Reference

Note: Please cite the publication below in study manuscripts using CLAMP. Please inform us of your publication for our reference.

2017

Ergin Soysal, Jingqi Wang, Min Jiang, Yonghui Wu, Serguei Pakhomov, Hongfang Liu, Hua Xu. CLAMP – a toolkit for efficiently building customized clinical natural language processing pipelines. JAMIA, Doi: 10.1093/jamia/ocx132 Full text link

Awards & Publications

CLAMP is built on award-winning methods. Our team has participated in a number of clinical NLP challenges and top ranked for various tasks (see below). Now we have integrated such proven methods into CLAMP and make them available to the community.

Relevant Publications

2017

Ergin Soysal, Jingqi Wang, Min Jiang, Yonghui Wu, Serguei Pakhomov, Hongfang Liu, Hua Xu. CLAMP – a toolkit for efficiently building customized clinical natural language processing pipelines. JAMIA, Doi: 10.1093/jamia/ Full text link Jun Xu*, Hee-Jin Lee*, Zongcheng Ji*, Jingqi Wang, Qiang Wei, and Hua Xu. UTH_CCB System for Adverse Drug Reaction Extraction from Drug Labels at TAC-ADR 2017. Proceedings of TAC, 2017. (* denotes equal contribution) Full text link

2016

Lee H, Zhang Y, Xu J, Moon S, Wang J, Wu Y, and Xu H, UTHealth at SemEval-2016 Task 12: an End-to-End System for Temporal Information Extraction from Clinical Notes. Proceedings of the 10th International Workshop on Semantic Evaluation (SemEval-2016), 1292-1297, San Diego, California, June, 2016. Full text link Xu J, Wu Y, Zhang Y, Wang J, Lee H-J, Xu H. CD-REST: a system for extracting chemical-induced disease relation in literature. Database: The Journal of Biological Databases and Curation. 2016;2016:baw036. doi:10.1093/database/baw036. Full text link Zhang Y, Xu J, Chen H, Wang J, Wu Y, Manu P, Xu H. Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning.Database (Oxford). 2016. doi: 10.1093/database/baw049. Full text link

2015

Xu J, Zhang Y, Wang J, Wu Y, Jiang M, Soysal E, and Xu H. UTH-CCB: The Participation of the SemEval 2015 Challenge – Task 14. Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015). Denver, Colorado. 2015:311-314. Full text link Xu J, Wu Y, Zhang Y, Wang J, Liu R, Wei Q, and Xu H. UTH-CCB@BioCreative V CDR Task: Identifying Chemical-induced Disease Relations in Biomedical Text. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 2015:254-259. Full text link Zhang Y, Xu J, Wang J, Wu Y, Parkasam M and Xu H. UTH-CCB@BioCreative V Track 2: Recognizing Chemical Entities in Patents. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 2015:147-148 Full text link

2014

Zhang Y, Wang J, Tang B, Wu Y, Jiang M, Chen Y, Xu H. UTH_CCB: A Report for SemEval 2014 – Task 7 Analysis of Clinical Text. SemEval 2014, 802–806, Dublin, Ireland, August 23-24, 2014. Full text link

2013

Tang B, Wu Y, Jiang M, and Xu H. A Machine Learning based System for Disorder Concept Extraction. 2013. Proceedings of CLEF 2013 Evaluation Labs and Workshop. Full text link Wu Y, Tang B, Jiang M, Moon S, Denny JC, Xu H. Clinical Acronym/Abbreviation Normalization using a Hybrid Approach. 2013. Proceedings of CLEF 2013 Evaluation Labs and Workshop. Full text link Tang B, Wu Y, Jiang M, Chen Y, Denny JC, Xu H. A hybrid system for temporal information extraction from clinical text. J Am Med Inform Assoc. 2013. Full text link

2011

Jiang M Chen Y Liu Met al. A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. J Am Med Inform Assoc  2011;18:601–6. Full text link Jiang M Chen Y Liu Met al. A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. J Am Med Inform Assoc  2011;18:601–6. Full text link

2010

Doan S Bastarache L Klimkowski Set al. Integrating existing natural language processing tools for medication extraction from discharge summaries. J Am Med Inform Assoc  2010;17:528–31. Full text link

Projects using CLAMP

Du J, Zhang Y, Luo J, Jia Y, Wei Q, Tao C, Xu H. Extracting psychiatric stressors for suicide from social media using deep learning. BMC medical informatics and decision making. 2018 Jul;18(2):43. https://doi.org/10.1186/s12911-018-0632-8 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. 2018 Jul;18(2):49. https://doi.org/10.1186/s12911-018-0627-5 Preum S, Shu S, Hotaki M, Williams R, Stankovic J, Alemzadeh H. CognitiveEMS: A Cognitive Assistant System for Emergency Medical Services. Malty AM, Jain SK, Yang PC, Harvey K, Warner JL. Computerized Approach to Creating a Systematic Ontology of Hematology/Oncology Regimens. JCO Clinical Cancer Informatics. 2018 May 11;2:1-1. Chen Q, Du J, Kim S, Wilbur WJ, Lu Z. Combining rich features and deep learning for finding similar sentences in electronic medical records. Sushil M, Šuster S, Luyckx K, Daelemans W. Patient representation learning and interpretable evaluation using clinical notes. Journal of biomedical informatics. 2018 Aug 1;84:103-13. Xu J, Lee HJ, Ji Z, Wang J, Wei Q, Xu H. UTH_CCB System for Adverse Drug Reaction Extraction from Drug Labels at TAC-ADR 2017. Šuster S, Sushil M, Daelemans W. Revisiting neural relation classification in clinical notes with external information. Van Le D, Montgomery J, Kirkby KC, Scanlan J. Risk prediction using natural language processing of electronic mental health records in an inpatient forensic psychiatry setting. Journal of biomedical informatics. 2018 Oct 1;86:49-58. Tang L, Xu J, Hu X, Wei Q, Xu H. Building a Biomedical Chinese-English Parallel Corpus from MEDLINE. MultilingualBIO: Multilingual Biomedical Text Processing. 2018 May 8:8. 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. 2017 Oct 1;62(10):2713-8. Chen X, Gururaj AE, Ozyurt B, Liu R, Soysal E, Cohen T, Tiryaki F, Li Y, Zong N, Jiang M, Rogith D. DataMed–an open source discovery index for finding biomedical datasets. Journal of the American Medical Informatics Association. 2018 Jan 13;25(3):300-8. Shin S, Hwang SG, Park H, Lee JH, Kwon SW, Rim KS, Kim G. Diagnostic Performance of Controlled Attenuation Parameter for Hepatic Steatosis in Patient with Chronic Liver Disease, Retrospectively. Gastroenterology. 2017 Apr 1;152(5):S1115. Karrar A, Kim S, Mohammad M, Addanki S, Abdelatif D, Tan D, Hassan M, Shaikh T, Felix S, Younoszai Z, Jeffers T. Lower Levels of Hepatokines Angiopoietin-Like 4 and RBP-4 are Independently Associated with Non-Alcoholic Steatohepatitis (NASH). Gastroenterology. 2017 Apr 1;152(5):S1115. Zhang Y, Li HJ, Wang J, Cohen T, Roberts K, Xu H. Adapting Word Embeddings from Multiple Domains to Symptom Recognition from Psychiatric Notes. AMIA Summits on Translational Science Proceedings. 2018;2017:281. Fleet SE, LeDuc CA, Leibel RL. Elucidating the Role of ILDR2 in the Unfolded Protein Response and its Effect on Nonalcoholic Steatohepatitis. Gastroenterology. 2017 Apr 1;152(5):S1114-5. Dakhoul L, Cummings OW, Weber R, Vuppalanchi R. Use of Vibration-Controlled Transient Elastography (VCTE) with Simultaneous Liver Stiffness Measurement (LSM) and Controlled Attenuation Parameter (CAP) in Patients Referred for Suspected Non-Alcoholic Fatty Liver Disease (NAFLD): A Prospective Study. Gastroenterology. 2017 Apr 1;152(5):S1115-6. Zhang OR, Zhang Y, Xu J, Roberts K, Zhang XY, Xu H. Interweaving Domain Knowledge and Unsupervised Learning for Psychiatric Stressor Extraction from Clinical Notes. InInternational Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems 2017 Jun 27 (pp. 396-406). Springer, Cham. Weng WH, Wagholikar KB, McCray AT, Szolovits P, Chueh HC. Medical subdomain classification of clinical notes using a machine learning-based natural language processing approach. BMC medical informatics and decision making. 2017 Dec;17(1):155. Shi J, Zheng M, Yao L, Ge Y. DIR—A semantic information resource for healthcare datasets. InBioinformatics and Biomedicine (BIBM), 2017 IEEE International Conference on 2017 Nov 13 (pp. 805-810). IEEE. Lee HJ, Zhang Y, Roberts K, Xu H. Leveraging existing corpora for de-identification of psychiatric notes using domain adaptation. InAMIA Annual Symposium Proceedings 2017 (Vol. 2017, p. 1070). American Medical Informatics Association. 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. 2017 Nov 1;75:S19-27. Zhang Y, Zhang O, Wu Y, Lee HJ, Xu J, Xu H, Roberts K. Psychiatric symptom recognition without labeled data using distributional representations of phrases and on-line knowledge. Journal of biomedical informatics. 2017 Nov 1;75:S129-37. Si Y, Weng C. An OMOP CDM-based Relational Database of Clinical Research Eligibility Criteria. Studies in health technology and informatics. 2017;245:950. Šuster S, Daelemans W. CliCR: A Dataset of Clinical Case Reports for Machine Reading Comprehension. arXiv preprint arXiv:1803.09720. 2018 Mar 26.

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Center for Computational Biomedicine

School of Biomedical Informatics

The University of Texas Health Science Center at Houston

7000 Fannin St, Houston, TX 77030

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Anupama E. Gururaj, PhD

anupama.e.gururaj@uth.tmc.edu

713-500-3619

Technical Support

Jingqi Wang, MS - Scientific Programmer

jingqi.wang@uth.tmc.edu

713-500-3620

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