:900-10. 2012
    ..This pilot network-assisted investigation of antipsychotics demonstrates that network-based analysis is useful for uncovering the molecular actions of antipsychotics...
  36. pmc ICD-9 tobacco use codes are effective identifiers of smoking status
    Laura K Wiley
    Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
    J Am Med Inform Assoc 20:652-8. 2013
    ..To evaluate the validity of, characterize the usage of, and propose potential research applications for International Classification of Diseases, Ninth Revision (ICD-9) tobacco codes in clinical populations...
  37. ncbi request reprint Facilitating cancer research using natural language processing of pathology reports
    Hua Xu
    Department of Biomedical Informatics, College of Physicians and Surgeons, Columbia University, 622 W 168th Street, VC 5, New York, NY 10032, USA
    Stud Health Technol Inform 107:565-72. 2004
    ..The evaluation outcome showed that the extended NLP system had a sensitivity of 90.6% and a precision of 91.6%. Results indicated that this system performed satisfactorily for capturing information for the cancer research project...
  38. pmc Opioid use after cardiac surgery in children with Down syndrome
    Sara L Van Driest
    1Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 2Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 3Department of Pharmaceutical Services, Vanderbilt University Medical Center, Nashville, TN 4The University of Texas School of Biomedical Informatics at Houston, Houston, TX 5Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville, TN
    Pediatr Crit Care Med 14:862-8. 2013
    ..To determine the cumulative opioid doses administered to patients with Down syndrome after cardiac surgery and compare them with patients without Down syndrome...
  39. pmc Comparing content coverage in medical curriculum to trainee-authored clinical notes
    Joshua C Denny
    Department of Biomedical Informatics, Vanderbilt University, Nashville, TN
    AMIA Annu Symp Proc 2010:157-61. 2010
    ..Such methods may prove useful for future curriculum evaluations and revisions...

Research Grants3

  1. An in-silico method for epidemiological studies using Electronic Medical Records
    Hua Xu; Fiscal Year: 2010
    ..The informatics approach will be validated on EMRs from two major hospitals to demonstrate its generalizability. Epidemiological findings from our study will be compared to reported findings for validation. ..
  2. An in-silico method for epidemiological studies using Electronic Medical Records
    Hua Xu; Fiscal Year: 2009
    ..The priority score reflects the average of all the scores given by the full committee after a thorough discussion. ..
  3. Real-time Disambiguation of Abbreviations in Clinical Notes
    Hua Xu; Fiscal Year: 2010
    ....