Selected Publications

Journal Articles

• Wu, Stephen, Kirk Roberts, Surabhi Datta, Jingcheng Du, Zongcheng Ji, Yuqi Si, Sarvesh Soni, Qiong Wang, Qiang Wei, Yang Xiang, Bo Zhao, Hua Xu. Deep Learning in Clinical Natural Language Processing: A Methodical Review.  J Am Med Inform Assoc. Volume 27, Issue 3, March 2020, Pages 457–470. [Supplemental Material]

• Wu, Stephen, Sijia Liu, Sunghwan Sohn, Sungrim Moon, Chung-il Wi, Young Juhn, Hongfang Liu. Modeling Asynchronous Event Sequences with RNNs. J Biomed Inform, 83:167-77. Jul 2018. [Author version]

• Sohn S, Wi CI, Wu ST, Liu H, Ryu E, Krusemark E, Seabright A, Voge GA, Juhn YJ. Ascertainment of asthma prognosis using natural language processing from electronic medical records. J Allergy Clin Immunol, 141(6):2292-2294.e3. doi: 10.1016/j.jaci.2017.12.1003. Jun 2018.

• Wu, Stephen T, Sijia Liu, Yanshan Wang, Tamara Timmons, Harsha Uppili, Steven Bedrick, William Hersh, and Hongfang Liu. Intra-institutional EHR Collections for Patient-Level Information Retrieval. Journal of the American Society for Information Science and Technology. doi:10.1002/asi.23884. September 2017.

• Wang, Yanshan, Stephen Wu, Dingcheng Li, Saeed Mehrabi, Hongfang Liu. A Part-Of-Speech term weighting scheme for biomedical information retrieval. J Biomed Inform, 63:379-389. Oct 2016.

• Wu, Stephen T, Young J Juhn, Sunghwan Sohn, Hongfang Liu.  Patient-level Temporal Aggregation for Text-based Asthma Ascertainment. J Am Med Inform Assoc. 21(5):876-884, 2014. Errata: there are publisher-introduced typos for p(t) and a(t), which should be written with a conditional probability P(... | f(0)=1) 

• Wu, Stephen T, Timothy Miller, James Masanz, Matt Coarr, Scott Halgrim, David Carrell, Cheryl Clark. Negation's not solved: Generalizability versus Optimizability in clinical natural language processing.  PLoS One. Nov 2014. [NLP Best Paper, 2015 IMIA Yearbook]

• Pathak, Jyotishman, Ashutosh Jadhav, ... Stephen Wu.  Comparative Analysis of Online Health Information Search Behavior.  J Med Internet Res. 16(7):e160. Jul 04, 2014.

• Dongqing Zhu*, Wu, Stephen T*, Ben Carterette, Hongfang Liu. Using large clinical corpora for query expansion in text-based cohort identification.  J Biomed Inform. 49:275–81, June 2014.     *Equal Contribution

• Pathak, Jyotishman, ...... Stephen Wu, ... Christopher G Chute. Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium. J Am Med Inform Assoc. 20:341-348. 2013.

• Wu, Stephen T, Sunghwan Sohn, Ravikumar K.E., Kavishwar Wagholikar, Siddhartha R. Jonnalagadda, Hongfang Liu, Young J Juhn. Automated Chart Review for Asthma Cohort Identification using Natural Language Processing: An Exploratory Study.  Ann Allergy Asthma Immunol.  111(5):364-369, November, 2013.

• Wu, Stephen T.  Computational Semantics in Clinical Text (editorial).  Biomedical Informatics Insights.  2013:Suppl. 1 3-5.

• Jonnalagadda S, Cohen T, Wu S, Liu H, Gonzalez G. Using empirically constructed lexical resources for named entity recognition. Biomed Inform Insights. 6(Suppl 1):17-27. 2013.

• Sohn S, Clark C, Halgrim SR, Murphy SP, Jonnalagadda SR, Wagholikar KB, Wu ST, Chute CG, Liu H. Analysis of cross-institutional medication description patterns in clinical narratives. Biomed Inform Insights. 6(Suppl 1):7-16. Epub 2013 Jun 24, 2013. 

• Wu, Stephen T, Vinod C Kaggal, Dmitriy Dligach, James J Masanz, Pei Chen, Lee Becker, Wendy W Chapman, Guergana K Savova, Hongfang Liu, Christopher G Chute.  A common type system for clinical natural language processing.  J Biomed Sem. 4:1. 2013.

• Sohn S, Torii M, Li D, Wagholikar K, Wu S, Liu H.  A Hybrid Approach to Sentiment Sentence Classification in Suicide Notes.  Biomed Inform Insights. 5(Suppl. 1):43-50; 2012.

• Jonnalagadda SR, Li D, Sohn S, Wu ST, Wagholikar K, Torii M, Liu H. Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules. J Am Med Inform Assoc.  19(5):867-74. 2012. 

• Wu, Stephen, Hongfang Liu, Dingcheng Li, Cui Tao, Mark Musen, Christopher Chute, and Nigam Shah.  UMLS Term Occurrences in Clinical Notes: A Large-scale Corpus Analysis. J Am Med Inform Assoc.  Published online first: 4 April, 2012.  doi:10.1136/amiajnl-2011-000744 [slides]

• Jonnalagadda, Siddhartha, Trevor Cohen, Stephen Wu, Graciela Gonzalez.  Enhancing clinical concept extraction with distributional semantics. Journal of Biomedical Informatics. Published online first: 7 November, 2011. 45(1):129-40, Elsevier, 2012.

• Schuler, William, Stephen Wu, and Lane Schwartz.  A Framework for Fast Incremental Interpretation during Speech Decoding. Computational Linguistics, 35(3):313–343, MIT Press, 2009.

Conference Papers

• Wu, Stephen Tze-Inn, Dan Demetriou, and Rudwan Husain. Honor Ethics: The Challenge of Globalizing Value Alignment in AI. Proceedings of FAccT '23: 2023 ACM Conference on Fairness, Accountability, and Transparency, Chicago, USA, June 2023.

• Mersha, Amanuel and Stephen Wu. Morphology-rich Alphasyllabary Embeddings. Proceedings of the 12th Edition of the Language Resources and Evaluation Conference (LREC). Marseilles, France. 2020.

• Wu, Stephen, Andrew Wen, Yanshan Wang, Sijia Liu, and Hongfang Liu. Aligned-layer text search in clinical notes. Proceedings of the 16th World Congress on Medical and Health Informatics (MedInfo 2017). Hangzhou, China. 2017.

• Liu, Sijia, Yanshan Wang, Na Hong, Feichen Shen, Stephen Wu, William Hersh, Hongfang Liu. On Mapping Textual Queries to a Common Data Model. 2017 IEEE International Conference on Healthcare Informatics (ICHI). Park City, Utah, 2017

• Wu, Stephen T., Tamara Timmons, Amy Yates, Meikun Wang, Steven Bedrick, William Hersh, and Hongfang Liu. On Developing Resources for Patient-level Information Retrieval.  Proceedings of the 10th Edition of its Language Resources and Evaluation Conference. Portorož, Slovenia. 2016.

• Wu, Stephen T., Chung-Il Wi, Sunghwan Sohn, Hongfang Liu, and Young J. Juhn. Staggered NLP-assisted refinement for Clinical Annotations of Chronic Disease Events.  Proceedings of the 10th Edition of the Language Resources and Evaluation Conference. Portorož, Slovenia. 2016. [poster]

• Zhu, Dongqing, Stephen Wu*, Ben Carterette, Hongfang Liu.  Using Discharge Summaries to Improve Information Retrieval in the Clinical Domain.  Proceedings of the CLEF eHealth Evaluation Lab. Valencia, Spain. 2013.    *Equal Contribution

• Wu, Stephen, Dongqing Zhu, William Hersh, and Hongfang Liu. Clinical Information Retrieval with Split-layer Language Models. In Proc ACM SIGIR Workshop on Health Search and Discovery (HSD). 2013.

• Wu, Stephen, Dongqing Zhu, Ben Carterette, Hongfang Liu.  MayoClinicNLP-CORE: Semantic representations for textual similarity.  Joint Conference on Lexical and Computational Semantics.  Atlanta, GA. 2013.

• Wagholikar KB, Boardman LA, Chaudhry R, Greenes RA, Wu Tsung-teh, Buehler SA, Larson DW, Sohn S, Wu ST, Kaggal VC, Liu H. Workflow-based Data Reconciliation for Clinical Decision Support: Case of Colorectal Cancer Screening and Surveillance. AMIA CRI. 2013.

• Wu, Stephen, James Masanz, Ravikumar K.E., Hongfang Liu.  Three Questions about Clinical Information Retrieval.  Text Retrieval Conference - Medical Records Track. 2012.

• Wagholikar, Kavishwar, Sunghwan Sohn, Stephen Wu, Vinod Kaggal, Sheila Buehler, Robert Greenes, Tsung-Teh Wu, David Larson, Hongfang Liu, Rajeev Chaudhry, Lisa Boardman. Clinical Decision Support for Colonoscopy Surveillance Using Natural Language Processing.  IEEE HISB. La Jolla, CA. 2012.

• Sohn, Sunghwan and Stephen Wu. Dependency Parser-based Negation Detection in Clinical Narratives.  AMIA CRI.  San Fransisco, CA. 2012.

• Liu, Hongfang, Kavishwar Wagholikar, and Stephen Tze-Inn Wu.  Using SNOMED CT to encode summary level data - a corpus analysis.  AMIA CRI.  San Fransisco, CA. 2012.

• Wu, Stephen, Kavishwar Wagholikar, Sunghwan Sohn, Vinod Kaggal, Hongfang Liu .  Empirical Ontologies for Cohort Identification.  Text REtrieval Conference - Medical Records Track. 2011. [poster]

• Wu, Stephen, and Hongfang Liu.  Semantic Characteristics of NLP-extracted Concepts in Clinical Notes vs. Biomedical Literature.  Proceedings of the Annual AMIA Fall Symposium.  Washington DC. 2011. [slides]

• Wu, Stephen T, Vinod C Kaggal, Guergana K Savova, Hongfang Liu, Dmitriy Dligach, Jiaping Zheng, Wendy W Chapman, and Christopher G Chute.  Generality and Reuse in a Common Type System for Clinical Natural Language Processing.  Proceedings of the First International Workshop on Managing Interoperability and compleXity in Health Systems.  Glasgow, Scotland.  2011. [slides]

• Schwartz, Lane, Chris Callison-Burch, William Schuler, and Stephen Wu.  Incremental Syntactic Language Models for Phrase-based Translation.  Proceedings of the Association for Computational Linguistics.  Portland, Oregon. 2011. [errata]

• Wu, Stephen, and William Schuler.  Structured Composition of Semantic Vectors.  Proceedings of the International Conference on Computational Semantics.  Oxford, UK. 2011.  [slides]

• Wu, Stephen, Asaf Bachrach, Carlos Cardenas, and William Schuler.  Complexity Metrics in an Incremental Right-corner Parser. Proceedings of the Association for Computational Linguistics.  Uppsala, Sweden.  2010.  [slides]

• Wu, Stephen, Lane Schwartz, and William Schuler. Referential Semantic Language Modeling for Data-Poor Domains. In Proceedings of the International Conference on Acoustics, Speech, and Signal Processing, Las Vegas, Nevada. 2008.

• Wu, Stephen, Lane Schwartz, William Schuler. Exploiting Referential Context in Spoken Language Interfaces for Data-Poor Domains. In Proceedings of the 2008 International Conference on Intelligent User Interfaces, Canary Islands, Spain. 2008.

• Schuler, William, Tim Miller, Andrew Exley, and Stephen Wu. Dynamic Evidence Models in a DBN Phone Recognizer. In Proceedings of the 9th International Conference on Spoken Language Processing, Pittsburgh, Pennsylvania. 2006.

Presentations

• Wu, Stephen T. Phenotyping with NLP. Mayo Clinic Bi-weekly Biomedical Informatics Webinar.  Rochester, MN. 2013.

• Wu, Stephen T. Meaning representations for Semantic Textual Similarity. Mayo Clinic Bi-weekly Biomedical Informatics Webinar.  Rochester, MN. 2013.

• Wu, Stephen T. Terms and Concepts in Clinical Notes: Large-scale Analysis and Application. UTHealth School of Biomedical Informatics Research Seminar.  Houston, TX. 2012.

• Wu, Stephen T.  UMLS Concepts and Terms in Clinical Notes: Large-scale Corpus Analysis.  NCBO Webinar.  2011. [slides]

Posters/Abstracts/Workshops

• Mersha, Amanuel and Stephen Wu. DistillEmb: Distilling word embeddings via contrastive learning. Widening NLP 2022. Abu Dhabi, UAE. 2022.

• Wu, Stephen T, Young J Juhn, Sunghwan Sohn, Ravikumar Komandur-Elayavilli, Kavishwar Wagholikar, Siddhartha Jonnalagadda, Hongfang Liu.  Automated Chart Review for Asthma Cohort Identification using Natural Language Processing.  Proceedings of the Annual AMIA Fall Symposium.  Chicago, IL.  2012.

• Wu, Stephen, Hongfang Liu, Dingcheng Li, Cui Tao, Mark Musen, Christopher Chute, and Nigam Shah.  UMLS Term Occurrences in Clinical Notes: A Large-scale Corpus Analysis.  AMIA CRI, journal-eligible.  San Fransisco, CA. 2012. [slides - see JAMIA article]

• Wu, Stephen, Sunghwan Sohn, Kavishwar Wagholikar, Sheila Buehler, Lisa Boardman.  Systematizing Colonoscopy Follow-up Recommendations.  AMIA CRI, San Fransisco, CA. 2012. [abstract|poster]

• Liu, Hongfang, Manabu Torii, Stephen Wu, Vinod Kaggal, Christopher Chute.  Modeling UIMA Type System Using Web Ontology Language - Towards Interoperability among UIMA NLP Tools.  AMIA CRI, San Fransisco, CA. 2012.

Other

• Mark L. Wieland, Stephen T. Wu, Vinod C. Kaggal, and Barbara P. Yawn.  Tracking Health Disparities Through Natural-Language Processing. American Journal of Public Health. Vol. 103, No. 3, pp. 448-449. March 2013.

Thesis

• Wu, Stephen.  Vectorial Representations of Meaning for a Computational Model of Language Comprehension.  University of Minnesota, 2010.