2019 (16)
An investigation of single-domain and multidomain medication and adverse drug event relation extraction from electronic health record notes using advanced deep learning models. Li, F.; and Yu, H. Journal of the American Medical Informatics Association, 26(7): 646–654. July 2019.
An investigation of single-domain and multidomain medication and adverse drug event relation extraction from electronic health record notes using advanced deep learning models [link]Paper   doi   bibtex   abstract
Detecting Hypoglycemia Incidents Reported in Patients’ Secure Messages: Using Cost-Sensitive Learning and Oversampling to Reduce Data Imbalance. Chen, J.; Lalor, J.; Liu, W.; Druhl, E.; Granillo, E.; Vimalananda, V. G.; and Yu, H. Journal of Medical Internet Research, 21(3): e11990. 2019.
Detecting Hypoglycemia Incidents Reported in Patients’ Secure Messages: Using Cost-Sensitive Learning and Oversampling to Reduce Data Imbalance [link]Paper   doi   bibtex   abstract
Learning Latent Parameters without Human Response Patterns: Item Response Theory with Artificial Crowds. Lalor, J. P.; Wu, H.; and Yu, H. In Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP), pages 4240–4250, Hong Kong, China, November 2019. Association for Computational Linguistics
Learning Latent Parameters without Human Response Patterns: Item Response Theory with Artificial Crowds [link]Paper   doi   bibtex   abstract
Overview of the First Natural Language Processing Challenge for Extracting Medication, Indication, and Adverse Drug Events from Electronic Health Record Notes (MADE 1.0). Jagannatha, A.; Liu, F.; Liu, W.; and Yu, H. Drug Safety. January 2019.
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QuikLitE, a Framework for Quick Literacy Evaluation in Medicine: Development and Validation. Zheng, J.; and Yu, H. Journal of Medical Internet Research, 21(2): e12525. 2019.
QuikLitE, a Framework for Quick Literacy Evaluation in Medicine: Development and Validation [link]Paper   doi   bibtex   abstract
Towards Drug Safety Surveillance and Pharmacovigilance: Current Progress in Detecting Medication and Adverse Drug Events from Electronic Health Records. Liu, F.; Jagannatha, A.; and Yu, H. Drug Safety. January 2019.
Towards Drug Safety Surveillance and Pharmacovigilance: Current Progress in Detecting Medication and Adverse Drug Events from Electronic Health Records [link]Paper   doi   bibtex
Generating Classical Chinese Poems from Vernacular Chinese. Yang, Z.; Cai, P.; Feng, Y.; Li, F.; Feng, W.; Chiu, E. S.; and yu , h. In Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP), pages 6156–6165, Hong Kong, China, November 2019. Association for Computational Linguistics
Generating Classical Chinese Poems from Vernacular Chinese [link]Paper   doi   bibtex   abstract
Automatic Detection of Hypoglycemic Events From the Electronic Health Record Notes of Diabetes Patients: Empirical Study. Jin, Y.; Li, F.; Vimalananda, V. G.; and Yu, H. JMIR Medical Informatics, 7(4): e14340. 2019.
Automatic Detection of Hypoglycemic Events From the Electronic Health Record Notes of Diabetes Patients: Empirical Study [link]Paper   doi   bibtex   abstract
Anticoagulant prescribing for non-valvular atrial fibrillation in the Veterans Health Administration. Rose, A.; Goldberg, R; McManus, D.; Kapoor, A; Wang, V; Liu, W; and Yu, H Journal of the American Heart Association. 2019.
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Clinical Question Answering from Electronic Health Records. In the MLHC 2019 research track proceedings. Singh, B.; Li, F.; and Yu, H. In The MLHC 2019 research track proceedings, 2019.
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Comparing Human and DNN-Ensemble Response Patterns for Item Response Theory Model Fitting. Lalor, J.; Wu, H.; and Yu, H. 2019 Annual Conference of the North American Chapter of the Association for Computational Linguistics (NAACL)The Workshop on Cognitive Modeling and Computational Linguistics (CMCL). 2019.
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Naranjo Question Answering using End-to-End Multi-task Learning Model. Rawat, B. P; Li, F.; and Yu, H. 25th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD). 2019.
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Method for Meta-Level Continual Learning. Yu, H.; and Munkhdalai, T. January 2019.
Method for Meta-Level Continual Learning [link]Paper   bibtex   abstract
Advancing Clinical Research Through Natural Language Processing on Electronic Health Records: Traditional Machine Learning Meets Deep Learning. Liu, F.; Weng, C.; and Yu, H. In Richesson, R. L.; and Andrews, J. E., editor(s), Clinical Research Informatics, of Health Informatics, pages 357–378. Springer International Publishing, Cham, 2019.
Advancing Clinical Research Through Natural Language Processing on Electronic Health Records: Traditional Machine Learning Meets Deep Learning [link]Paper   doi   bibtex   abstract
Improving Electronic Health Record Note Comprehension With NoteAid: Randomized Trial of Electronic Health Record Note Comprehension Interventions With Crowdsourced Workers. Lalor, J. P.; Woolf, B.; and Yu, H. Journal of Medical Internet Research, 21(1): e10793. 2019.
Improving Electronic Health Record Note Comprehension With NoteAid: Randomized Trial of Electronic Health Record Note Comprehension Interventions With Crowdsourced Workers [link]Paper   doi   bibtex   abstract
Automatic extraction of quantitative data from ClinicalTrials.gov to conduct meta-analyses. Pradhan, R.; Hoaglin, D. C.; Cornell, M.; Liu, W.; Wang, V.; and Yu, H. Journal of Clinical Epidemiology, 105: 92–100. January 2019.
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  2018 (19)
A Natural Language Processing System That Links Medical Terms in Electronic Health Record Notes to Lay Definitions: System Development Using Physician Reviews. Chen, J.; Druhl, E.; Polepalli Ramesh, B.; Houston, T. K.; Brandt, C. A.; Zulman, D. M.; Vimalananda, V. G.; Malkani, S.; and Yu, H. Journal of Medical Internet Research, 20(1): e26. January 2018.
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Clinical Relation Extraction Toward Drug Safety Surveillance Using Electronic Health Record Narratives: Classical Learning Versus Deep Learning. Munkhdalai, T.; Liu, F.; and Yu, H. JMIR public health and surveillance, 4(2): e29. April 2018.
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Detecting Hypoglycemia Incidence from Patients’ Secure Messages. Chen, J; and Yu, H In 2018.
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Extraction of Information Related to Adverse Drug Events from Electronic Health Record Notes: Design of an End-to-End Model Based on Deep Learning. Li, F.; Liu, W.; and Yu, H. JMIR medical informatics, 6(4): e12159. November 2018.
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Inadequate diversity of information resources searched in US-affiliated systematic reviews and meta-analyses: 2005-2016. Pradhan, R.; Garnick, K.; Barkondaj, B.; Jordan, H. S.; Ash, A.; and Yu, H. Journal of Clinical Epidemiology, 102: 50–62. October 2018.
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Sentence Simplification with Memory-Augmented Neural Networks. Vu, T.; Hu, B.; Munkhdalai, T.; and Yu, H. In North American Chapter of the Association for Computational Linguistics: Human Language Technologies, 2018.
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Assessing the Readability of Medical Documents: A Ranking Approach. Zheng, J.; and Yu, H. JMIR medical informatics, 6(1): e17. March 2018.
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ComprehENotes, an Instrument to Assess Patient Reading Comprehension of Electronic Health Record Notes: Development and Validation. Lalor, J. P.; Wu, H.; Chen, L.; Mazor, K. M.; and Yu, H. Journal of Medical Internet Research, 20(4): e139. April 2018.
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Recent Trends in Oral Anticoagulant Use and Post-Discharge Complications Among Atrial Fibrillation Patients with Acute Myocardial Infarction. Kundu, A.; Day, K. O.; Lessard, D. M.; Gore, J. M.; Lubitz, S. A.; Yu, H.; Akhter, M. W.; Fisher, D. Z.; Hayward, R. M.; Henninger, N.; Saczynski, J. S.; Walkey, A. J.; Kapoor, A.; Yarzebski, J.; Goldberg, R. J.; and McManus, D. D. Journal of Atrial Fibrillation, 10(5): 1749. February 2018.
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Accuracy of International Classification of Disease Clinical Modification Codes for Detecting Bleeding Events in Electronic Health Records and When to Use Them. Wang, V; McManus, D; Ash, A; Hoaglin, D; and Yu, H In 2018.
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Understanding Deep Learning Performance through an Examination of Test Set Difficulty: A Psychometric Case Study. Lalor, J.; Wu, H.; Munkhdalai, T.; and Yu, H. In EMNLP, 2018.
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Soft Label Memorization-Generalization for Natural Language Inference. Lalor, J.; Wu, H.; and Yu, H. In 2018.
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Recent Trends In Oral Anticoagulant Use and Post-Discharge Complications Among Atrial Fibrillation Patients With Acute Myocardial Infarction. Amartya Kundu; Kevin O ’Day; Darleen M. Lessard; Joel M. Gore1; Steven A. Lubitz; Hong Yu; Mohammed W. Akhter; Daniel Z. Fisher; Robert M. Hayward Jr.; Nils Henninger; Jane S. Saczynski; Allan J. Walkey; Alok Kapoor; Jorge Yarzebski; Robert J. Goldberg; and David D. McManus In 2018. Journal of Atrial Fibrillation
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Frontiers of Clinical Information Extraction: Current Progress in Medication and Adverse Drug Event Detection from Electronic Health Records. Abhyuday Jagannatha; Feifan Liu; Weisong Liu; and Hong Yu In 9th Annual Pharmacy Informatics Conference, 2018.
Frontiers of Clinical Information Extraction: Current Progress in Medication and Adverse Drug Event Detection from Electronic Health Records [link]Paper   bibtex
Panel – Deep Learning for Healthcare - Hype or the Real Thing?. J. Sun; B. Westover; H. Yu; D. Sontag; and M. Ghassemi In AMIA 2018 Informatics Summit, 2018.
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Panel - Frontiers of Clinical Information Extraction: Current Progress in Medication and Adverse Drug Event Detection from Electronic Health Records. Feifan Liu; Abhyuday Jagannatha; and Hong Yu In AMIA 2018 Informatics Summit, 2018.
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Reference Standard Development to Train Natural Language Processing Algorithms to Detect Problematic Buprenorphine-Naloxone Therapy. Celena B Peters; Fran Cunningham; Adam Gordon; Hong Yu; Cedric Salone; Jessica Zacher; Ronald Carico; Jianwei Leng; Nikolh Durley; Weisong Liu; Chao-Chin Lu; Emily Druhl; Feifan Liu; and Brian C Sauer In VA Pharmacy Informatics Conference 2018, 2018.
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Zheng JP and Yu H. 2018. Assessing Readability of Medical Documents: A Ranking Approach. The Journal of Medical Internet Research Medical Informatics. Accepted. . 2018.
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Lalor JP, Chen L, Mazor K, and Yu H. 2018. ComprehENotes: An Instrument to Assess Patient EHR Note Reading Comprehension. The Journal of Medical Internet Research. Accepted. . 2018.
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  2017 (14)
Neural Semantic Encoders. Munkhdalai, T; and Yu, H. In European Chapter of the Association for Computational Linguistics 2017 (EACL), 2017.
Neural Semantic Encoders [pdf]Paper   bibtex
Readability Formulas and User Perceptions of Electronic Health Records Difficulty: A Corpus Study. Zheng, J.; and Yu, H. Journal of Medical Internet Research, 19(3): e59. 2017.
Readability Formulas and User Perceptions of Electronic Health Records Difficulty: A Corpus Study [link]Paper   doi   bibtex   abstract
Reasoning with memory augmented neural networks for language comprehension. Munkhdalai, T.; and Yu, H. 5th International Conference on Learning Representations (ICLR). 2017.
Reasoning with memory augmented neural networks for language comprehension. [link]Paper   bibtex
Detecting Opioid-Related Aberrant Behavior using Natural Language Processing. Lingeman, J. M.; Wang, P.; Becker, W.; and Yu, H. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2017: 1179–1185. 2017.
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An Analysis of Machine Learning Intelligence. Lalor, J. P.; Wu, H.; Munkhdalai, T.; and Yu, H. arXiv:1702.04811 [cs]. February 2017. arXiv: 1702.04811
An Analysis of Machine Learning Intelligence [link]Paper   bibtex   abstract
CIFT: Crowd-Informed Fine-Tuning to Improve Machine Learning Ability. Lalor, J. P.; Wu, H.; and Yu, H. arXiv preprint arXiv:1702.08563. 2017.
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Ranking Medical Terms to Support Expansion of Lay Language Resources for Patient Comprehension of Electronic Health Record Notes: Adapted Distant Supervision Approach. Chen, J.; Jagannatha, A. N.; Fodeh, S. J.; and Yu, H. JMIR medical informatics, 5(4): e42. October 2017.
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J. Lalor, H. Wu, L. Chen, K. Mazor, H. Yu. Generating a Test of Electronic Health Record Narrative Comprehension with Item Response Theory. American Medical Informatics Association (AMIA) Annual Symposium Podium Abstract. In 2017.
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J. Lalor, H. Wu, H. Yu. CIFT: Crowd-Informed Fine-Tuning to Improve Machine Learning Ability. Human Computation and Crowdsourcing (HCOMP) Works-in-Progress. In 2017.
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Lingeman J and Yu H. 2017. Detecting Opioid-Related Aberrant Behavior using Natural Language Processing. AMIA Fall Symposium. In 2017.
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Li R and Yu H. 2017. A Hybrid Neural Network Model for Joint Prediction of Medical Presence and Period Assertions in Clinical Notes. AMIA Fall Symposium. In 2017.
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Zheng J and Yu H. 2017. Assessing Electronic Health Record Readability. AMIA Fall Symposium. In 2017.
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Meta Networks. Munkhdalai, T.; and Yu, H. In ICML, Sydney, Australia, 2017.
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Improving Machine Learning Ability with Fine-Tuning. Lalor, J.; Wu, H.; and Yu, H. In ICML, 2017.
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  2016 (11)
Condensed Memory Networks for Clinical Diagnostic Inferencing. Prakash, A.; Zhao, S.; Hasan, S. A.; Datla, V.; Lee, K.; Qadir, A.; Liu, J.; and Farri, O. arXiv:1612.01848 [cs]. December 2016. arXiv: 1612.01848
Condensed Memory Networks for Clinical Diagnostic Inferencing [link]Paper   bibtex   abstract
Finding Important Terms for Patients in Their Electronic Health Records: A Learning-to-Rank Approach Using Expert Annotations. Chen, J.; Zheng, J.; and Yu, H. JMIR medical informatics, 4(4): e40. November 2016.
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RETAIN: An Interpretable Predictive Model for Healthcare using Reverse Time Attention Mechanism. Choi, E.; Bahadori, M. T.; Sun, J.; Kulas, J.; Schuetz, A.; and Stewart, W. In Advances in Neural Information Processing Systems, pages 3504–3512, 2016.
RETAIN: An Interpretable Predictive Model for Healthcare using Reverse Time Attention Mechanism [link]Paper   bibtex
Structured prediction models for RNN based sequence labeling in clinical text. Jagannatha, A. N.; and Yu, H. In Proceedings of the Conference on Empirical Methods in Natural Language Processing, volume 2016, pages 856–865, November 2016.
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EHR Note Paraphrasing for NoteAid Evaluation. Yu, H. In SBM, 2016.
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Mismatch between Patient Information-Seeking and Physician Expectation at a Diabetes Outpatient Clinic. Yu, H.; Makkapati, S.; Maranda, L.; and Malkani, S. In SBM, 2016.
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Learning to Rank Scientific Documents from the Crowd. Lingeman, J. M; and Yu, H. arXiv:1611.01400. November 2016.
Learning to Rank Scientific Documents from the Crowd [pdf]Paper   bibtex
Learning for Biomedical Information Extraction: Methodological Review of Recent Advances. Liu, F.; Chen, J.; Jagannatha, A.; and Yu, H. arXiv:1606.07993. June 2016.
Learning for Biomedical Information Extraction: Methodological Review of Recent Advances [pdf]Paper   bibtex
Citation Analysis with Neural Attention Models. Munkhdalai, M; Lalor, J; and Yu, H In Proceedings of the Seventh International Workshop on Health Text Mining and Information Analysis (LOUHI) ,, pages 69–77, Austin, TX, November 2016. Association for Computational Linguistics
Citation Analysis with Neural Attention Models [pdf]Paper   bibtex
Building an Evaluation Scale using Item Response Theory. Lalor, J. P.; Wu, H.; and Yu, H. arXiv:1605.08889 [cs]. May 2016. arXiv: 1605.08889
Building an Evaluation Scale using Item Response Theory [link]Paper   bibtex   abstract
Bidirectional Recurrent Neural Networks for Medical Event Detection in Electronic Health Records. Jagannatha, A.; and Yu, H. arXiv:1606.07953 [cs]. June 2016. arXiv: 1606.07953
Bidirectional Recurrent Neural Networks for Medical Event Detection in Electronic Health Records [link]Paper   bibtex   abstract
  2015 (10)
Methods for Linking EHR Notes to Education Materials. Zheng, J.; and Yu, H. AMIA Joint Summits on Translational Science proceedings AMIA Summit on Translational Science, 2015: 209–215. 2015.
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Figure-Associated Text Summarization and Evaluation. Polepalli Ramesh, B.; Sethi, R. J.; and Yu, H. PLOS ONE, 10(2): e0115671. February 2015.
Figure-Associated Text Summarization and Evaluation [link]Paper   doi   bibtex
Identifying Key Concepts from EHR Notes Using Domain Adaptation. Zheng, J.; Yu, H.; and Bedford, M. A. In SIXTH INTERNATIONAL WORKSHOP ON HEALTH TEXT MINING AND INFORMATION ANALYSIS (LOUHI), pages 115, 2015.
Identifying Key Concepts from EHR Notes Using Domain Adaptation [link]Paper   bibtex
Improving Concept Identification for linking EHR notes to education materials. Zheng, J; and Yu, H. In Empirical Methods in Natural Language Processing, Lisboa, Portugal, 2015.
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Towards Mining Electronic Health Records for Opioid ADE Surveillance. Yu, H; Brandt, C; Becker, W; and Kem, R In The 2015 HSR&D/QUERI National Conference, 2015.
Towards Mining Electronic Health Records for Opioid ADE Surveillance [link]Paper   bibtex   abstract
Translating Electronic Health Record Notes from English to Spanish: A Preliminary Study. Liu, W.; Cai, S.; Balaji, R.; Chiriboga, G.; Knight, K.; and Yu, H. In ACL-IJCNLP, pages 134, Bei Jing, China, July 2015.
Translating Electronic Health Record Notes from English to Spanish: A Preliminary Study [pdf]Paper   bibtex
Learning to rank scientific articles. Lingerman, J; and Hong, Y. In AMIA Fall Symposium, 2015.
Learning to rank scientific articles. [pdf]Paper   bibtex
Systems for helping Veterans Comprehend their own EHR notes. Yu, H; Brandt, C; and Houston, T In 2015 HSR&D/QUERI National Conference, 2015.
Systems for helping Veterans Comprehend their own EHR notes. [link]Paper   bibtex   abstract
Learning Distributed Word Representations and Applications in Biomedial Natural Language Processing. Zheng, J.; and Yu, H. In MEDINFO 2015: EHealth-enabled Health: Proceedings of the 15th World Congress on Health and Biomedical Informatics, 2015.
Learning Distributed Word Representations and Applications in Biomedial Natural Language Processing [pdf]Paper   bibtex
DeTEXT: A Database for Evaluating Text Extraction from Biomedical Literature Figures. Yin, X.; Yang, C.; Pei, W.; Man, H.; Zhang, J.; Learned-Miller, E.; and Yu, H. PLoS ONE, 10(5). May 2015.
DeTEXT: A Database for Evaluating Text Extraction from Biomedical Literature Figures [link]Paper   doi   bibtex   abstract
  2014 (5)
A robust data-driven approach for gene ontology annotation. Li, Y.; and Yu, H. Database: The Journal of Biological Databases and Curation, 2014: bau113. 2014. 00000
A robust data-driven approach for gene ontology annotation [link]Paper   doi   bibtex   abstract
Automatically Recognizing Medication and Adverse Event Information From Food and Drug Administration’s Adverse Event Reporting System Narratives. Polepalli Ramesh, B.; Belknap, S. M; Li, Z.; Frid, N.; West, D. P; and Yu, H. JMIR Medical Informatics, 2(1): e10. June 2014.
Automatically Recognizing Medication and Adverse Event Information From Food and Drug Administration’s Adverse Event Reporting System Narratives [link]Paper   doi   bibtex
Learning to Rank Figures within a Biomedical Article. Liu, F.; and Yu, H. PLoS ONE, 9(3): e61567. March 2014.
Learning to Rank Figures within a Biomedical Article [link]Paper   doi   bibtex
Treatment of acute venous thromboembolism with dabigatran or warfarin and pooled analysis. Schulman, S.; Kakkar, A. K.; Goldhaber, S. Z.; Schellong, S.; Eriksson, H.; Mismetti, P.; Christiansen, A. V.; Friedman, J.; Le Maulf, F.; Peter, N.; Kearon, C.; and RE-COVER II Trial Investigators Circulation, 129(7): 764–772. February 2014.
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Computational Approaches for Predicting Biomedical Research Collaborations. Zhang, Q.; and Yu, H. PLoS ONE, 9(11): e111795. November 2014.
Computational Approaches for Predicting Biomedical Research Collaborations [link]Paper   doi   bibtex
  2013 (2)
Systems for Improving Electronic Health Record Note Comprehension. Polepalli Ramesh, B.; and Yu, H. In ACM SIGIR Workshop on Health Search & Discovery, 2013.
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CiteGraph: A Citation Network System for MEDLINE Articles and Analysis. Qing, Z.; and Hong, Y. Studies in Health Technology and Informatics,832–836. 2013.
CiteGraph: A Citation Network System for MEDLINE Articles and Analysis [link]Paper   doi   bibtex   abstract
  2012 (4)
Automatic discourse connective detection in biomedical text. Ramesh, B. P.; Prasad, R.; Miller, T.; Harrington, B.; and Yu, H. Journal of the American Medical Informatics Association: JAMIA, 19(5): 800–808. October 2012.
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Beyond Captions: Linking Figures with Abstract Sentences in Biomedical Articles. Bockhorst, J. P.; Conroy, J. M.; Agarwal, S.; O’Leary, D. P.; and Yu, H. PLoS ONE, 7(7): e39618. July 2012.
Beyond Captions: Linking Figures with Abstract Sentences in Biomedical Articles [link]Paper   doi   bibtex
Natural Language Processing, Electronic Health Records, and Clinical Research. Liu, F.; Weng, C.; and Yu, H. In Clinical Research Informatics, pages 293–310. Springer London, 2012.
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MedTxting: learning based and knowledge rich SMS-style medical text contraction. Liu, F.; Moosavinasab, S.; Houston, T. K.; and Yu, H. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2012: 558–567. 2012.
MedTxting: learning based and knowledge rich SMS-style medical text contraction [link]Paper   bibtex   abstract
  2011 (12)
An investigation into the feasibility of spoken clinical question answering. Miller, T.; Ravvaz, K.; Cimino, J. J.; and Yu, H. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2011: 954–959. 2011.
An investigation into the feasibility of spoken clinical question answering [link]Paper   bibtex   abstract
Apixaban versus warfarin in patients with atrial fibrillation. Granger, C. B.; Alexander, J. H.; McMurray, J. J. V.; Lopes, R. D.; Hylek, E. M.; Hanna, M.; Al-Khalidi, H. R.; Ansell, J.; Atar, D.; Avezum, A.; Bahit, M. C.; Diaz, R.; Easton, J. D.; Ezekowitz, J. A.; Flaker, G.; Garcia, D.; Geraldes, M.; Gersh, B. J.; Golitsyn, S.; Goto, S.; Hermosillo, A. G.; Hohnloser, S. H.; Horowitz, J.; Mohan, P.; Jansky, P.; Lewis, B. S.; Lopez-Sendon, J. L.; Pais, P.; Parkhomenko, A.; Verheugt, F. W. A.; Zhu, J.; Wallentin, L.; ARISTOTLE Committees; and Investigators The New England Journal of Medicine, 365(11): 981–992. September 2011.
Apixaban versus warfarin in patients with atrial fibrillation [link]Paper   doi   bibtex   abstract
AskHERMES: An online question answering system for complex clinical questions. Cao, Y.; Liu, F.; Simpson, P.; Antieau, L.; Bennett, A.; Cimino, J. J; Ely, J.; and Yu, H. Journal of Biomedical Informatics, 44(2): 277–288. April 2011.
AskHERMES: An online question answering system for complex clinical questions [link]Paper   doi   bibtex   abstract
Automatic figure classification in bioscience literature. Kim, D.; Ramesh, B. P.; and Yu, H. Journal of Biomedical Informatics, 44(5): 848–858. October 2011.
Automatic figure classification in bioscience literature [link]Paper   doi   bibtex
Figure summarizer browser extensions for PubMed Central. Agarwal, S.; and Yu, H. Bioinformatics, 27(12): 1723–1724. June 2011.
Figure summarizer browser extensions for PubMed Central [link]Paper   doi   bibtex
Figure Text Extraction in Biomedical Literature. Kim, D.; and Yu, H. PLoS ONE, 6(1): e15338. January 2011.
Figure Text Extraction in Biomedical Literature [link]Paper   doi   bibtex
Parsing citations in biomedical articles using conditional random fields. Zhang, Q.; Cao, Y.; and Yu, H. Computers in Biology and Medicine, 41(4): 190–194. April 2011.
Parsing citations in biomedical articles using conditional random fields [link]Paper   doi   bibtex
The biomedical discourse relation bank. Prasad, R.; McRoy, S.; Frid, N.; Joshi, A.; and Yu, H. BMC Bioinformatics, 12(1): 188. May 2011.
The biomedical discourse relation bank [link]Paper   doi   bibtex   abstract
Toward automated consumer question answering: Automatically separating consumer questions from professional questions in the healthcare domain. Liu, F.; Antieau, L. D.; and Yu, H. Journal of Biomedical Informatics, 44(6): 1032–1038. December 2011.
Toward automated consumer question answering: Automatically separating consumer questions from professional questions in the healthcare domain [link]Paper   doi   bibtex
Towards spoken clinical-question answering: evaluating and adapting automatic speech-recognition systems for spoken clinical questions. Liu, F.; Tur, G.; Hakkani-Tür, D.; and Yu, H. Journal of the American Medical Informatics Association: JAMIA, 18(5): 625–630. October 2011.
Towards spoken clinical-question answering: evaluating and adapting automatic speech-recognition systems for spoken clinical questions [link]Paper   doi   bibtex   abstract
Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions. Agarwal, S.; Liu, F.; and Yu, H. BMC Bioinformatics, 12(Suppl 8): S10. 2011.
Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions [link]Paper   doi   bibtex
BioN∅T: A searchable database of biomedical negated sentences. Agarwal, S.; Yu, H.; and Kohane, I. BMC Bioinformatics, 12(1): 420. 2011.
BioN∅T: A searchable database of biomedical negated sentences [link]Paper   doi   bibtex
  2010 (8)
An IR-aided machine learning framework for the BioCreative II.5 Challenge. Cao, Y.; Li, Z.; Liu, F.; Agarwal, S.; Zhang, Q.; and Yu, H. IEEE/ACM Transactions on Computational Biology and Bioinformatics / IEEE, ACM, 7(3): 454–461. September 2010.
An IR-aided machine learning framework for the BioCreative II.5 Challenge [link]Paper   doi   bibtex   abstract
Automatic Figure Ranking and User Interfacing for Intelligent Figure Search. Yu, H.; Liu, F.; and Ramesh, B. P. PLoS ONE, 5(10): e12983. October 2010.
Automatic Figure Ranking and User Interfacing for Intelligent Figure Search [link]Paper   doi   bibtex
Automatically extracting information needs from complex clinical questions. Best Paper in International Medical Informatics Association (IMIA) Yearbook 2011. Cao, Y.; Cimino, J. J; Ely, J.; and Yu, H. Journal of Biomedical Informatics. July 2010.
Automatically extracting information needs from complex clinical questions. Best Paper in International Medical Informatics Association (IMIA) Yearbook 2011 [link]Paper   doi   bibtex   abstract
Biomedical negation scope detection with conditional random fields. Agarwal, S.; and Yu, H. Journal of the American Medical Informatics Association: JAMIA, 17(6): 696–701. November 2010. 00033
Biomedical negation scope detection with conditional random fields [link]Paper   doi   bibtex   abstract
Detecting hedge cues and their scope in biomedical text with conditional random fields. Agarwal, S.; and Yu, H. Journal of Biomedical Informatics, 43(6): 953–961. December 2010.
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Identifying discourse connectives in biomedical text. Ramesh, B. P.; and Yu, H. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2010: 657–661. November 2010.
Identifying discourse connectives in biomedical text [link]Paper   bibtex   abstract
Lancet: a high precision medication event extraction system for clinical text. Li, Z.; Liu, F.; Antieau, L.; Cao, Y.; and Yu, H. Journal of the American Medical Informatics Association: JAMIA, 17(5): 563–567. October 2010.
Lancet: a high precision medication event extraction system for clinical text [link]Paper   doi   bibtex   abstract
Automatically classifying the role of citations in biomedical articles. Agarwal, S.; Choubey, L.; and Yu, H. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2010: 11–15. November 2010.
Automatically classifying the role of citations in biomedical articles [link]Paper   bibtex
  2009 (9)
Are figure legends sufficient? Evaluating the contribution of associated text to biomedical figure comprehension. Yu, H.; Agarwal, S.; Johnston, M.; and Cohen, A. Journal of Biomedical Discovery and Collaboration, 4(1): 1. 2009.
Are figure legends sufficient? Evaluating the contribution of associated text to biomedical figure comprehension [link]Paper   doi   bibtex   abstract
Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion. Agarwal, S.; and Yu, H. Bioinformatics, 25(23): 3174–3180. December 2009.
Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion [link]Paper   doi   bibtex
Evaluation of the clinical question answering presentation. Cao, Y.; Ely, J.; Antieau, L.; and Yu, H. In Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing, pages 171, 2009. Association for Computational Linguistics
Evaluation of the clinical question answering presentation [link]Paper   doi   bibtex
FigSum: automatically generating structured text summaries for figures in biomedical literature. Agarwal, S.; and Yu, H. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2009: 6–10. November 2009.
FigSum: automatically generating structured text summaries for figures in biomedical literature [link]Paper   bibtex   abstract
Hierarchical image classification in the bioscience literature. Kim, D.; and Yu, H. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2009: 327–331. November 2009.
Hierarchical image classification in the bioscience literature [link]Paper   bibtex   abstract
Investigating and annotating the role of citation in biomedical full-text articles. Yu, H.; Agarwal, S.; and Frid, N. In Bioinformatics and Biomedicine Workshop, pages 308–313, November 2009. IEEE
Investigating and annotating the role of citation in biomedical full-text articles [link]Paper   doi   bibtex
Using the Weighted Keyword Model to Improve Information Retrieval for Answering Biomedical Questions. Yu, H.; and Cao, Y. Summit on translational bioinformatics, 2009: 143. 2009.
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Evaluating the weighted-keyword model to improve clinical question answering. Cao, Y.; Ely, J.; and Yu, H. In Bioinformatics and Biomedicine Workshop, pages 331–335, November 2009. IEEE
Evaluating the weighted-keyword model to improve clinical question answering [link]Paper   doi   bibtex
A Survey of Artificial Immune Theory-based Computer Defense Technology. YU, H.; and TAN, M. Journal of University of South China (Science and Technology), 3: 011. 2009.
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  2008 (3)
A pilot annotation to investigate discourse connectivity in biomedical text. Yu, H.; Frid, N.; McRoy, S.; Prasad, R.; Lee, A.; and Joshi, A. In Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing, pages 92–93, 2008. Association for Computational Linguistics
A pilot annotation to investigate discourse connectivity in biomedical text [pdf]Paper   bibtex
Automatically extracting information needs from Ad Hoc clinical questions. Yu, H.; and Cao, Y. AMIA ... Annual Symposium proceedings. AMIA Symposium,96–100. November 2008.
Automatically extracting information needs from Ad Hoc clinical questions [link]Paper   bibtex   abstract
Translating biology: text mining tools that work. Cohen, K B.; Yu, H.; Bourne, P. E; and Hirschman, L. In Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, volume 13, pages 551, 2008.
Translating biology: text mining tools that work [pdf]Paper   bibtex
  2007 (5)
A cognitive evaluation of four online search engines for answering definitional questions posed by physicians. Yu, H.; and Kaufman, D. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing,328–339. 2007.
A cognitive evaluation of four online search engines for answering definitional questions posed by physicians [pdf]Paper   bibtex   abstract
Development, implementation, and a cognitive evaluation of a definitional question answering system for physicians. Yu, H.; Lee, M.; Kaufman, D.; Ely, J.; Osheroff, J. A.; Hripcsak, G.; and Cimino, J. Journal of Biomedical Informatics, 40(3): 236–251. June 2007.
Development, implementation, and a cognitive evaluation of a definitional question answering system for physicians [link]Paper   doi   bibtex
Frontiers of biomedical text mining: current progress. Zweigenbaum, P.; Demner-Fushman, D.; Yu, H.; and Cohen, K. B Briefings in Bioinformatics, 8(5): 358–75. September 2007.
Frontiers of biomedical text mining: current progress [link]Paper   doi   bibtex   abstract
Using MEDLINE as a knowledge source for disambiguating abbreviations and acronyms in full-text biomedical journal articles. Yu, H.; Kim, W.; Hatzivassiloglou, V.; and Wilbur, W. J. Journal of Biomedical Informatics, 40(2): 150–159. April 2007.
Using MEDLINE as a knowledge source for disambiguating abbreviations and acronyms in full-text biomedical journal articles [link]Paper   doi   bibtex
The efficacy and safety of apixaban, an oral, direct factor Xa inhibitor, as thromboprophylaxis in patients following total knee replacement. Lassen, M. R.; Davidson, B. L.; Gallus, A.; Pineo, G.; Ansell, J.; and Deitchman, D. Journal of Thrombosis and Haemostasis, 5(12): 2368–2375. December 2007.
The efficacy and safety of apixaban, an oral, direct factor Xa inhibitor, as thromboprophylaxis in patients following total knee replacement [link]Paper   doi   bibtex
  2006 (8)
Towards answering biological questions with experimental evidence: automatically identifying text that summarize image content in full-text articles. Yu, H. AMIA ... Annual Symposium proceedings. AMIA Symposium,834–838. 2006.
Towards answering biological questions with experimental evidence: automatically identifying text that summarize image content in full-text articles [link]Paper   bibtex   abstract
Accessing bioscience images from abstract sentences. Yu, H.; and Lee, M. Bioinformatics, 22(14): e547–e556. July 2006. 00039 PMID: 16873519
Accessing bioscience images from abstract sentences [link]Paper   doi   bibtex   abstract
Beyond information retrieval–medical question answering. Lee, M.; Cimino, J.; Zhu, H. R.; Sable, C.; Shanker, V.; Ely, J.; and Yu, H. AMIA ... Annual Symposium proceedings. AMIA Symposium,469–473. 2006.
Beyond information retrieval–medical question answering [link]Paper   bibtex   abstract
BioEx: a novel user-interface that accesses images from abstract sentences. Yu, H.; and Lee, M. In Proceedings of the Human Language Technology Conference of the NAACL, Companion Volume: Short Papers, pages 189–192, 2006. Association for Computational Linguistics
BioEx: a novel user-interface that accesses images from abstract sentences [link]Paper   bibtex
Exploring supervised and unsupervised methods to detect topics in biomedical text. Lee, M.; Wang, W.; and Yu, H. BMC bioinformatics, 7: 140. March 2006.
Exploring supervised and unsupervised methods to detect topics in biomedical text [link]Paper   doi   bibtex   abstract
Exploring text and image features to classify images in bioscience literature. Rafkind, B.; Lee, M.; Chang, S.; and Yu, H. In Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology, pages 73, 2006. Association for Computational Linguistics
Exploring text and image features to classify images in bioscience literature [link]Paper   doi   bibtex
The semantics of a definiendum constrains both the lexical semantics and the lexicosyntactic patterns in the definiens. Yu, H.; and Wei, Y. In Proceedings of the BioNLP Workshop on Linking Natural Language Processing and Biology at HLT-NAACL, pages 1–8, New York, USA, 2006.
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System and methods for automatically identifying answerable questions. Yu, H. June 2006. 00012 US Patent App. 11/479,645
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  2005 (1)
Question analysis for biomedical question answering. Sable, C.; Lee, M.; Zhu, H. R.; and Yu, H. AMIA ... Annual Symposium proceedings. AMIA Symposium,1102. 2005.
Question analysis for biomedical question answering [link]Paper   bibtex   abstract
  2004 (4)
GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. Rzhetsky, A.; Iossifov, I.; Koike, T.; Krauthammer, M.; Kra, P.; Morris, M.; Yu, H.; Duboué, P. A.; Weng, W.; Wilbur, W. J.; Hatzivassiloglou, V.; and Friedman, C. Journal of Biomedical Informatics, 37(1): 43–53. February 2004. 00251
doi   bibtex   abstract
Using MEDLINE as a knowledge source for disambiguating abbreviations in full-text biomedical journal articles. Yu, H.; Kim, W.; Hatzivassiloglou, V.; and John Wilbur, W In Computer-Based Medical Systems, 2004. CBMS 2004. Proceedings. 17th IEEE Symposium on, pages 27–32, 2004. IEEE
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Automatic extraction of opinion propositions and their holders. Bethard, S.; Yu, H.; Thornton, A.; Hatzivassiloglou, V.; and Jurafsky, D. 2004 AAAI Spring Symposium on Exploring Attitude and Affect in Text,2224. 2004.
Automatic extraction of opinion propositions and their holders [pdf]Paper   bibtex
Methods and systems for extracting synonymous gene and protein terms from biological literature. Yu, H.; and Rzhetsky, A. August 2004.
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  2003 (2)
Extracting synonymous gene and protein terms from biological literature. Yu, H.; and Agichtein, E. Bioinformatics, 19(Suppl 1): i340–i349. July 2003.
Extracting synonymous gene and protein terms from biological literature [link]Paper   doi   bibtex