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Hongfang Liu

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2024
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Sunyang Fu, Liwei Wang, Huan He, Andrew Wen, Nansu Zong, Anamika Kumari, Feifan Liu, Sicheng Zhou, Rui Zhang, Chenyu Li, Yanshan Wang, Jennifer St Sauver, Hongfang Liu, Sunghwan Sohn:
A taxonomy for advancing systematic error analysis in multi-site electronic health record-based clinical concept extraction. J. Am. Medical Informatics Assoc. 31(7): 1493-1502 (2024)
[j142]
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Yang Ren, Yuqi Wu, Jungwei W. Fan, Aditya Khurana, Sunyang Fu, Dezhi Wu, Hongfang Liu, Ming Huang:
Automatic uncovering of patient primary concerns in portal messages using a fusion framework of pretrained language models. J. Am. Medical Informatics Assoc. 31(8): 1714-1724 (2024)
[j141]
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Satya S. Sahoo, Joseph M. Plasek, Hua Xu, Özlem Uzuner, Trevor Cohen, Meliha Yetisgen, Hongfang Liu, Stéphane M. Meystre, Yanshan Wang:
Large language models for biomedicine: foundations, opportunities, challenges, and best practices. J. Am. Medical Informatics Assoc. 31(9): 2114-2124 (2024)
[j140]
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Sunyang Fu, Heling Jia, Maria Vassilaki, Vipina Kuttichi Keloth, Yifang Dang, Yujia Zhou, Muskan Garg, Ronald C. Petersen, Jennifer St Sauver, Sungrim Moon, Liwei Wang, Andrew Wen, Fang Li, Hua Xu, Cui Tao, Jungwei Fan, Hongfang Liu, Sunghwan Sohn:
FedFSA: Hybrid and federated framework for functional status ascertainment across institutions. J. Biomed. Informatics 152: 104623 (2024)
[j139]
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Sonish Sivarajkumar, Haneef Ahamed Mohammad, David Oniani, Kirk Roberts, William R. Hersh, Hongfang Liu, Daqing He, Shyam Visweswaran, Yanshan Wang:
Clinical Information Retrieval: A Literature Review. J. Heal. Informatics Res. 8(2): 313-352 (2024)
[j138]
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Zhao Wang, Hongfang Liu, Yuhu Liu:
Nordhaus-Gaddum-Type Results for the k-Independent Number of Graphs. J. Interconnect. Networks 24(1): 2350007:1-2350007:9 (2024)
[j137]
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Evangelia Katsoulakis, Qi Wang, Huanmei Wu, Leili Shahriyari, Richard Fletcher, Jinwei Liu, Luke Achenie, Hongfang Liu, Pamela R. Jackson, Ying Xiao, Tanveer F. Syeda-Mahmood, Richard Tuli, Jun Deng:
Digital twins for health: a scoping review. npj Digit. Medicine 7(1) (2024)
[c249]
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Liwei Wang, Qiuhao Lu, Rui Li, Sunyang Fu, Hongfang Liu:
Wonder at Chemotimelines 2024: MedTimeline: An End-to-End NLP System for Timeline Extraction from Clinical Narratives. ClinicalNLP@NAACL 2024: 483-487
[c248]
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Shenda Hong, Daoxin Yin, Gongzheng Tang, Tianfan Fu, Liantao Ma, Junyi Gao, Mengling Feng, Mai Wang, Yu Yang, Fei Wang, Hongfang Liu, Luxia Zhang:
Artificial Intelligence and Data Science for Healthcare: Bridging Data-Centric AI and People-Centric Healthcare. KDD 2024: 6720-6721
[i28]
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  - journals/corr/abs-2406-10459
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Mingchen Li, Anne H. Blaes, Steven Johnson, Hongfang Liu, Hua Xu, Rui Zhang:
CancerLLM: A Large Language Model in Cancer Domain. CoRR abs/2406.10459 (2024)
[i27]
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Qiuhao Lu, Rui Li, Andrew Wen, Jinlian Wang, Liwei Wang, Hongfang Liu:
Large Language Models Struggle in Token-Level Clinical Named Entity Recognition. CoRR abs/2407.00731 (2024)
[i26]
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  - journals/corr/abs-2409-18878
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Zehan Li, Yan Hu, Scott Lane, Salih Selek, Lokesh Shahani, Rodrigo Machado-Vieira, Jair Soares, Hua Xu, Hongfang Liu, Ming Huang:
Suicide Phenotyping from Clinical Notes in Safety-Net Psychiatric Hospital Using Multi-Label Classification with Pre-Trained Language Models. CoRR abs/2409.18878 (2024)
[i25]
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  - journals/corr/abs-2410-01855
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Qiuhao Lu, Rui Li, Elham Sagheb, Andrew Wen, Jinlian Wang, Liwei Wang, Jungwei W. Fan, Hongfang Liu:
Explainable Diagnosis Prediction through Neuro-Symbolic Integration. CoRR abs/2410.01855 (2024)
2023
[j136]
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Xiaoyang Ruan, Liwei Wang, Charat Thongprayoon, Wisit Cheungpasitporn, Hongfang Liu:
GRU-D-Weibull: A novel real-time individualized endpoint prediction. Artif. Intell. Medicine 146: 102696 (2023)
[j135]
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Jungwei Fan, Wanjing Wang, Ming Huang, Hongfang Liu, W. M. Hooten:
Retrospective content analysis of consumer product reviews related to chronic pain. Frontiers Digit. Health 5 (2023)
[j134]
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Yifang Dang, Fang Li, Xinyue Hu, Vipina Kuttichi Keloth, Meng Zhang, Sunyang Fu, Muhammad F. Amith, J. Wilfred Fan, Jingcheng Du, Evan Yu, Hongfang Liu, Xiaoqian Jiang, Hua Xu, Cui Tao:
Systematic design and data-driven evaluation of social determinants of health ontology (SDoHO). J. Am. Medical Informatics Assoc. 30(9): 1465-1473 (2023)
[j133]
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Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert T. Miller, Andrew E. Williams, Daniel R. Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-El-Rub, Dalton Schutte, Rui Zhang, Masoud Rouhizadeh, John D. Osborne, Yongqun He, Umit Topaloglu, Stephanie S. Hong, Joel H. Saltz, Thomas Schaffter, Emily R. Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu:
An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C). J. Am. Medical Informatics Assoc. 30(12): 2036-2040 (2023)
[j132]
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Vipina Kuttichi Keloth, Juan M. Banda, Michael J. Gurley, Paul M. Heider, Georgina Kennedy, Hongfang Liu, Feifan Liu, Timothy A. Miller, Karthik Natarajan, Olga V. Patterson, Yifan Peng, Kalpana Raja, Ruth M. Reeves, Masoud Rouhizadeh, Jianlin Shi, Xiaoyan Wang, Yanshan Wang, Wei-Qi Wei, Andrew E. Williams, Rui Zhang, Rimma Belenkaya, Christian G. Reich, Clair Blacketer, Patrick B. Ryan, George Hripcsak, Noémie Elhadad, Hua Xu:
Representing and utilizing clinical textual data for real world studies: An OHDSI approach. J. Biomed. Informatics 142: 104343 (2023)
[j131]
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Carlo Combi, Julio C. Facelli, Peter Haddawy, John H. Holmes, Sabine Koch, Hongfang Liu, Jochen Meyer, Mor Peleg, Giuseppe Pozzi, Gregor Stiglic, Pierangelo Veltri, Christopher C. Yang:
The IHI Rochester Report 2022 on Healthcare Informatics Research: Resuming After the CoViD-19. J. Heal. Informatics Res. 7(2): 169-202 (2023)
[j130]
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Andrew Wen, Huan He, Sunyang Fu, Sijia Liu, Kurt Miller, Liwei Wang, Kirk E. Roberts, Steven Bedrick, William R. Hersh, Hongfang Liu:
The IMPACT framework and implementation for accessible in silico clinical phenotyping in the digital era. npj Digit. Medicine 6 (2023)
[c247]
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Rui Li, Andrew Wen, Jing Gao, Hongfang Liu:
MLGAN: a Meta-Learning based Generative Adversarial Network adapter for rare disease differentiation tasks. BCB 2023: 11:1-11:10
[c246]
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Yang Ren, Dezhi Wu, Aditya Khurana, George M. Mastorakos, Sunyang Fu, Nansu Zong, Jungwei Fan, Hongfang Liu, Ming Huang:
Classification of Patient Portal Messages with BERT-based Language Models. ICHI 2023: 176-182
[c245]
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Ziyi Chen, Ren Yang, Sunyang Fu, Nansu Zong, Hongfang Liu, Ming Huang:
Detecting Reddit Users with Depression Using a Hybrid Neural Network SBERT-CNN. ICHI 2023: 193-199
[c244]
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Ming Huang, Aditya Khurana, George M. Mastorakos, Jiawei Zhou, Nansu Zong, Yue Yu, Julie E. Prigge, Christi A. Patten, Hongfang Liu, Brian Costello:
Characterizing the Users of Patient Portal Messaging: A Single Institutional Cohort Study. ICHI 2023: 381-387
[c243]
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Christina Letter, Puneet Gupta, Annie Kim, Guang-Ting Cong, Hongfang Liu, Ahmad P. Tafti:
Gender-Specific Machine Learning Models to Predict Unplanned Return to Operating Room Following Primary Total Shoulder Arthroplasty. ICHI 2023: 717-721
[c242]
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Carlo Combi, Julio C. Facelli, Peter Haddawy, John H. Holmes, Sabine Koch, Hongfang Liu, Jochen Meyer, Mor Peleg, Giuseppe Pozzi, Gregor Stiglic, Pierangelo Veltri, Christopher C. Yang:
Resuming HealthCare Informatics Research after CoViD-19: the HealthCare System Perspective. ICHI 2023: 760-762
[i24]
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  - journals/corr/abs-2302-02759
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Ziyi Chen, Ren Yang, Sunyang Fu, Nansu Zong, Hongfang Liu, Ming Huang:
Detecting Reddit Users with Depression Using a Hybrid Neural Network. CoRR abs/2302.02759 (2023)
[i23]
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Sicheng Zhou, Nan Wang, Liwei Wang, Ju Sun, Anne H. Blaes, Hongfang Liu, Rui Zhang:
A Cross-institutional Evaluation on Breast Cancer Phenotyping NLP Algorithms on Electronic Health Records. CoRR abs/2303.08448 (2023)
[i22]
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Kai Zhang, Jun Yu, Zhiling Yan, Yixin Liu, Eashan Adhikarla, Sunyang Fu, Xun Chen, Chen Chen, Yuyin Zhou, Xiang Li, Lifang He, Brian D. Davison, Quanzheng Li, Yong Chen, Hongfang Liu, Lichao Sun:
BiomedGPT: A Unified and Generalist Biomedical Generative Pre-trained Transformer for Vision, Language, and Multimodal Tasks. CoRR abs/2305.17100 (2023)
[i21]
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  - journals/corr/abs-2308-07452
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Xiaoyang Ruan, Liwei Wang, Charat Thongprayoon, Wisit Cheungpasitporn, Hongfang Liu:
GRU-D-Weibull: A Novel Real-Time Individualized Endpoint Prediction. CoRR abs/2308.07452 (2023)
2022
[j129]
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Nansu Zong, Ning Li, Andrew Wen, Victoria Ngo, Yue Yu, Ming Huang, Shaika Chowdhury, Chao Jiang, Sunyang Fu, Richard Weinshilboum, Guoqian Jiang, Lawrence Hunter, Hongfang Liu:
BETA: a comprehensive benchmark for computational drug-target prediction. Briefings Bioinform. 23(4) (2022)
[j128]
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Huan He, Sunyang Fu, Liwei Wang, Sijia Liu, Andrew Wen, Hongfang Liu:
MedTator: a serverless annotation tool for corpus development. Bioinform. 38(6): 1776-1778 (2022)
[j127]
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Yiqing Zhao, Matthew Brush, Chen Wang, Alex H. Wagner, Hongfang Liu, Robert R. Freimuth:
Leveraging a pharmacogenomics knowledgebase to formulate a drug response phenotype terminology for genomic medicine. Bioinform. 38(23): 5279-5287 (2022)
[j126]
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Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-Hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng, Anna Maria Masci, Liwei Wang, Hongfang Liu, Fatima Zohra Smaili, Robert Hoehndorf, Zoë May Pendlington, Paola Roncaglia, Xianwei Ye, Jiangan Xie, Yi-Wei Tang, Xiaolin Yang, Suyuan Peng, Luxia Zhang, Luonan Chen, Junguk Hur, Gilbert S. Omenn, Brian D. Athey, Barry Smith:
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. J. Biomed. Semant. 13(1): 25 (2022)
[j125]
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Sunyang Fu, Maria Vassilaki, Omar A. Ibrahim, Ronald C. Petersen, Sandeep R. Pagali, Jennifer St Sauver, Sungrim Moon, Liwei Wang, Jungwei Fan, Hongfang Liu, Sunghwan Sohn:
Quality assessment of functional status documentation in EHRs across different healthcare institutions. Frontiers Digit. Health 4 (2022)
[j124]
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Sunyang Fu, Bjoerg Thorsteinsdottir, Xin Zhang, Guilherme S. Lopes, Sandeep R. Pagali, Nathan K. LeBrasseur, Andrew Wen, Hongfang Liu, Walter A. Rocca, Janet E. Olson, Jennifer St. Sauver, Sunghwan Sohn:
A hybrid model to identify fall occurrence from electronic health records. Int. J. Medical Informatics 162: 104736 (2022)
[j123]
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Sicheng Zhou, Nan Wang, Liwei Wang, Hongfang Liu, Rui Zhang:
CancerBERT: a cancer domain-specific language model for extracting breast cancer phenotypes from electronic health records. J. Am. Medical Informatics Assoc. 29(7): 1208-1216 (2022)
[j122]
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Jason A. Thomas, Randi E. Foraker, Noa Zamstein, Jon D. Morrow, Philip R. O. Payne, Adam B. Wilcox, Melissa A. Haendel, Christopher G. Chute, Kenneth R. Gersing, Anita Walden, Tellen D. Bennett, David A. Eichmann, Justin Guinney, Warren A. Kibbe, Hongfang Liu, Emily R. Pfaff, Peter N. Robinson, Joel H. Saltz, Heidi Spratt, Justin Starren, Christine Suver, Chunlei Wu, Davera Gabriel, Stephanie S. Hong, Kristin Kostka, Harold P. Lehmann, Richard A. Moffitt, Michele Morris, Matvey B. Palchuk, Xiaohan Tanner Zhang, Richard L. Zhu, Benjamin R. C. Amor, Mark M. Bissell, Marshall Clark, Andrew T. Girvin, Adam M. Lee, Robert T. Miller, Kellie M. Walters, Yooree Chae, Connor Cook, Alexandra Dest, Racquel R. Dietz, Thomas Dillon, Patricia A. Francis, Rafael Fuentes, Alexis Graves, Andrew J. Neumann, Shawn T. O'Neil, Usman Sheikh, Andréa M. Volz, Elizabeth Zampino, Christopher P. Austin, Samuel Bozzette, Mariam Deacy, Nicole Garbarini, Michael G. Kurilla, Sam G. Michael, Joni L. Rutter, Meredith Temple-O'Connor, Katie Rebecca Bradwell, Amin Manna, Nabeel Qureshi, Mary Morrison Saltz, Julie A. McMurry, Carolyn T. Bramante, Jeremy Richard Harper, Wenndy Hernandez, Farrukh M. Koraishy, Federico Mariona, Saidulu Mattapally, Amit Saha, Satyanarayana Vedula, Yujuan Fu, Nisha Mathews, Ofer Mendelevitch:
Demonstrating an approach for evaluating synthetic geospatial and temporal epidemiologic data utility: results from analyzing >1.8 million SARS-CoV-2 tests in the United States National COVID Cohort Collaborative (N3C). J. Am. Medical Informatics Assoc. 29(8): 1350-1365 (2022)
[j121]
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Xiaoyang Ruan, Sunyang Fu, Curtis B. Storlie, Kellie L. Mathis, David W. Larson, Hongfang Liu:
Real-time risk prediction of colorectal surgery-related post-surgical complications using GRU-D model. J. Biomed. Informatics 135: 104202 (2022)
[j120]
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Nansu Zong, Andrew Wen, Sungrim Moon, Sunyang Fu, Liwei Wang, Yiqing Zhao, Yue Yu, Ming Huang, Yanshan Wang, Gang Zheng, Michelle M. Mielke, James R. Cerhan, Hongfang Liu:
Computational drug repurposing based on electronic health records: a scoping review. npj Digit. Medicine 5 (2022)
[c241]
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Sunyang Fu, Maria Vassilaki, Omar A. Ibrahim, Ronald C. Petersen, Jennifer St. Sauver, Liwei Wang, Jungwei Fan, Hongfang Liu, Sunghwan Sohn:
Quality Assessment of Functional Status Documentation in EHR Across Institutions. AMIA 2022
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Huan He, Sunyang Fu, Liwei Wang, Andrew Wen, Sijia Liu, Sungrim Moon, Kurt Miller, Hongfang Liu:
Towards User-centered Corpus Development: Lessons Learnt from Designing and Developing MedTator. AMIA 2022
[c239]
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Huan He, Irbaz Bin Riaz, Syed Arsalan Ahmed Naqvi, Rabbia Siddiqi, Noureen Asghar, Mohammad Hassan Murad, Hongfang Liu, Mahnoor Islam:
Real-time Exploration of Pairwise Meta-analysis Results by Applying Serverless Architecture Design. AMIA 2022
[c238]
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Kurt Miller, Ming Huang, Sunyang Fu, Kris Abah, Andrea Maraboto Escarria, Kevin J. Peterson, Hongfang Liu, Lacey Hart, Nelly Tan:
Probing Radiology Patient Experience Feedbacks with Aspect-based Sentiment Analysis. AMIA 2022
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Sungrim Moon, Liwei Wang, Xuan Chen, Nan Wang, Sheila Manemann, Nicholas B. Larson, Suzette J. Bielinski, Hongfang Liu:
Bridging the Granularity Gap in Family History Information Extracted from Clinical Narratives. AMIA 2022
[c236]
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Sungrim Moon, Liwei Wang, Xuan Chen, Nan Wang, Sheila Manemann, Nicholas B. Larson, Suzette J. Bielinski, Hongfang Liu:
Mapping Family History Information from Clinical Narratives to Ontologies or Terminological Resources. AMIA 2022
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Irbaz Bin Riaz, Huan He, Syed Arsalan Ahmed Naqvi, Rabbia Siddiqi, Noureen Asghar, Mahnoor Islam, Mohammad Hassan Murad, Hongfang Liu:
A Hybrid Approach to Semi-automate the Evaluation of the Certainty of Evidence for Living Systematic Reviews and Meta-analysis. AMIA 2022
[c234]
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Liwei Wang, Sungrim Moon, Sicheng Zhou, Huan He, Hongfang Liu:
Annotation Enhancement of Synthetic Family History Corpus. AMIA 2022
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Sungrim Moon, Huan He, Hongfang Liu:
Sublanguage Characteristics of Clinical Documents. BIBM 2022: 3280-3286
[c232]
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Kurt Miller, Sunyang Fu, Kris Abah, Andrea Maraboto Escarria, Kevin J. Peterson, Hongfang Liu, Lacey Hart, Nelly Tan, Ming Huang:
Aspect-based Sentiment Analysis of Radiology Patient Experience Surveys: A Cohort Study. ICHI 2022: 90-96
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Jiawei Zhou, Rosa I. Arriaga, Hongfang Liu, Ming Huang:
A Tale of Two Perspectives: Harvesting System Views and User Views to Understand Patient Portal Engagement. ICHI 2022: 373-383
[c230]
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Ray Oian, Sunyang Fu, Hongfang Liu:
Evaluation of Document-Level Identification of Pulmonary Nodules in Radiology Reports Using FLAIR Natural Language Processing Framework. ICHI 2022: 515-516
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Liwei Wang, Sunyang Fu, Andrew Wen, Xiaoyang Ruan, Huan He, Sijia Liu, Sungrim Moon, Michelle Mai, Irbaz Bin Riaz, Nan Wang, Ping Yang, Hua Xu, Jeremy L. Warner, Hongfang Liu:
Evaluation of mCODE Coverage in EHR: a Scoping Review of Cancer Natural Language Processing. ICHI 2022: 517-518
[c228]
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Huan He, Sunyang Fu, Liwei Wang, Andrew Wen, Sijia Liu, Hongfang Liu:
MedTator: A Serverless Web-based Tool for Corpus Annotation. ICHI 2022: 530-531
[i20]
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  - journals/corr/abs-2201-02517
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Sungrim Moon, Huan He, Hongfang Liu, Jungwei Fan:
RxWhyQA: a clinical question-answering dataset with the challenge of multi-answer questions. CoRR abs/2201.02517 (2022)
[i19]
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  - journals/corr/abs-2206-14181
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Yao Yan, Thomas Yu, Kathleen Muenzen, Sijia Liu, Connor Boyle, George Koslowski, Jiaxin Zheng, Nicholas J. Dobbins, Clement Essien, Hongfang Liu, Larsson Omberg, Meliha Yestigen, Bradley Taylor, James A. Eddy, Justin Guinney, Sean D. Mooney, Thomas Schaffter:
The NLP Sandbox: an efficient model-to-data system to enable federated and unbiased evaluation of clinical NLP models. CoRR abs/2206.14181 (2022)
[i18]
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  - journals/corr/abs-2212-01941
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Yifang Dang, Fang Li, Xinyue Hu, Vipina Kuttichi Keloth, Meng Zhang, Sunyang Fu, Jingcheng Du, J. Wilfred Fan, Muhammad F. Amith, Evan Yu, Hongfang Liu, Xiaoqian Jiang, Hua Xu, Cui Tao:
Systematic Design and Evaluation of Social Determinants of Health Ontology (SDoHO). CoRR abs/2212.01941 (2022)
[i17]
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  - journals/corr/abs-2212-09606
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Xiaoyang Ruan, Liwei Wang, Michelle Mai, Charat Thongprayoon, Wisit Cheungpasitporn, Hongfang Liu:
Discrimination, calibration, and point estimate accuracy of GRU-D-Weibull architecture for real-time individualized endpoint prediction. CoRR abs/2212.09606 (2022)
2021
[j119]
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Nansu Zong, Daniel J. Stone, Deepak K. Sharma, Andrew Wen, Chen Wang, Yue Yu, Ming Huang, Sijia Liu, Hongfang Liu, Qian Shi, Guoqian Jiang:
Modeling cancer clinical trials using HL7 FHIR to support downstream applications: A case study with colorectal cancer data. Int. J. Medical Informatics 145: 104308 (2021)
[j118]
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Carolyn Petersen, Jeffery Smith, Robert R. Freimuth, Kenneth W. Goodman, Gretchen Purcell Jackson, Joseph L. Kannry, Hongfang Liu, Subha Madhavan, Dean F. Sittig, Adam Wright:
Recommendations for the safe, effective use of adaptive CDS in the US healthcare system: an AMIA position paper. J. Am. Medical Informatics Assoc. 28(4): 677-684 (2021)
[j117]
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Jianfu Li, Yujia Zhou, Xiaoqian Jiang, Karthik Natarajan, Serguei V. S. Pakhomov, Hongfang Liu, Hua Xu:
Are synthetic clinical notes useful for real natural language processing tasks: A case study on clinical entity recognition. J. Am. Medical Informatics Assoc. 28(10): 2193-2201 (2021)
[j116]
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Andrew Wen, Liwei Wang, Huan He, Sijia Liu, Sunyang Fu, Sunghwan Sohn, Jacob A. Kugel, Vinod C. Kaggal, Ming Huang, Yanshan Wang, Feichen Shen, Jungwei Fan, Hongfang Liu:
An aberration detection-based approach for sentinel syndromic surveillance of COVID-19 and other novel influenza-like illnesses. J. Biomed. Informatics 113: 103660 (2021)
[j115]
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Yiqing Zhao, Saravut J. Weroha, Ellen L. Goode, Hongfang Liu, Chen Wang:
Generating real-world evidence from unstructured clinical notes to examine clinical utility of genetic tests: use case in BRCAness. BMC Medical Informatics Decis. Mak. 21(1): 3 (2021)
[j114]
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Jungwon Yoon, Heather Billings, Chung-Il Wi, Elissa Hall, Sunghwan Sohn, Jung Hyun Kwon, Euijung Ryu, Pragya Shrestha, Hongfang Liu, Young J. Juhn:
Establishing an expert consensus for the operational definitions of asthma-associated infectious and inflammatory multimorbidities for computational algorithms through a modified Delphi technique. BMC Medical Informatics Decis. Mak. 21(1): 310 (2021)
[c227]
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Chao Jiang, Victoria Ngo, Richard Chapman, Hongfang Liu, Guoqian Jiang, Nansu Zong:
Automatic Construction of Biomedical Knowledge Graph from Covid-19 Literature. AMIA 2021
[c226]
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Ming Huang, Aditya Khurana, George M. Mastorakos, Andrew Wen, Huan He, Liwei Wang, Sijia Liu, Yanshan Wang, Julie E. Prigge, Brian Costello, Nilay D. Shah, Henry Ting, Christi A. Patten, Jungwei Fan, Hongfang Liu:
Patient Asynchronous Response to Coronavirus Disease 2019 (COVID-19): A Retrospective Analysis of Patient Portal Messages. AMIA 2021
[c225]
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  - conf/amia/Estiri0LTL21
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Hossein Estiri, Yuan Luo, Hongfang Liu, Suzanne Tamang, Harold P. Lehmann:
Addressing Bias in the Application of Machine Learning on Real-World Data. AMIA 2021
[c224]
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  - conf/amia/HeRNSAML21
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Huan He, Irbaz Bin Riaz, Syed Arsalan Ahmed Naqvi, Rabbia Siddiqi, Noureen Asghar, Mohammad Hassan Murad, Hongfang Liu:
A Hybrid Approach to Semi-Automate the Screening Process for Living Systematic Reviews and Meta-Analysis. AMIA 2021
[c223]
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Huan He, Liwei Wang, Andrew Wen, Ming Huang, Yanshan Wang, Hongfang Liu:
COVID-19 Dashboard: Visual Exploration of the Regional Pandemic Trend. AMIA 2021
[c222]
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Ming Huang, Andrew Wen, Huan He, Liwei Wang, Sijia Liu, Yanshan Wang, Nansu Zong, Yue Yu, Julie E. Prigge, Brian Costello, Nilay D. Shah, Henry Ting, Chyke Doubeni, Jungwei Fan, Hongfang Liu, Christi A. Patten:
Disparity analysis of patient portal messaging use for COVID-19 in urban versus rural locality. AMIA 2021
[c221]
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  - conf/amia/RiazHNSAML21
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Irbaz Bin Riaz, Huan He, Syed Arsalan Ahmed Naqvi, Rabbia Siddiqi, Noureen Asghar, Mohammad Hassan Murad, Hongfang Liu:
An Interactive Data Extraction System to Create the Living Systematic Reviews and Meta-Analysis. AMIA 2021
[c220]
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  - conf/amia/StoneLLWZRABPWT21
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Daniel J. Stone, Sijia Liu, Yuan Luo, Andrew Wen, Nansu Zong, Luke V. Rasmussen, Prakash Adekkanattu, Pascal S. Brandt, Jennifer A. Pacheco, Fei Wang, Cui Tao, Jyotishman Pathak, Hongfang Liu, Guoqian Jiang:
FHIRTime: Standardizing Temporal Patterns Identified from Clinical Narratives Using HL7 FHIR. AMIA 2021
[c219]
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Andrew Wen, Luke V. Rasmussen, Daniel J. Stone, Sijia Liu, Prakash Adekkanattu, Pascal S. Brandt, Jennifer A. Pacheco, Yuan Luo, Fei Wang, Jyotishman Pathak, Hongfang Liu, Guoqian Jiang:
On Constraints and Considerations for Extending Support for Natural Language Processing-Based FHIR Resource Generation. AMIA 2021
[c218]
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Yiqing Zhao, Matthew Brush, Hongfang Liu, Robert R. Freimuth:
Modeling Variant Annotation (VA) Therapeutic Association Statements using a SEPIO-Based Workflow. AMIA 2021
[c217]
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Sicheng Zhou, Liwei Wang, Nan Wang, Sunyang Fu, Chetan Shenoy, Anne H. Blaes, Hongfang Liu, Rui Zhang:
Deep Learning Approaches for Breast Cancer Characteristics Extraction from Electronic Health Records. AMIA 2021
[c216]
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  - conf/medinfo/FuWPZSSFL21
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Sunyang Fu, Andrew Wen, Sandeep R. Pagali, Nansu Zong, Jennifer St Sauver, Sunghwan Sohn, Jungwei Fan, Hongfang Liu:
The Implication of Latent Information Quality to the Reproducibility of Secondary Use of Electronic Health Records. MedInfo 2021: 173-177
[c215]
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Yanbo Guo, Chen Wang, Raymond M. Moore, Hongfang Liu, Feichen Shen:
POKR: Building a Computable Heterogeneous Knowledge Resource for Precision Oncology. MedInfo 2021: 243-247
[e3]
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  - conf/ijcai/2021ai4function
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Denis Newman-Griffis, Bart Desmet, Ayah Zirikly, Suzanne Tamang, Hongfang Liu:
Proceedings of the Second Workshop on Artificial Intelligence for Function, Disability, and Health co-located with the 2021 International Joint Conference on Artificial Intelligence, AI4Function@IJCAI 2021, Online, August 20-21, 2021. CEUR Workshop Proceedings 2926, CEUR-WS.org 2021 [contents]
[i16]
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  - journals/corr/abs-2101-05866
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David Oniani, Chen Wang, Yiqing Zhao, Andrew Wen, Hongfang Liu, Feichen Shen:
Comparisons of Graph Neural Networks on Cancer Classification Leveraging a Joint of Phenotypic and Genetic Features. CoRR abs/2101.05866 (2021)
[i15]
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  - journals/corr/abs-2103-16316
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David Oniani, Chen Wang, Yiqing Zhao, Andrew Wen, Hongfang Liu, Feichen Shen:
Leveraging a Joint of Phenotypic and Genetic Features on Cancer Patient Subgrouping. CoRR abs/2103.16316 (2021)
[i14]
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  - journals/corr/abs-2108-02255
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Greg M. Silverman, Raymond L. Finzel, Michael V. Heinz, Jake Vasilakes, Jacob C. Solinsky, Reed McEwan, Benjamin C. Knoll, Christopher J. Tignanelli, Hongfang Liu, Hua Xu, Xiaoqian Jiang, Genevieve B. Melton, Serguei V. S. Pakhomov:
An Empirical Study of UMLS Concept Extraction from Clinical Notes using Boolean Combination Ensembles. CoRR abs/2108.02255 (2021)
[i13]
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  - journals/corr/abs-2108-11303
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Sicheng Zhou, Liwei Wang, Nan Wang, Hongfang Liu, Rui Zhang:
CancerBERT: a BERT model for Extracting Breast Cancer Phenotypes from Electronic Health Records. CoRR abs/2108.11303 (2021)
[i12]
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  - journals/corr/abs-2110-10780
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Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert T. Miller, Andrew E. Williams, Daniel R. Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-El-Rub, Rui Zhang, John D. Osborne, Masoud Rouhizadeh, Yongqun He, Emily R. Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu:
An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C). CoRR abs/2110.10780 (2021)
2020
[j113]
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  - journals/ijseke/WangCWPL20
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Haitao Wang, Yanli Chen, Juan Wang, Hao Peng, Hongfang Liu:
Mutual Inference Model for User Roles and Urban Functional Zones. Int. J. Softw. Eng. Knowl. Eng. 30(4): 503-521 (2020)
[j112]
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  - journals/jamia/KronzerWLDSC20
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Vanessa L. Kronzer, Liwei Wang, Hongfang Liu, John M. Davis III, Jeffrey A. Sparks, Cynthia S. Crowson:
Investigating the impact of disease and health record duration on the eMERGE algorithm for rheumatoid arthritis. J. Am. Medical Informatics Assoc. 27(4): 601-605 (2020)
[j111]
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Fang Li, Jingcheng Du, Yongqun He, Hsing-yi Song, Mohcine Madkour, Guozheng Rao, Yang Xiang, Yi Luo, Henry W. Chen, Sijia Liu, Liwei Wang, Hongfang Liu, Hua Xu, Cui Tao:
Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events. J. Am. Medical Informatics Assoc. 27(7): 1046-1056 (2020)
[j110]
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  - journals/jamia/OnianiJLS20
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David Oniani, Guoqian Jiang, Hongfang Liu, Feichen Shen:
Constructing co-occurrence network embeddings to assist association extraction for COVID-19 and other coronavirus infectious diseases. J. Am. Medical Informatics Assoc. 27(8): 1259-1267 (2020)
[j109]
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Xiao Dong, Jianfu Li, Ekin Soysal, Jiang Bian, Scott L. DuVall, Elizabeth Hanchrow, Hongfang Liu, Kristine E. Lynch, Michael E. Matheny, Karthik Natarajan, Lucila Ohno-Machado, Serguei Pakhomov, Ruth Madeleine Reeves, Amy M. Sitapati, Swapna Abhyankar, Theresa Cullen, Jami Deckard, Xiaoqian Jiang, Robert Murphy, Hua Xu:
COVID-19 TestNorm: A tool to normalize COVID-19 testing names to LOINC codes. J. Am. Medical Informatics Assoc. 27(9): 1437-1442 (2020)
[j108]
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Yanshan Wang, Yiqing Zhao, Terry M. Therneau, Elizabeth J. Atkinson, Ahmad P. Tafti, Nan Zhang, Shreyasee Amin, Andrew H. Limper, Sundeep Khosla, Hongfang Liu:
Unsupervised machine learning for the discovery of latent disease clusters and patient subgroups using electronic health records. J. Biomed. Informatics 102: 103364 (2020)
[j107]
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Sunyang Fu, David Chen, Huan He, Sijia Liu, Sungrim Moon, Kevin J. Peterson, Feichen Shen, Liwei Wang, Yanshan Wang, Andrew Wen, Yiqing Zhao, Sunghwan Sohn, Hongfang Liu:
Clinical concept extraction: A methodology review. J. Biomed. Informatics 109: 103526 (2020)
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Kevin J. Peterson, Guoqian Jiang, Hongfang Liu:
A corpus-driven standardization framework for encoding clinical problems with HL7 FHIR. J. Biomed. Informatics 110: 103541 (2020)
[j105]
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  - journals/lre/WangAFWSRL20
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Yanshan Wang, Naveed Afzal, Sunyang Fu, Liwei Wang, Feichen Shen, Majid Rastegar-Mojarad, Hongfang Liu:
MedSTS: a resource for clinical semantic textual similarity. Lang. Resour. Evaluation 54(1): 57-72 (2020)
[j104]
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Sunyang Fu, Lester Y. Leung, Anne-Olivia Raulli, David F. Kallmes, Kristin A. Kinsman, Kristoff B. Nelson, Michael S. Clark, Patrick H. Luetmer, Paul R. Kingsbury, David M. Kent, Hongfang Liu:
Assessment of the impact of EHR heterogeneity for clinical research through a case study of silent brain infarction. BMC Medical Informatics Decis. Mak. 20(1): 60 (2020)
[c214]
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Sijia Liu, Sunyang Fu, Sungrim Moon, Andrew Wen, Hongfang Liu:
Predicting Section Location of Clinical Sentences using BERT Encoder - A Pilot Study. AMIA 2020
[c213]
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Luke A. Carlson, Molly M. Jeffery, Sunyang Fu, Huan He, Rozalina G. McCoy, Yanshan Wang, W. M. Hooten, Jennifer L. St. Sauver, Hongfang Liu, Jungwei Fan:
Annotating Chronic Pain Episodes in EHR Text: Guideline Development and Corpus Analysis. AMIA 2020
[c212]
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Luke A. Carlson, Jennifer St. Sauver, Sunyang Fu, Ahmad P. Tafti, Jungwei Fan, Molly M. Jeffery, Rozalina G. McCoy, Hongfang Liu, Yanshan Wang:
Big Impact from Small Data: Unsupervised Machine Learning Approaches for Chronic Pain Patient Subgrouping. AMIA 2020
[c211]
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Huan He, Feichen Shen, Michael Lin, Hongfang Liu:
Identifying Rare Disease Studies by Natural Language Processing. AMIA 2020
[c210]
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Hongfang Liu, Xiaoqian Jiang, Serguei V. S. Pakhomov, Chunhua Weng, Hua Xu:
The Open Health Natural Language Processing Collaboratory. AMIA 2020
[c209]
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Irbaz Bin Riaz, Huan He, Yiqing Zhao, Rabbia Siddiqi, Vitaly Herasevich, Per Olav Vandvik, Victor Montori, Allan Bryce, Mohammad Hassan Murad, Hongfang Liu:
A Living Network Meta-Analysis of First Line Treatment of Metastatic Kidney Cancer. AMIA 2020
[c208]
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Elham Sagheb, Jungwon Yoon, Chung-Il Wi, Pragya Shrestha, Euijung Ryu, Miguel Park, Barbara P. Yawn, Hongfang Liu, Young J. Juhn, Sunghwan Sohn:
Assessing Clinician's Adherence to Asthma Guidelines for Asthma Control Status using Natural Language Processing in a Primary Care Setting. AMIA 2020
[c207]
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Andrew Wen, Sunyang Fu, Feichen Shen, Hongfang Liu:
Accelerating Development of Learning Healthcare Systems via Distantly Supervised Knowledge Discovery. AMIA 2020
[c206]
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Yiqing Zhao, Hanzhong Yu, Luke A. Carlson, Feichen Shen, Sunyang Fu, Hongfang Liu, Chen Wang:
Extracting Patient Genetic Information from Unstructured Clinical Notes. AMIA 2020
[c205]
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  - conf/cbms/ShenWL20
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Feichen Shen, Andrew Wen, Hongfang Liu:
Enrich Rare Disease Phenotypic Characterizations via a Graph Convolutional Network Based Recommendation System. CBMS 2020: 37-40
[c204]
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  - conf/cbms/ShenWL20a
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Feichen Shen, Andrew Wen, Hongfang Liu:
Subgrouping Rare Disease Patients Leveraging the Human Phenotype Ontology Embeddings. CBMS 2020: 169-172
[c203]
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Andrew Wen, Feichen Shen, Sungrim Moon, Hongfang Liu, Jungwei Fan:
A Deep Profiling and Visualization Framework to Audit Clinical Assessment Variation. CBMS 2020: 546-551
[c202]
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  - conf/isvc/YanRSFSLLKCTKT20
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Shi Yan, Taghi Ramazanian, Elham Sagheb, Sunyang Fu, Sunghwan Sohn, David G. Lewallen, Hongfang Liu, Walter K. Kremers, Vipin Chaudhary, Michael J. Taunton, Hilal Maradit Kremers, Ahmad P. Tafti:
DeepTKAClassifier: Brand Classification of Total Knee Arthroplasty Implants Using Explainable Deep Convolutional Neural Networks. ISVC (2) 2020: 154-165
[c201]
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Steve Chamberlin, Steven Bedrick, Aaron M. Cohen, Yanshan Wang, Andrew Wen, Sijia Liu, Hongfang Liu, William R. Hersh:
A Query Taxonomy Describes Performance of Patient-Level Retrieval from Electronic Health Record Data. HSDM@WSDM 2020: 27-33
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Denis Newman-Griffis, Serguei V. S. Pakhomov, Suzanne Tamang, Ayah Zirikly, Bart Desmet, Hongfang Liu, Junichi Tsujii:
Proceedings of the First Workshop on Artificial Intelligence for Function, Disability, and Health co-located with the 2020 International Joint Conference on Artificial Intelligence - Pacific Rim Conference on Artificial Intelligence (IJCAI-PRICAI 2020), Online, January 7-8, 2021. CEUR Workshop Proceedings 2760, CEUR-WS.org 2020 [contents]

2010 – 2019

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2019
[j103]
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Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C. Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C. Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altinel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu:
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database J. Biol. Databases Curation 2019: bay147 (2019)
[j102]
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Sungrim Moon, Sijia Liu, Christopher Scott, Sujith Samudrala, Mohamed M. Abidian, Jeffrey B. Geske, Peter A. Noseworthy, Jane L. Shellum, Rajeev Chaudhry, Steve Ommen, Rick Nishimura, Hongfang Liu, Adelaide M. Arruda-Olson:
Automated extraction of sudden cardiac death risk factors in hypertrophic cardiomyopathy patients by natural language processing. Int. J. Medical Informatics 128: 32-38 (2019)
[j101]
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Xin Zhou, Yanshan Wang, Sunghwan Sohn, Terry M. Therneau, Hongfang Liu, David S. Knopman:
Automatic extraction and assessment of lifestyle exposures for Alzheimer's disease using natural language processing. Int. J. Medical Informatics 130 (2019)
[j100]
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  - journals/jbi/ShenPFWLWWL19
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Feichen Shen, Suyuan Peng, Yadan Fan, Andrew Wen, Sijia Liu, Yanshan Wang, Liwei Wang, Hongfang Liu:
HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology. J. Biomed. Informatics 96 (2019)
[j99]
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  - journals/jbi/HongWSTKRPAWLPL19
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Na Hong, Andrew Wen, Daniel J. Stone, Shintaro Tsuji, Paul R. Kingsbury, Luke V. Rasmussen, Jennifer A. Pacheco, Prakash Adekkanattu, Fei Wang, Yuan Luo, Jyotishman Pathak, Hongfang Liu, Guoqian Jiang:
Developing a FHIR-based EHR phenotyping framework: A case study for identification of patients with obesity and multiple comorbidities from discharge summaries. J. Biomed. Informatics 99 (2019)
[j98]
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  - journals/jbi/LiuTRLLBSKWSLEF19
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Cong Liu, Casey N. Ta, James R. Rogers, Ziran Li, Junghwan Lee, Alex M. Butler, Ning Shang, Fabricio Sampaio Peres Kury, Liwei Wang, Feichen Shen, Hongfang Liu, Lyudmila Ena, Carol Friedman, Chunhua Weng:
Ensembles of natural language processing systems for portable phenotyping solutions. J. Biomed. Informatics 100 (2019)
[j97]
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Feichen Shen, Vipin Chaudhary, Yan Liu, Che Ngufor, Hongfang Liu:
Special Issue on Healthcare Knowledge Discovery and Management. J. Heal. Informatics Res. 3(2): 157-158 (2019)
[j96]
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Sungrim Moon, Sijia Liu, David Chen, Yanshan Wang, Douglas L. Wood, Rajeev Chaudhry, Hongfang Liu, Paul R. Kingsbury:
Salience of Medical Concepts of Inside Clinical Texts and Outside Medical Records for Referred Cardiovascular Patients. J. Heal. Informatics Res. 3(2): 200-219 (2019)
[j95]
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Feichen Shen, David W. Larson, James M. Naessens, Elizabeth B. Habermann, Hongfang Liu, Sunghwan Sohn:
Detection of Surgical Site Infection Utilizing Automated Feature Generation in Clinical Notes. J. Heal. Informatics Res. 3(3): 267-282 (2019)
[j94]
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Yanshan Wang, Sunghwan Sohn, Sijia Liu, Feichen Shen, Liwei Wang, Elizabeth J. Atkinson, Shreyasee Amin, Hongfang Liu:
A clinical text classification paradigm using weak supervision and deep representation. BMC Medical Informatics Decis. Mak. 19(1): 1:1-1:13 (2019)
[j93]
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Feichen Shen, Yiqing Zhao, Liwei Wang, Majid Rastegar-Mojarad, Yanshan Wang, Sijia Liu, Hongfang Liu:
Rare disease knowledge enrichment through a data-driven approach. BMC Medical Informatics Decis. Mak. 19(1): 32:1-32:11 (2019)
[j92]
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  - journals/midm/SadatAMPLJ19
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Md. Nazmus Sadat, Md Momin Al Aziz, Noman Mohammed, Serguei Pakhomov, Hongfang Liu, Xiaoqian Jiang:
A privacy-preserving distributed filtering framework for NLP artifacts. BMC Medical Informatics Decis. Mak. 19(1): 183:1-183:10 (2019)
[j91]
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Liwei Wang, Yanshan Wang, Feichen Shen, Majid Rastegar-Mojarad, Hongfang Liu:
Discovering associations between problem list and practice setting. BMC Medical Informatics Decis. Mak. 19-S(3): 13-22 (2019)
[j90]
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Yanshan Wang, Saeed Mehrabi, Sunghwan Sohn, Elizabeth J. Atkinson, Shreyasee Amin, Hongfang Liu:
Natural language processing of radiology reports for identification of skeletal site-specific fractures. BMC Medical Informatics Decis. Mak. 19-S(3): 23-29 (2019)
[j89]
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Liwei Wang, Lei Luo, Yanshan Wang, Jason A. Wampfler, Ping Yang, Hongfang Liu:
Natural language processing for populating lung cancer clinical research data. BMC Medical Informatics Decis. Mak. 19-S(5): 2 (2019)
[j88]
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Sijia Liu, Yanshan Wang, Hongfang Liu:
Selected articles from the BioCreative/OHNLP challenge 2018. BMC Medical Informatics Decis. Mak. 19-S(10): 262 (2019)
[j87]
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  - journals/mlc/ZhouZFLYL19
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Guoqiang Zhou, Shuai Zhang, Yi Fan, Jingjin Li, Wenbo Yao, Hongfang Liu:
Recommendations based on user effective point-of-interest path. Int. J. Mach. Learn. Cybern. 10(10): 2887-2899 (2019)
[j86]
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  - journals/npjdm/00030KSSHNLL19
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David Chen, Sijia Liu, Paul R. Kingsbury, Sunghwan Sohn, Curtis B. Storlie, Elizabeth B. Habermann, James M. Naessens, David W. Larson, Hongfang Liu:
Deep learning and alternative learning strategies for retrospective real-world clinical data. npj Digit. Medicine 2 (2019)
[j85]
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Andrew Wen, Sunyang Fu, Sungrim Moon, Mohamed El Wazir, Andrew Rosenbaum, Vinod C. Kaggal, Sijia Liu, Sunghwan Sohn, Hongfang Liu, Jungwei Fan:
Desiderata for delivering NLP to accelerate healthcare AI advancement and a Mayo Clinic NLP-as-a-service implementation. npj Digit. Medicine 2 (2019)
[c200]
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  - conf/amia/ChaudhryMKWRLSC19
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Alisha Chaudhry, Sungrim Moon, Vinod Kaggal, Paul Wennberg, Thom Rooke, David Liedl, Christopher Scott, Ana Casanegra, Iftikhar J. Kullo, Robert McBane, Jane L. Shellum, Rick Nishimura, Rajeev Chaudhry, Hongfang Liu, Adelaide M. Arruda-Olson:
Usability Evaluation of a Clinical Decision Support Tool for Management of Peripheral Artery Disease Patients. AMIA 2019
[c199]
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  - conf/amia/MoonKSLCA19
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Sungrim Moon, Vinod Kaggal, Sunghwan Sohn, Hongfang Liu, Rajeev Chaudhry, Adelaide M. Arruda-Olson:
Adaptation of a Natural Language Processing Algorithm Following Implementation of a New Electronic Health Record. AMIA 2019
[c198]
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  - conf/amia/PetersonL19
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Kevin J. Peterson, Hongfang Liu:
A Data-Driven System for Defining Interoperable Semantic Models of Clinical Concepts using HL7 FHIR Profiles: A Proposed Framework. AMIA 2019
[c197]
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Feichen Shen, Yiqing Zhao, Hongfang Liu:
Leveraging a Data-Driven Strategy to Enrich Rare Disease Knowledge. AMIA 2019
[c196]
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Ahmad P. Tafti, Edin Cubro, Hongfang Liu, Brian W. Pickering, Vitaly Herasevich:
Privacy-preserving and non-intrusive video recognition technique to count the number of patient room visits during patient deterioration: a simulation study. AMIA 2019
[c195]
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Liwei Wang, Suzette J. Bielinski, Paul A. Decker, Jill M. Killian, Nicholas B. Larson, Rui Zhang, Hongfang Liu:
Association between Cardiotoxic Chemotherapy and Myocardial Infarction. AMIA 2019
[c194]
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Liwei Wang, Jason A. Wampfler, Angela Dispenzieri, Hua Xu, Ping Yang, Hongfang Liu:
Achievability to Extract Specific Date Information for Cancer Research. AMIA 2019
[c193]
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Yanshan Wang, Andrew Wen, Sijia Liu, Jennifer L. St. Sauver, Adil E. Bharucha, Chunhua Weng, Hongfang Liu:
Clinical Use of an Information Retrieval Framework for Cohort Discovery from Electronic Health Records. AMIA 2019
[c192]
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Yiqing Zhao, Yanshan Wang, Paul R. Kingsbury, Michael Panzer, Richard Van Ert, Hongfang Liu:
Summarization of Patient Education Material for New Media Platform. AMIA 2019
[c191]
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Ahmad P. Tafti, Yanshan Wang, Feichen Shen, Elham Sagheb, Paul R. Kingsbury, Hongfang Liu:
Integrating word embedding neural networks with PubMed abstracts to extract keyword proximity of chronic diseases. BHI 2019: 1-4
[c190]
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Ahmad P. Tafti, Sunyang Fu, Aditya Khurana, George M. Mastorakos, Kenneth G. Poole, Stephen J. Traub, James A. Yiannias, Hongfang Liu:
Artificial intelligence to organize patient portal messages: a journey from an ensemble deep learning text classification to rule-based named entity recognition. BIBM 2019: 1380-1387
[c189]
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Andrew Wen, Yanshan Wang, Vinod C. Kaggal, Sijia Liu, Hongfang Liu, Jungwei Fan:
Enhancing Clinical Information Retrieval through Context-Aware Queries and Indices. IEEE BigData 2019: 2800-2807
[c188]
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Liwei Wang, Lei Luo, Yanshan Wang, Jason A. Wampfler, Ping Yang, Hongfang Liu:
Information Extraction for Populating Lung Cancer Clinical Research Data. ICHI 2019: 1-2
[c187]
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Ergin Soysal, Jeremy L. Warner, Jingqi Wang, Min Jiang, Krysten Harvey, Sandeep Kumar Jain, Xiao Dong, Hsing-yi Song, Harish Siddhanamatha, Liwei Wang, Qi Dai, Qingxia Chen, Xianglin Du, Cui Tao, Ping Yang, Joshua Charles Denny, Hongfang Liu, Hua Xu:
Developing Customizable Cancer Information Extraction Modules for Pathology Reports Using CLAMP. MedInfo 2019: 1041-1045
[c186]
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Ahmad P. Tafti, Yue Dong, Elizabeth B. Habermann, Hongfang Liu, Vitaly Herasevich:
Relationship Between Very Cold Outside Weather and Surgical Outcome: Integrating Shallow and Deep Artificial Neural Nets. MedInfo 2019: 1783-1784
[c185]
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Graciela Gonzalez, Zhiyong Lu, Robert Leaman, Davy Weissenbacher, Mary Regina Boland, Yong Chen, Jingcheng Du, Juliane Fluck, Casey S. Greene, John H. Holmes, Aditya Kashyap, Rikke Linnemann Nielsen, Zhengqing Ouyang, Sebastian Schaaf, Jaclyn N. Taroni, Cui Tao, Yuping Zhang, Hongfang Liu:
Text Mining and Machine Learning for Precision Medicine. PSB 2019: 449-454
[i11]
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  - journals/corr/abs-1901-07601
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Sijia Liu, Yanshan Wang, Andrew Wen, Liwei Wang, Na Hong, Feichen Shen, Steven Bedrick, William R. Hersh, Hongfang Liu:
CREATE: Cohort Retrieval Enhanced by Analysis of Text from Electronic Health Records using OMOP Common Data Model. CoRR abs/1901.07601 (2019)
[i10]
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  - journals/corr/abs-1905-10309
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Yanshan Wang, Yiqing Zhao, Terry M. Therneau, Elizabeth J. Atkinson, Ahmad P. Tafti, Nan Zhang, Shreyasee Amin, Andrew H. Limper, Hongfang Liu:
Unsupervised Machine Learning for the Discovery of Latent Disease Clusters and Patient Subgroups Using Electronic Health Records. CoRR abs/1905.10309 (2019)
[i9]
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  - journals/corr/abs-1906-09543
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Jun Jiang, Shumao Pang, Xia Zhao, Liwei Wang, Andrew Wen, Hongfang Liu, Qianjin Feng:
Cross-lingual Data Transformation and Combination for Text Classification. CoRR abs/1906.09543 (2019)
[i8]
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  - journals/corr/abs-1908-10678
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Yanshan Wang, Krishna B. Soundararajan, Sunyang Fu, Luke A. Carlson, Rebecca A. Smith, David S. Knopman, Hongfang Liu:
How Good is Artificial Intelligence at Automatically Answering Consumer Questions Related to Alzheimer's Disease? CoRR abs/1908.10678 (2019)
[i7]
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  - journals/corr/abs-1910-11377
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Sunyang Fu, David Chen, Sijia Liu, Sungrim Moon, Kevin J. Peterson, Feichen Shen, Yanshan Wang, Liwei Wang, Andrew Wen, Yiqing Zhao, Sunghwan Sohn, Hongfang Liu:
Development of Clinical Concept Extraction Applications: A Methodology Review. CoRR abs/1910.11377 (2019)
2018
[j84]
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K. E. Ravikumar, Kathy L. MacLaughlin, Marianne R. Scheitel, Maya Kessler, Kavishwar B. Wagholikar, Hongfang Liu, Rajeev Chaudhry:
Improving the Accuracy of a Clinical Decision Support System for Cervical Cancer Screening and Surveillance. Appl. Clin. Inform. 09(01): 62-71 (2018)
[j83]
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  - journals/biodb/LiuSEWRCL18
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Sijia Liu, Feichen Shen, Ravikumar Komandur Elayavilli, Yanshan Wang, Majid Rastegar-Mojarad, Vipin Chaudhary, Hongfang Liu:
Extracting chemical-protein relations using attention-based neural networks. Database J. Biol. Databases Curation 2018: bay102 (2018)
[j82]
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  - journals/ijmi/AfzalMSLCSKA18
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Naveed Afzal, Vishnu Priya Mallipeddi, Sunghwan Sohn, Hongfang Liu, Rajeev Chaudhry, Christopher Scott, Iftikhar J. Kullo, Adelaide M. Arruda-Olson:
Natural language processing of clinical notes for identification of critical limb ischemia. Int. J. Medical Informatics 111: 83-89 (2018)
[j81]
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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. J. Am. Medical Informatics Assoc. 25(3): 331-336 (2018)
[j80]
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Sunghwan Sohn, Yanshan Wang, Chung-Il Wi, Elizabeth A. Krusemark, Euijung Ryu, Mir H. Ali, Young J. Juhn, Hongfang Liu:
Clinical documentation variations and NLP system portability: a case study in asthma birth cohorts across institutions. J. Am. Medical Informatics Assoc. 25(3): 353-359 (2018)
[j79]
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Yanshan Wang, Liwei Wang, Majid Rastegar-Mojarad, Sungrim Moon, Feichen Shen, Naveed Afzal, Sijia Liu, Yuqun Zeng, Saeed Mehrabi, Sunghwan Sohn, Hongfang Liu:
Clinical information extraction applications: A literature review. J. Biomed. Informatics 77: 34-49 (2018)
[j78]
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Stephen T. Wu, Sijia Liu, Sunghwan Sohn, Sungrim Moon, Chung-Il Wi, Young J. Juhn, Hongfang Liu:
Modeling asynchronous event sequences with RNNs. J. Biomed. Informatics 83: 167-177 (2018)
[j77]
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Yanshan Wang, Sijia Liu, Naveed Afzal, Majid Rastegar-Mojarad, Liwei Wang, Feichen Shen, Paul R. Kingsbury, Hongfang Liu:
A comparison of word embeddings for the biomedical natural language processing. J. Biomed. Informatics 87: 12-20 (2018)
[j76]
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  - journals/midm/ZhaoFLL18
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Yiqing Zhao, Nooshin J. Fesharaki, Hongfang Liu, Jake Luo:
Using data-driven sublanguage pattern mining to induce knowledge models: application in medical image reports knowledge representation. BMC Medical Informatics Decis. Mak. 18(1): 61:1-61:13 (2018)
[j75]
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Na Hong, Ning Zhang, Huawei Wu, Shanshan Lu, Yue Yu, Li Hou, Yinying Lu, Hongfang Liu, Guoqian Jiang:
Preliminary exploration of survival analysis using the OHDSI common data model: a case study of intrahepatic cholangiocarcinoma. BMC Medical Informatics Decis. Mak. 18(S-5): 81-88 (2018)
[c184]
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Sijia Liu, Liwei Wang, Sunghwan Sohn, Liping Xia, Hongfang Liu:
ARETA: A Corpus for Asthma Related Event Temporal Association. AMIA 2018
[c183]
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  - conf/amia/Arruda-OlsonAMS18
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Adelaide M. Arruda-Olson, Naveed Afzal, Vishnu Priya Mallipeddi, Ahmad Said, Homam Moussa Pacha, Sungrim Moon, Alisha Chaudhry, Christopher Scott, Kent Bailey, Vinod Kaggal, Gustavo Oderich, Iftikhar J. Kullo, Rick Nishimura, Rajeev Chaudhry, Hongfang Liu:
Leveraging the Electronic Health Record to Create an Automated Real-time Prognostic Tool for Peripheral Arterial Disease. AMIA 2018
[c182]
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Sunyang Fu, Lester Y. Leung, Anne-Olivia Raulli, David F. Kallmes, Kristin A. Kinsman, Kristoff B. Nelson, Michael S. Clark, Patrick H. Luetmer, Paul R. Kingsbury, David M. Kent, Hongfang Liu:
Natural Language Processing for the Identification of Silent Brain Infractions from Neuroimaging Reports. AMIA 2018
[c181]
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Na Hong, Andrew Wen, Majid Rastegar-Mojarad, Sunghwan Sohn, Hongfang Liu, Guoqian Jiang:
Standardizing Heterogeneous Annotation Corpora Using HL7 FHIR for Facilitating their Reuse and Integration in Clinical NLP. AMIA 2018
[c180]
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  - conf/amia/JacobsonCLPZ18
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Rebecca Crowley Jacobson, Wendy W. Chapman, Hongfang Liu, Olga V. Patterson, Daniel S. Zisook:
Natural Language Processing at Scale - Perspectives from Five Healthcare Organizations. AMIA 2018
[c179]
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  - conf/amia/Moon0SSGNOCNLA18
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Sungrim Moon, Sijia Liu, Sujith Samudrala, Jane L. Shellum, Jeffrey B. Geske, Peter A. Noseworthy, Steve Ommen, Rajeev Chaudhry, Rick Nishimura, Hongfang Liu, Adelaide M. Arruda-Olson:
Leveraging Electronic Health Records for Identification of Features Associated with Sudden Death for Hypertrophic Cardiomyopathy Patients. AMIA 2018
[c178]
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Kevin J. Peterson, Hongfang Liu:
The Sublanguage of Clinical Problem Lists: A Corpus Analysis. AMIA 2018
[c177]
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Feichen Shen, Hongfang Liu:
Incorporating Knowledge-Driven Insights into a Collaborative Filtering Model to Facilitate the Differential Diagnosis of Rare Diseases. AMIA 2018
[c176]
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Feichen Shen, Hongfang Liu:
Combining Knowledge and Data Driven Insights to Facilitate the Differential Diagnosis of Rare Diseases. AMIA 2018
[c175]
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Liwei Wang, Lei Luo, Yanshan Wang, Jason A. Wampfler, Ping Yang, Hongfang Liu:
Information Extraction for Data Population in Lung Cancer Clinical Research. AMIA 2018
[c174]
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  - conf/amia/WangW0L18
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Yanshan Wang, Andrew Wen, Sijia Liu, Hongfang Liu:
EMIRS: An Electronic Medical Information Retrieval System by Leveraging both Structured and Unstructured Electronic Health Records. AMIA 2018
[c173]
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  - conf/bcb/Rastegar-Mojarad18
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Majid Rastegar-Mojarad, Sijia Liu, Yanshan Wang, Naveed Afzal, Liwei Wang, Feichen Shen, Sunyang Fu, Hongfang Liu:
BioCreative/OHNLP Challenge 2018. BCB 2018: 575
[c172]
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  - conf/bibm/PengFWWLLS18
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Su-Yuan Peng, Yadan Fan, Liwei Wang, Andrew Wen, Xusheng Liu, Hongfang Liu, Feichen Shen:
Leveraging Association Rule Mining to Detect Pathophysiological Mechanisms of Chronic Kidney Disease Complicated by Metabolic Syndrome. BIBM 2018: 1302-1309
[c171]
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Yiqing Zhao, Yanshan Wang, Henry Wang, Benjamin Yan, Feichen Shen, Kevin J. Peterson, Walter A. Rocca, Jennifer St. Sauver, Hongfang Liu:
Annotating Cohort Data Elements with OHDSI Common Data Model to Promote Research Reproducibility. BIBM 2018: 1310-1317
[c170]
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  - conf/ichi/WangREWL18
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Liwei Wang, Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Yanshan Wang, Hongfang Liu:
Identification of Genetic Causality Statements in Medline Abstracts Leveraging Distant Supervision. ICHI Workshops 2018: 1-8
[c169]
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Feichen Shen, Sijia Liu, Yanshan Wang, Liwei Wang, Andrew Wen, Andrew H. Limper, Hongfang Liu:
Constructing Node Embeddings for Human Phenotype Ontology to Assist Phenotypic Similarity Measurement. ICHI Workshops 2018: 29-33
[c168]
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  - conf/ichi/WangWSRL18
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Liwei Wang, Yanshan Wang, Feichen Shen, Majid Rastegar-Mojarad, Hongfang Liu:
Predicting Practice Setting Using Topic Modeling. ICHI Workshops 2018: 62-63
[c167]
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  - conf/ichi/Wang0SAAL18
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Yanshan Wang, Saeed Mehrabi, Sunghwan Sohn, Elizabeth J. Atkinson, Shreyasee Amin, Hongfang Liu:
Automatic Extraction of Major Osteoporotic Fractures from Radiology Reports using Natural Language Processing. ICHI Workshops 2018: 64-65
[c166]
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  - conf/ichi/ZhouLW18
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Xin Zhou, Hongfang Liu, Yanshan Wang:
A Comparison of Lifestyle Interventions for Alzheimer's Disease Extracted from Clinical Notes and Literature. ICHI Workshops 2018: 74-75
[c165]
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  - conf/psb/Gonzalez-Hernandez18
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  - https://dblp.org/rec/conf/psb/Gonzalez-Hernandez18
Graciela Gonzalez-Hernandez, Abeed Sarker, Karen O'Connor, Casey S. Greene, Hongfang Liu:
Session Introduction. PSB 2018: 559-565
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Yanshan Wang, Andrew Wen, Sijia Liu, Hongfang Liu:
MayoNLPTeam at the TREC 2018 Precision Medicine Track: Simple Information Retrieval Approach Is the Best. TREC 2018
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Amarda Shehu, Cathy H. Wu, Christina Boucher, Jing Li, Hongfang Liu, Mihai Pop:
Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2018, Washington, DC, USA, August 29 - September 01, 2018. ACM 2018 [contents]
[i6]
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Yanshan Wang, Sijia Liu, Naveed Afzal, Majid Rastegar-Mojarad, Liwei Wang, Feichen Shen, Paul R. Kingsbury, Hongfang Liu:
A Comparison of Word Embeddings for the Biomedical Natural Language Processing. CoRR abs/1802.00400 (2018)
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  - journals/corr/abs-1803-08850
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Feichen Shen, David W. Larson, James M. Naessens, Elizabeth B. Habermann, Hongfang Liu, Sunghwan Sohn:
Detection of Surgical Site Infection Utilizing Automated Feature Generation in Clinical Notes. CoRR abs/1803.08850 (2018)
[i4]
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  - journals/corr/abs-1804-07814
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Yanshan Wang, Sunghwan Sohn, Sijia Liu, Feichen Shen, Liwei Wang, Elizabeth J. Atkinson, Shreyasee Amin, Hongfang Liu:
A Deep Representation Empowered Distant Supervision Paradigm for Clinical Information Extraction. CoRR abs/1804.07814 (2018)
[i3]
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  - journals/corr/abs-1808-09397
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Yanshan Wang, Naveed Afzal, Sunyang Fu, Liwei Wang, Feichen Shen, Majid Rastegar-Mojarad, Hongfang Liu:
MedSTS: A Resource for Clinical Semantic Textual Similarity. CoRR abs/1808.09397 (2018)
2017
[j74]
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K. E. Ravikumar, Majid Rastegar-Mojarad, Hongfang Liu:
BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences. Database J. Biol. Databases Curation 2017: baw156 (2017)
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Yanshan Wang, Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Hongfang Liu:
Leveraging word embeddings and medical entity extraction for biomedical dataset retrieval using unstructured texts. Database J. Biol. Databases Curation 2017: bax091 (2017)
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Yanshan Wang, In-Chan Choi, Hongfang Liu:
Generalized ensemble model for document ranking in information retrieval. Comput. Sci. Inf. Syst. 14(1): 123-151 (2017)
[j71]
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Majid Rastegar-Mojarad, Sunghwan Sohn, Liwei Wang, Feichen Shen, Troy C. Bleeker, William A. Cliby, Hongfang Liu:
Need of informatics in designing interoperable clinical registries. Int. J. Medical Informatics 108: 78-84 (2017)
[j70]
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Stephen T. Wu, Sijia Liu, Yanshan Wang, Tamara Timmons, Harsha Uppili, Steven Bedrick, William R. Hersh, Hongfang Liu:
Intrainstitutional EHR collections for patient-level information retrieval. J. Assoc. Inf. Sci. Technol. 68(11): 2636-2648 (2017)
[c163]
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Naveed Afzal, Yanshan Wang, Feichen Shen, Liwei Wang, Hongfang Liu:
A Resource for Clinical Semantic Textual Similarity. AMIA 2017
[c162]
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Zhengping Che, Jennifer L. St. Sauver, Hongfang Liu, Yan Liu:
Deep Learning Solutions for Classifying Patients on Opioid Use. AMIA 2017
[c161]
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Gregory P. Finley, Benjamin C. Knoll, Reed McEwan, Genevieve B. Melton, Hongfang Liu, Hua Xu, Serguei V. S. Pakhomov:
AMICUS: A Metasystem for Interoperation and Combination of UIMA Systems. AMIA 2017
[c160]
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Vishnu Priya Mallipeddi, Naveed Afzal, Iftikhar J. Kullo, Hongfang Liu, Rajeev Chaudhry, Adelaide M. Arruda-Olson:
Guideline Based Recommended Therapies in PAD Patients Identified by NLP: A Quality Assessment Project. AMIA 2017
[c159]
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Sungrim Moon, Donna M. Ihrke, Yuqun Zeng, Hongfang Liu:
Distinction between medical and non-medical usages of short forms in clinical narratives. AMIA 2017
[c158]
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Che Ngufor, Matthew A. Warner, Dennis Murphree, Hongfang Liu, Rickey E. Carter, Curtis B. Storlie, Daryl J. Kor:
Identification of Clinically Meaningful Plasma Transfusion Subgroups Using Unsupervised Random Forest Clustering. AMIA 2017
[c157]
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Kevin J. Peterson, Guoqian Jiang, Scott M. Brue, Feichen Shen, Hongfang Liu:
Mining Hierarchies and Similarity Clusters from Value Set Repositories. AMIA 2017
[c156]
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Feichen Shen, Sijia Liu, Yanshan Wang, Liwei Wang, Naveed Afzal, Hongfang Liu:
Leveraging Collaborative Filtering to Accelerate Rare Disease Diagnosis. AMIA 2017
[c155]
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Feichen Shen, Sijia Liu, Yanshan Wang, Liwei Wang, Naveed Afzal, Hongfang Liu:
Accelerating Rare Disease Diagnosis with Collaborative Filtering. AMIA 2017
[c154]
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Sunghwan Sohn, Young J. Juhn, Sungrim Moon, Chung-Il Wi, Katherine S. King, Euijung Ryu, Hongfang Liu:
Bayesian Prediction of Asthma Exacerbation in Children. AMIA 2017
[c153]
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Yanshan Wang, Naveed Afzal, Liwei Wang, Feichen Shen, Hongfang Liu:
Semantic Representations of Medical Terms: A Comparison Study of Word Embeddings Trained on Clinical Notes and PubMed Articles. AMIA 2017
[c152]
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Yuqun Zeng, Yanshan Wang, Feichen Shen, Sijia Liu, Liwei Wang, Majid Rastegar-Mojarad, Xusheng Liu, Hongfang Liu:
Recommending education materials for diabetic questions using information retrieval approaches. AMIA 2017
[c151]
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  - conf/bcb/WangLRWSLL17
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Yanshan Wang, Sijia Liu, Majid Rastegar-Mojarad, Liwei Wang, Feichen Shen, Fei Liu, Hongfang Liu:
Dependency and AMR Embeddings for Drug-Drug Interaction Extraction from Biomedical Literature. BCB 2017: 36-43
[c150]
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  - conf/bibm/Moon0KCWSCL17
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Sungrim Moon, Sijia Liu, Paul R. Kingsbury, David Chen, Yanshan Wang, Feichen Shen, Rajeev Chaudhry, Hongfang Liu:
Medical concept intersection between outside medical records and consultant notes: A case study in transferred cardiovascular patients. BIBM 2017: 1495-1500
[c149]
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Sijia Liu, Liwei Wang, Donna M. Ihrke, Vipin Chaudhary, Cui Tao, Chunhua Weng, Hongfang Liu:
Correlating Lab Test Results in Clinical Notes with Structured Lab Data: A Case Study in HbA1c and Glucose. CRI 2017
[c148]
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Naveed Afzal, Sunghwan Sohn, Christopher Scott, Hongfang Liu, Iftikhar J. Kullo, Adelaide M. Arruda-Olson:
Surveillance of Peripheral Arterial Disease Cases Using Natural Language Processing of Clinical Notes. CRI 2017
[c147]
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  - conf/cri/Arruda-OlsonAPS17
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Adelaide M. Arruda-Olson, Naveed Afzal, Homam Moussa Pacha, Ahmad Said, Bradley Lewis, Christopher Scott, Kent Bailey, Hongfang Liu, Iftikhar J. Kullo:
Mortality Prognostic Model for Peripheral Arterial Disease. CRI 2017
[c146]
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  - conf/cri/FinleyKLXMP17
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Gregory P. Finley, Benjamin C. Knoll, Hongfang Liu, Hua Xu, Genevieve B. Melton, Serguei V. S. Pakhomov:
Using ensembles of NLP engines without a common type system to improve abbreviation disambiguation. CRI 2017
[c145]
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Feichen Shen, Sunghwan Sohn, Majid Rastegar-Mojarad, Sijia Liu, Joshua J. Pankratz, Michael Hatton, Nancy Sowada, Om Shrestha, Shawna Shurson, Hongfang Liu:
Populating Physician Biographical Pages Based on EMR Data. CRI 2017
[c144]
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Yanshan Wang, Liwei Wang, Majid Rastegar-Mojarad, Sijia Liu, Feichen Shen, Hongfang Liu:
Content Analysis of Free-Text Family History. CRI 2017
[c143]
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  - conf/cri/ZhouLHNLS17
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Yangmei Zhou, David W. Larson, Elizabeth B. Habermann, James M. Naessens, Hongfang Liu, Sunghwan Sohn:
Prediction of Organ Space Colorectal Surgical Site Infections Using Prognostic Bayesian Networks. CRI 2017
[c142]
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Yangmei Zhou, David W. Larson, Elizabeth B. Habermann, James M. Naessens, Hongfang Liu, Sunghwan Sohn:
Locally Generated Bayesian Network Prediction of Colorectal Surgical Site Infections. CRI 2017
[c141]
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Majid Rastegar-Mojarad, Jenna K. Lovely, Joshua J. Pankratz, Sunghwan Sohn, Donna M. Ihrke, Amit Merchea, David W. Larson, Hongfang Liu:
Using Unstructured Data to Identify Readmitted Patients. ICHI 2017: 1-4
[c140]
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Sijia Liu, Yanshan Wang, Na Hong, Feichen Shen, Stephen T. Wu, William R. Hersh, Hongfang Liu:
On Mapping Textual Queries to a Common Data Model. ICHI 2017: 21-25
[c139]
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Feichen Shen, Liwei Wang, Hongfang Liu:
Phenotypic Analysis of Clinical Narratives Using Human Phenotype Ontology. MedInfo 2017: 581-585
[c138]
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Stephen T. Wu, Andrew Wen, Yanshan Wang, Sijia Liu, Hongfang Liu:
Aligned-Layer Text Search in Clinical Notes. MedInfo 2017: 629-633
[c137]
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Sunghwan Sohn, Chung-Il Wi, Young J. Juhn, Hongfang Liu:
Analysis of Clinical Variations in Asthma Care Documented in Electronic Health Records Between Staff and Resident Physicians. MedInfo 2017: 1170-1174
[c136]
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Feichen Shen, Liwei Wang, Hongfang Liu:
Using Human Phenotype Ontology for Phenotypic Analysis of Clinical Notes. MedInfo 2017: 1285
[c135]
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  - conf/semeval/LiuSCL17
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Sijia Liu, Feichen Shen, Vipin Chaudhary, Hongfang Liu:
MayoNLP at SemEval 2017 Task 10: Word Embedding Distance Pattern for Keyphrase Classification in Scientific Publications. SemEval@ACL 2017: 956-960
[c134]
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Yanshan Wang, Ravikumar Komandur Elayavilli, Majid Rastegar-Mojarad, Hongfang Liu:
Leveraging both Structured and Unstructured Data for Precision Information Retrieval. TREC 2017
2016
[j69]
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  - journals/bib/OellrichCGRSBBG16
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Anika Oellrich, Nigel Collier, Tudor Groza, Dietrich Rebholz-Schuhmann, Nigam Shah, Olivier Bodenreider, Mary Regina Boland, Ivo I. Georgiev, Hongfang Liu, Kevin M. Livingston, Augustin Luna, Ann-Marie Mallon, Prashanti Manda, Peter N. Robinson, Gabriella Rustici, Michelle Simon, Liqin Wang, Rainer Winnenburg, Michel Dumontier:
The digital revolution in phenotyping. Briefings Bioinform. 17(5): 819-830 (2016)
[j68]
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Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Hongfang Liu:
BELTracker: evidence sentence retrieval for BEL statements. Database J. Biol. Databases Curation 2016 (2016)
[j67]
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Ravikumar Komandur Elayavilli, Kavishwar B. Wagholikar, Dingcheng Li, Jean-Pierre A. Kocher, Hongfang Liu:
Erratum to: Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature. BMC Bioinform. 17: 162 (2016)
[j66]
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Thomas A. Oniki, Ning Zhuo, Calvin E. Beebe, Hongfang Liu, Joseph F. Coyle, Craig G. Parker, Harold R. Solbrig, Kyle Marchant, Vinod Kaggal, Christopher G. Chute, Stanley M. Huff:
Clinical element models in the SHARPn consortium. J. Am. Medical Informatics Assoc. 23(2): 248-256 (2016)
[j65]
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Na Hong, Dingcheng Li, Yue Yu, Qiongying Xiu, Hongfang Liu, Guoqian Jiang:
A computational framework for converting textual clinical diagnostic criteria into the quality data model. J. Biomed. Informatics 63: 11-21 (2016)
[j64]
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Yanshan Wang, Stephen T. Wu, Dingcheng Li, Saeed Mehrabi, Hongfang Liu:
A Part-Of-Speech term weighting scheme for biomedical information retrieval. J. Biomed. Informatics 63: 379-389 (2016)
[j63]
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Guoqiang Zhou, Hongfang Liu, Ziyuan Wang:
去随意推荐的信任评估模型 (Trust Evaluation Model with Eliminating Random Recommendation). 计算机科学 43(4): 155-159 (2016)
[c133]
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Mei Li, Yuying Cao, Liwei Wang, Hongfang Liu, Yongqun He:
Ontology-Based Analysis of Adverse Drug Reactions Associated with Anti-infection Drugs in China. AMIA 2016
[c132]
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Dingcheng Li, Sijia Liu, Majid Rastegar-Mojarad, Yanshan Wang, Xiaodi Li, Vipin Chaudhary, Terry M. Therneau, Hongfang Liu:
A Topic-modeling Based Framework for Drug-drug Interaction Classification from Biomedical Text. AMIA 2016
[c131]
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Dingcheng Li, Sijia Liu, Majid Rastegar-Mojarad, Yanshan Wang, Xiaodi Li, Vipin Chaudhary, Terry M. Therneau, Hongfang Liu:
Drug-drug Interaction Detection with A Topic-modeling Based Framework Augmented with Distant-supervision. AMIA 2016
[c130]
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  - conf/amia/MeystreLXAWPSWZ16
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Stéphane M. Meystre, Hongfang Liu, Rong Xu, Sivaram Arabandi, Kavishwar B. Wagholikar, Jon D. Patrick, Guergana K. Savova, Chunhua Weng, Pierre Zweigenbaum, Dina Demner-Fushman, Özlem Uzuner, Hua Xu:
Natural Language Processing Working Group Pre-Symposium: Graduate Student Consortium and 'Hackathon'. AMIA 2016
[c129]
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Kevin J. Peterson, Guoqian Jiang, Scott M. Brue, Hongfang Liu:
Leveraging Terminology Services for Extract-Transform-Load Processes: A User-Centered Approach. AMIA 2016
[c128]
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Sunghwan Sohn, Yanshan Wang, Chung-Il Wi, Elizabeth A. Krusemark, Euijung Ryu, Mir H. Ali, Young J. Juhn, Hongfang Liu:
Asthma Ascertainment NLP System Portability across Institutions. AMIA 2016
[c127]
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Liwei Wang, Dingcheng Li, Majid Rastegar-Mojarad, Hongfang Liu:
Discovering Associations between Problem List and Practice Setting. AMIA 2016
[c126]
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Yanshan Wang, Stephen T. Wu, Dingcheng Li, Hongfang Liu:
A Part-Of-Speech Weighting Scheme for Clinical Information Retrieval. AMIA 2016
[c125]
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Stephen T. Wu, Yanshan Wang, Sunghwan Sohn, Chung-Il Wi, Elizabeth A. Krusemark, Hongfang Liu, Young J. Juhn:
Probabilistic Population-level Modeling of Disease Event Timelines. AMIA 2016
[c124]
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Yuqun Zeng, Liwei Wang, Yanshan Wang, Dingcheng Li, Hongfang Liu:
Answering patients' questions using expert-vetted online resources: A case study of diabetes. AMIA 2016
[c123]
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Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Liwei Wang, Rashmi Prasad, Hongfang Liu:
Prioritizing Adverse Drug Reaction and Drug Repositioning Candidates Generated by Literature-Based Discovery. BCB 2016: 289-296
[c122]
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  - conf/bhi/AfzalSALKA16
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Naveed Afzal, Sunghwan Sohn, Sara Abram, Hongfang Liu, Iftikhar J. Kullo, Adelaide M. Arruda-Olson:
Identifying peripheral arterial disease cases using natural language processing of clinical notes. BHI 2016: 126-131
[c121]
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  - conf/bhi/KnollMLXP16
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Benjamin C. Knoll, Genevieve B. Melton, Hongfang Liu, Hua Xu, Serguei V. S. Pakhomov:
Using synthetic clinical data to train an HMM-based POS tagger. BHI 2016: 252-255
[c120]
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Yuqun Zeng, Xusheng Liu, Liwei Wang, Hongfang Liu, Yanshan Wang:
Answering diabetic patients' questions using expert-vetted online resources: A case study. BIBM 2016: 525-528
[c119]
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Yanshan Wang, Stephen T. Wu, Hongfang Liu:
MayoNLPTeam at the 2016 CLEF eHealth Information Retrieval Task 1. CLEF (Working Notes) 2016: 198-204
[c118]
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Sijia Liu, Yanshan Wang, Saeed Mehrabi, Dingcheng Li, Hongfang Liu:
MayoBMI at ImageCLEF 2016 Handwritten Document Retrieval Task. CLEF (Working Notes) 2016: 347-355
[c117]
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Sijia Liu, Hongfang Liu, Vipin Chaudhary, Dingcheng Li:
An Infinite Mixture Model for Coreference Resolution in Clinical Notes. CRI 2016
[c116]
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Saeed Mehrabi, Yanshan Wang, Donna M. Ihrke, Hongfang Liu:
Exploring Gaps of Family History Documentation in EHR for Precision Medicine - A Case Study of Familial Hypercholesterolemia Ascertainment. CRI 2016
[c115]
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Sunghwan Sohn, Young J. Juhn, Chung-Il Wi, Euijung Ryu, Hongfang Liu:
Ascertaining Asthma Predictive Index through Natural Language Processing. CRI 2016
[c114]
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Yanshan Wang, Dingcheng Li, Stephen T. Wu, Hongfang Liu:
POS-MRF: A Part-Of-Speech Weighted Markov Random Field Model for Clinical Information Retrieval. CRI 2016
[c113]
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  - conf/icbo/ElayavilliRL16
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Ravikumar Komandur Elayavilli, Majid Rastegar-Mojarad, Hongfang Liu:
MutD - A PubMed Scale Resource for Protein Mutation-Disease Relations through Bio-Medical Literature Mining. ICBO/BioCreative 2016
[c112]
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Sijia Liu, Vipin Chaudhary, Liwei Wang, Hongfang Liu:
LabLinker: Finding Links of Laboratory Test Results between Structured Records and Clinical Notes. ICHI 2016: 302
[c111]
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Stephen T. Wu, Tamara Timmons, Amy Yates, Meikun Wang, Steven Bedrick, William R. Hersh, Hongfang Liu:
On Developing Resources for Patient-level Information Retrieval. LREC 2016
[c110]
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Stephen T. Wu, Chung-Il Wi, Sunghwan Sohn, Hongfang Liu, Young J. Juhn:
Staggered NLP-assisted refinement for Clinical Annotations of Chronic Disease Events. LREC 2016
[c109]
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  - conf/semeval/AfzalWL16
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Naveed Afzal, Yanshan Wang, Hongfang Liu:
MayoNLP at SemEval-2016 Task 1: Semantic Textual Similarity based on Lexical Semantic Net and Deep Learning Semantic Model. SemEval@NAACL-HLT 2016: 674-679
[c108]
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Yanshan Wang, Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Sijia Liu, Hongfang Liu:
An Ensemble Model of Clinical Information Extraction and Information Retrieval for Clinical Decision Support. TREC 2016
[c107]
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  - conf/vldb/OverbyRL16
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Casey Lynnette Overby, Louiqa Raschid, Hongfang Liu:
Exploiting HPO to Predict a Ranked List of Phenotype Categories for LiverTox Case Reports. DMAH@VLDB 2016: 3-9
[i2]
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Yanshan Wang, Hongfang Liu:
MatLM: a Matrix Formulation for Probabilistic Language Models. CoRR abs/1610.00735 (2016)
2015
[j62]
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Liwei Wang, Hongfang Liu, Christopher G. Chute, Qian Zhu:
Cancer based pharmacogenomics network supported with scientific evidences: from the view of drug repurposing. BioData Min. 8: 9 (2015)
[j61]
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Dingcheng Li, Janet Okamoto, Hongfang Liu, Scott Leischow:
A bibliometric analysis on tobacco regulation investigators. BioData Min. 8: 11 (2015)
[j60]
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Guoqian Jiang, Hongfang Liu, Harold R. Solbrig, Christopher G. Chute:
Mining severe drug-drug interaction adverse events using Semantic Web technologies: a case study. BioData Min. 8: 12 (2015)
[j59]
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Yuji Zhang, Qian Zhu, Hongfang Liu:
Next generation informatics for big data in precision medicine era. BioData Min. 8: 34 (2015)
[j58]
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  - journals/bmcbi/RavikumarWLKL15
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Ravikumar Komandur Elayavilli, Kavishwar B. Wagholikar, Dingcheng Li, Jean-Pierre A. Kocher, Hongfang Liu:
Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature. BMC Bioinform. 16: 185:1-185:15 (2015)
[j57]
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Hua Xu, Melinda C. Aldrich, Qingxia Chen, Hongfang Liu, Neeraja B. Peterson, Qi Dai, Mia A. Levy, Anushi Shah, Han Xue, Xiaoyang Ruan, Min Jiang, Ying Li, Jamii St Julien, Jeremy L. Warner, Carol Friedman, Dan M. Roden, Joshua C. Denny:
Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality. J. Am. Medical Informatics Assoc. 22(1): 179-191 (2015)
[j56]
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Saeed Mehrabi, Anand Krishnan, Sunghwan Sohn, Alexandra M. Roch, Heidi Schmidt, Joe Kesterson, Chris Beesley, Paul R. Dexter, C. Max Schmidt, Hongfang Liu, Mathew J. Palakal:
DEEPEN: A negation detection system for clinical text incorporating dependency relation into NegEx. J. Biomed. Informatics 54: 213-219 (2015)
[j55]
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  - journals/jbi/ZhengVLWSUGBARP15
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Kai Zheng, V. G. Vinod Vydiswaran, Yang Liu, Yue Wang, Amber Stubbs, Özlem Uzuner, Anupama E. Gururaj, Samuel Bayer, John S. Aberdeen, Anna Rumshisky, Serguei Pakhomov, Hongfang Liu, Hua Xu:
Ease of adoption of clinical natural language processing software: An evaluation of five systems. J. Biomed. Informatics 58: S189-S196 (2015)
[j54]
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Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M. Lowe, Roger A. Sayle, Riza Theresa Batista-Navarro, Rafal Rak, Torsten Huber, Tim Rocktäschel, Sérgio Matos, David Campos, Buzhou Tang, Hua Xu, Tsendsuren Munkhdalai, Keun Ho Ryu, S. V. Ramanan, P. Senthil Nathan, Slavko Zitnik, Marko Bajec, Lutz Weber, Matthias Irmer, Saber A. Akhondi, Jan A. Kors, Shuo Xu, Xin An, Utpal Kumar Sikdar, Asif Ekbal, Masaharu Yoshioka, Thaer M. Dieb, Miji Choi, Karin Verspoor, Madian Khabsa, C. Lee Giles, Hongfang Liu, Ravikumar Komandur Elayavilli, Andre Lamurias, Francisco M. Couto, Hong-Jie Dai, Richard Tzong-Han Tsai, Caglar Ata, Tolga Can, Anabel Usie, Rui Alves, Isabel Segura-Bedmar, Paloma Martínez, Julen Oyarzabal, Alfonso Valencia:
The CHEMDNER corpus of chemicals and drugs and its annotation principles. J. Cheminformatics 7(S-1): S2 (2015)
[j53]
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Qian Zhu, Hongfang Liu, Christopher G. Chute, Matthew Ferber:
EHR based Genetic Testing Knowledge Base (iGTKB) Development. BMC Medical Informatics Decis. Mak. 15-S(4): S3 (2015)
[c106]
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Dingcheng Li, Saeed Mehrabi, Yue Yu, Hongfang Liu:
A Deep Learning Framework for Improving Medical Information Retrieval. AMIA 2015
[c105]
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Kathy L. MacLaughlin, Ravikumar Komandur Elayavilli, Kavishwar B. Wagholikar, Marianne R. Scheitel, Hongfang Liu, Rajeev Chaudhry:
Evaluation of the accuracy of CDS for cervical cancer screening and surveillance. AMIA 2015
[c104]
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Saeed Mehrabi, Mayya S. Safarova, Iftikhar J. Kullo, Hongfang Liu:
Exploring Gaps of Family History Documentation in EHR for Precision Medicine - A Case Study of Familial Hypercholesterolemia Ascertainment. AMIA 2015
[c103]
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Majid Rastegar-Mojarad, Hongfang Liu, Priya Nambisan:
Social Media use for Drug Repurposing: Understanding the consumer perspective. AMIA 2015
[c102]
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K. E. Ravikumar, Rajeev Chaudhry, James J. Masanz, Joshua J. Pankratz, Jane L. Shellum, Steve G. Peters, Ronald A. Hankey, Daniel J. Cronk, Jennifer J. Boysen, Kristin Pavek, Robert Roden, Hongfang Liu:
Natural Language Processing facilitates delivery of individualized recommendations at the point of care. AMIA 2015
[c101]
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K. E. Ravikumar, Rajeev Chaudhry, James J. Masanz, Joshua J. Pankratz, Jane L. Shellum, Steve G. Peters, Ronald A. Hankey, Daniel J. Cronk, Jennifer J. Boysen, Kristin Pavek, Robert Roden, Hongfang Liu:
Natural Language Processing facilitates delivery of individualized recommendations at the point of care. AMIA 2015
[c100]
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  - conf/amia/ScheitelLSHPC15
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Marianne R. Scheitel, Hongfang Liu, Jane L. Shellum, Ronald A. Hankey, Steve G. Peters, Rajeev Chaudhry:
Automating risk score calculations and care recommendations by an EMR agnostic solution and potential time saving for providers. AMIA 2015
[c99]
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Sunghwan Sohn, Majid Rastegar-Mojarad, James M. Naessens, Elizabeth B. Habermann, David W. Larson, Hongfang Liu:
Detection of Colorectal Surgical Site Infections Using Bayesian Network and Natural Language Processing. AMIA 2015
[c98]
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Sunghwan Sohn, Majid Rastegar-Mojarad, James M. Naessens, Elizabeth B. Habermann, David W. Larson, Hongfang Liu:
Prediction of Colorectal Surgical Site Infections Using Risk Factors. AMIA 2015
[c97]
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  - conf/bcb/LiREWMYSLAL15
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Dingcheng Li, Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Yanshan Wang, Saeed Mehrabi, Yue Yu, Sunghwan Sohn, Yanpeng Li, Naveed Afzal, Hongfang Liu:
A frequency-filtering strategy of obtaining PHI-free sentences from clinical data repository. BCB 2015: 315-324
[c96]
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Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Dingcheng Li, Rashmi Prasad, Hongfang Liu:
A new method for prioritizing drug repositioning candidates extracted by literature-based discovery. BIBM 2015: 669-674
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Feichen Shen, Hongfang Liu, Sunghwan Sohn, David W. Larson, Yugyung Lee:
BmQGen: Biomedical query generator for knowledge discovery. BIBM 2015: 1092-1097
[c94]
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Na Hong, Dingcheng Li, Yue Yu, Hongfang Liu, Christopher G. Chute, Guoqian Jiang:
Representing Clinical Diagnostic Criteria in Quality Data Model Using Natural Language Processing. BioNLP@IJCNLP 2015: 177-182
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  - conf/ichi/MehrabiSLPTSLP15
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Saeed Mehrabi, Sunghwan Sohn, Dingcheng Li, Joshua J. Pankratz, Terry M. Therneau, Jennifer L. St. Sauver, Hongfang Liu, Mathew J. Palakal:
Temporal Pattern and Association Discovery of Diagnosis Codes Using Deep Learning. ICHI 2015: 408-416
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Yanshan Wang, Saeed Mehrabi, Majid Rastegar-Mojarad, Dingcheng Li, Hongfang Liu:
Retrieval of Semantically Similar Healthcare Questions in Healthcare Forums. ICHI 2015: 517-518
[c91]
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Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Dingcheng Li, Hongfang Liu:
Assessing the Need of Discourse-Level Analysis in Identifying Evidence of Drug-Disease Relations in Scientific Literature. MedInfo 2015: 539-543
[c90]
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Saeed Mehrabi, Anand Krishnan, Alexandra M. Roch, Heidi Schmidt, Dingcheng Li, Joe Kesterson, Chris Beesley, Paul R. Dexter, C. Max Schmidt, Mathew J. Palakal, Hongfang Liu:
Identification of Patients with Family History of Pancreatic Cancer - Investigation of an NLP System Portability. MedInfo 2015: 604-608
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Dingcheng Li, Majid Rastegar-Mojarad, Yanpeng Li, Sunghwan Sohn, Saeed Mehrabi, Ravikumar Komandur Elayavilli, Yue Yu, Hongfang Liu:
A Frequency-based Strategy of Obtaining Sentences from Clinical Data Repository for Crowdsourcing. MedInfo 2015: 1033-1034
[i1]
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Yanshan Wang, Dingcheng Li, Hongfang Liu, In-Chan Choi:
Generalized Ensemble Model for Document Ranking. CoRR abs/1507.08586 (2015)
2014
[j52]
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Yuqing Mao, Kimberly Van Auken, Donghui Li, Cecilia N. Arighi, Peter McQuilton, G. Thomas Hayman, Susan Tweedie, Mary L. Schaeffer, Stanley J. F. Laulederkind, Shur-Jen Wang, Julien Gobeill, Patrick Ruch, Anh Tuan Luu, Jung-Jae Kim, Jung-Hsien Chiang, Yu-De Chen, Chia-Jung Yang, Hongfang Liu, Dongqing Zhu, Yanpeng Li, Hong Yu, Ehsan Emadzadeh, Graciela Gonzalez, Jian-Ming Chen, Hong-Jie Dai, Zhiyong Lu:
Overview of the gene ontology task at BioCreative IV. Database J. Biol. Databases Curation 2014 (2014)
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Dongqing Zhu, Dingcheng Li, Ben Carterette, Hongfang Liu:
Integrating information retrieval with distant supervision for Gene Ontology annotation. Database J. Biol. Databases Curation 2014 (2014)
[j50]
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Manabu Torii, Kavishwar B. Wagholikar, Hongfang Liu:
Detecting concept mentions in biomedical text using hidden Markov model: multiple concept types at once or one at a time? J. Biomed. Semant. 5: 3 (2014)
[j49]
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Yuji Zhang, Cui Tao, Guoqian Jiang, Asha A. Nair, Jian Su, Christopher G. Chute, Hongfang Liu:
Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network. J. Biomed. Semant. 5: 33 (2014)
[j48]
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Liwei Wang, Guoqian Jiang, Dingcheng Li, Hongfang Liu:
Standardizing adverse drug event reporting data. J. Biomed. Semant. 5: 36 (2014)
[j47]
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Sunghwan Sohn, Cheryl Clark, Scott R. Halgrim, Sean P. Murphy, Christopher G. Chute, Hongfang Liu:
Research and applications: MedXN: an open source medication extraction and normalization tool for clinical text. J. Am. Medical Informatics Assoc. 21(5): 858-865 (2014)
[j46]
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Stephen T. Wu, Young J. Juhn, Sunghwan Sohn, Hongfang Liu:
Research and applications: Patient-level temporal aggregation for text-based asthma status ascertainment. J. Am. Medical Informatics Assoc. 21(5): 876-884 (2014)
[j45]
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Dongqing Zhu, Stephen T. Wu, Ben Carterette, Hongfang Liu:
Using large clinical corpora for query expansion in text-based cohort identification. J. Biomed. Informatics 49: 275-281 (2014)
[j44]
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Guixian Xu, Lirong Qiu, Hongfang Liu:
Study on Hot Topic Discovery from Chinese Texts. J. Digit. Inf. Manag. 12(4): 267-273 (2014)
[c88]
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Ravikumar Komandur Elayavilli, Kavishwar B. Wagholikar, Hongfang Liu:
NLP enhances Quality Care Measures in Heart Failure. AMIA 2014
[c87]
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Siddhartha Jonnalagadda, Soheil Moosavinasab, Chinmoy Nath, Dingcheng Li, Christopher G. Chute, Hongfang Liu:
An Automated Approach for Ranking Journals to Help in Clinician Decision Support. AMIA 2014
[c86]
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Dingcheng Li, Zhen Wang, Feichen Shen, Mohammad Hassan Murad, Hongfang Liu:
Reducing the Screening Burden of Systematic Review with a Multiple-level Relevance Ranking System. AMIA 2014
[c85]
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Sunghwan Sohn, Hongfang Liu:
Analysis of Medication and Indication Occurrences in Clinical Notes. AMIA 2014
[c84]
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Sunghwan Sohn, Hongfang Liu:
Exploration of Potential Drug Off-label Uses in Clinical Practice. AMIA 2014
[c83]
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Stephen T. Wu, Dingcheng Li, James J. Masanz, Hongfang Liu:
Layered Spaces for Clinical Information Retrieval. AMIA 2014
[c82]
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Qian Zhu, Hongfang Liu, Christopher G. Chute, Matthew Ferber:
iGenetics: An Individualized Genetic Test Recommendation System Based on EHRs. AMIA 2014
[c81]
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  - conf/bcb/RavikumarWL14
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K. E. Ravikumar, Kavishwar B. Wagholikar, Hongfang Liu:
Challenges in adapting text mining for full text articles to assist pathway curation. BCB 2014: 551-558
[c80]
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Dingcheng Li, Janet Okamoto, Hongfang Liu, Scott Leischow:
An author topic analysis on NCI DCP/DCCPS PIs. BCB 2014: 607-608
[c79]
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Feichen Shen, Dingcheng Li, Hongfang Liu, Yugyung Lee, Jyotishman Pathak, Christopher G. Chute, Cui Tao:
Using semantic web technologies for quality measure phenotyping algorithm representation and automatic execution on EHR data. BHI 2014: 531-534
[c78]
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Dingcheng Li, Zhen Wang, Feichen Shen, Mohammad Hassan Murad, Hongfang Liu:
Towards a multi-level framework for supporting systematic review - A pilot study. BIBM 2014: 43-50
[c77]
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Qian Zhu, Hongfang Liu, Christopher G. Chute, Matthew Ferber:
Genetic testing knowledge base (GTKB) towards individualized genetic test recommendation - An experimental study. BIBM 2014: 574-577
[c76]
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Dingcheng Li, Janet Okamoto, Scott Leischow, Hongfang Liu:
An Author Topic Analysis of Tobacco Regulation Investigators. PAKDD Workshops 2014: 616-627
[c75]
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Guoqian Jiang, Hongfang Liu, Harold R. Solbrig, Christopher G. Chute:
Mining Severe Drug-Drug Interaction Adverse Events Using Semantic Web Technologies: A Case Study. PAKDD Workshops 2014: 628-638
[c74]
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Liwei Wang, Hongfang Liu, Christopher G. Chute, Qian Zhu:
Cancer Based Pharmacogenomics Network for Drug Repurposing. PAKDD Workshops 2014: 639-651
[c73]
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K. E. Ravikumar, Kavishwar B. Wagholikar, Hongfang Liu:
Towards Pathway Curation Through Literature Mining - A Case Study Using PharmGKB. Pacific Symposium on Biocomputing 2014: 352-363
2013
[j43]
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Stephen T. Wu, Vinod Kaggal, Dmitriy Dligach, James J. Masanz, Pei J. Chen, Lee Becker, Wendy Webber Chapman, Guergana K. Savova, Hongfang Liu, Christopher G. Chute:
A common type system for clinical natural language processing. J. Biomed. Semant. 4: 1 (2013)
[j42]
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Kavishwar B. Wagholikar, Manabu Torii, Siddhartha Jonnalagadda, Hongfang Liu:
Pooling annotated corpora for clinical concept extraction. J. Biomed. Semant. 4: 3 (2013)
[j41]
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Yuji Zhang, Cui Tao, Yongqun He, Pradip Kanjamala, Hongfang Liu:
Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology. J. Biomed. Semant. 4: 33 (2013)
[j40]
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Kavishwar B. Wagholikar, Kathy L. MacLaughlin, Thomas M. Kastner, Petra M. Casey, Michael R. Henry, Robert A. Greenes, Hongfang Liu, Rajeev Chaudhry:
Research and applications: Formative evaluation of the accuracy of a clinical decision support system for cervical cancer screening. J. Am. Medical Informatics Assoc. 20(4): 749-757 (2013)
[j39]
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Sunghwan Sohn, Kavishwar B. Wagholikar, Dingcheng Li, Siddhartha Jonnalagadda, Cui Tao, Ravikumar Komandur Elayavilli, Hongfang Liu:
Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification. J. Am. Medical Informatics Assoc. 20(5): 836-842 (2013)
[j38]
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Siddhartha Jonnalagadda, Guilherme Del Fiol, Richard Medlin, Charlene R. Weir, Marcelo Fiszman, Javed Mostafa, Hongfang Liu:
Automatically extracting sentences from Medline citations to support clinicians' information needs. J. Am. Medical Informatics Assoc. 20(5): 995-1000 (2013)
[c72]
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Siddhartha Jonnalagadda, Christopher G. Chute, Hongfang Liu:
Prioritize journals relevant to a clinical topic: A survey of US cardiologists about heart failure. AMIA 2013
[c71]
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Dingcheng Li, Liwei Wang, Cui Tao, Christopher G. Chute, Hongfang Liu:
Coreference Resolution from Medical Corpus with Topic Modeling. AMIA 2013
[c70]
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Sunghwan Sohn, Cheryl Clark, Scott R. Halgrim, Sean P. Murphy, Christopher G. Chute, Hongfang Liu:
Medication Extraction and Normalization from Clinical Notes. AMIA 2013
[c69]
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Sunghwan Sohn, Cheryl Clark, Scott R. Halgrim, Sean P. Murphy, Christopher G. Chute, Hongfang Liu:
Clinical Drug Extraction and Normalization from Clinical Notes. AMIA 2013
[c68]
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Kavishwar B. Wagholikar, Ronald A. Hankey, Hongfang Liu, Rajeev Chaudhry:
Decision Support can Improve Time Efficiency of Healthcare Providers for Deciding Preventive Care Recommendations. AMIA 2013
[c67]
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Siddhartha Jonnalagadda, Soheil Moosavinasab, Dingcheng Li, Martin D. Abel, Christopher G. Chute, Hongfang Liu:
Prioritizing journals relevant to a topic for addressing clinicians' information needs. BIBM 2013: 5-6
[c66]
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Liwei Wang, Hongfang Liu:
Profiling adverse drug events of cancer drug ingredients using normalized AERS data. BIBM 2013: 46-52
[c65]
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Yuji Zhang, Dingcheng Li, Cui Tao, Feichen Shen, Hongfang Liu:
An integrative computational approach to identify disease-specific networks from PubMed literature information. BIBM 2013: 72-75
[c64]
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Dingcheng Li, Hongfang Liu, Christopher G. Chute, Siddhartha Jonnalagadda:
Towards assigning references using semantic, journal and citation relevance. BIBM 2013: 499-503
[c63]
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Hongfang Liu, Kavishwar B. Wagholikar, Siddhartha Jonnalagadda, Sunghwan Sohn:
Integrated cTAKES for Concept Mention Detection and Normalization. CLEF (Working Notes) 2013
[c62]
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Dongqing Zhu, Dingcheng Li, Ben Carterette, Hongfang Liu:
An Incremental Approach for MEDLINE MeSH Indexing. BioASQ@CLEF 2013
[c61]
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Dongqing Zhu, Stephen T. Wu, James J. Masanz, Ben Carterette, Hongfang Liu:
Using Discharge Summaries to Improve Information Retrieval in Clinical Domain. CLEF (Working Notes) 2013
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Yuji Zhang, Cui Tao, Yongqun He, Pradip Kanjamala, Hongfang Liu:
Analysis of Vaccine-related Networks using Semantic MEDLINE and the Vaccine Ontology. VDOS+DO@ICBO 2013
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Cui Tao, Dingcheng Li, Feichen Shen, Zonghui Lian, Jyotishman Pathak, Hongfang Liu, Christopher G. Chute:
Phenotyping on EHR Data Using OWL and Semantic Web Technologies. ICSH 2013: 31-32
[c58]
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Guoqian Jiang, Liwei Wang, Hongfang Liu, Harold R. Solbrig, Christopher G. Chute:
Building a Knowledge Base of Severe Adverse Drug Events Based on AERS Reporting Data Using Semantic Web Technologies. MedInfo 2013: 496-500
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Mingyuan Zhang, Guilherme Del Fiol, Randall Grout, Siddhartha Jonnalagadda, Richard Medlin, Rashmi Mishra, Charlene R. Weir, Hongfang Liu, Javed Mostafa, Marcelo Fiszman:
Automatic Identification of Comparative Effectiveness Research from Medline Citations to Support Clinicians' Treatment Information Needs. MedInfo 2013: 846-850
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Liwei Wang, Guoqian Jiang, Dingcheng Li, Hongfang Liu:
Standardizing Drug Adverse Event Reporting Data. MedInfo 2013: 1101
[c55]
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Stephen T. Wu, Dongqing Zhu, Ben Carterette, Hongfang Liu:
MayoClinicNLP-CORE: Semantic representations for textual similarity. *SEM@NAACL-HLT 2013: 148-154
2012
[j37]
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Kavishwar B. Wagholikar, Kathy L. MacLaughlin, Michael R. Henry, Robert A. Greenes, Ronald A. Hankey, Hongfang Liu, Rajeev Chaudhry:
Clinical decision support with automated text processing for cervical cancer screening. J. Am. Medical Informatics Assoc. 19(5): 833-839 (2012)
[j36]
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Siddhartha Jonnalagadda, Dingcheng Li, Sunghwan Sohn, Stephen Tze-Inn Wu, Kavishwar B. Wagholikar, Manabu Torii, Hongfang Liu:
Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules. J. Am. Medical Informatics Assoc. 19(5): 867-874 (2012)
[j35]
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Stephen T. Wu, Hongfang Liu, Dingcheng Li, Cui Tao, Mark A. Musen, Christopher G. Chute, Nigam H. Shah:
Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis. J. Am. Medical Informatics Assoc. 19(e1) (2012)
[c54]
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Suzette J. Bielinski, Jyotishman Pathak, Hongfang Liu, Sunghwan Sohn, Gail P. Jarvik, David Carrell, Naveen Pereira, Véronique L. Roger:
Using Electronic Health Records to Identify Heart Failure Cohorts with Differentiation for Preserved and Reduced Ejection Fraction. AMIA 2012
[c53]
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Mei Liu, Anushi Shah, Min Jiang, Neeraja B. Peterson, Qi Dai, Melinda Aldrich, Qingxia Chen, Erica A. Bowton, Hongfang Liu, Joshua C. Denny, Hua Xu:
A Study of Transportability of an Existing Smoking Status Detection Module across Institutions. AMIA 2012
[c52]
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Hongfang Liu, Stephen T. Wu, Dingcheng Li, Siddhartha Jonnalagadda, Sunghwan Sohn, Kavishwar B. Wagholikar, Peter J. Haug, Stanley M. Huff, Christopher G. Chute:
Towards a semantic lexicon for clinical natural language processing. AMIA 2012
[c51]
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Kavishwar B. Wagholikar, Kathy L. MacLaughlin, Michael R. Henry, Robert A. Greenes, Ronald A. Hankey, Hongfang Liu, Rajeev Chaudhry:
Clinical Decision Support with Natural Language Processing for Cervical Cancer Screening. AMIA 2012
[c50]
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Liwei Wang, Guoqian Jiang, Wei Wang, Hongfang Liu:
A Preliminary Study on Normalizing AERS Drug Names Using RxNorm. AMIA 2012
[c49]
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Stephen T. Wu, Young J. Juhn, Sunghwan Sohn, Ravikumar Komandur Elayavilli, Kavishwar B. Wagholikar, Siddhartha Jonnalagadda, Hongfang Liu:
Asthma Status Identification with Natural Language Processing. AMIA 2012
[c48]
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Stephen T. Wu, Mark Wieland, Vinod Kaggal, Hongfang Liu, Christopher G. Chute:
Tracking Immigrant Health with Natural Language Processing. AMIA 2012
[c47]
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Hua Xu, Melinda Aldrich, Qingxia Chen, Neeraja B. Peterson, Qi Dai, Mia A. Levy, Anushi Shah, Han Xue, Ying Li, Carol Friedman, Hongfang Liu, Joshua C. Denny:
Electronic health record data suggests metformin improves cancer survival: A new model for drug repurposing studies. AMIA 2012
[c46]
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Bo Xu, Hongfei Lin, Zhihao Yang, Kavishwar B. Wagholikar, Hongfang Liu:
Classifying protein complexes from candidate subgraphs using fuzzy machine learning model. BIBM Workshops 2012: 640-647
[c45]
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Dingcheng Li, Cui Tao, Hongfang Liu, Christopher G. Chute:
Ontology-Based Temporal Relation Modeling with MapReduce Latent Dirichlet Allocations for Big EHR Data. CGC 2012: 708-715
[c44]
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Hongfang Liu, Stephen T. Wu, Cui Tao, Christopher G. Chute:
Modeling UIMA type system using web ontology language: towards interoperability among UIMA-based NLP tools. MIX-HS 2012: 31-36
[c43]
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Kavishwar B. Wagholikar, Sunghwan Sohn, Stephen T. Wu, Vinod Kaggal, Sheila Buehler, Robert A. Greenes, Tsung-Teh Wu, David W. Larson, Hongfang Liu, Rajeev Chaudhry, Lisa Boardman:
Clinical Decision Support for Colonoscopy Surveillance Using Natural Language Processing. HISB 2012: 12-21
[c42]
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Siddhartha Jonnalagadda, Guilherme Del Fiol, Richard Medlin, Charlene R. Weir, Marcelo Fiszman, Javed Mostafa, Hongfang Liu:
Automatically Extracting Sentences from Medline Citations to Support Clinicians' Information Needs. HISB 2012: 72
[c41]
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Sunghwan Sohn, Sean P. Murphy, Siddhartha Jonnalagadda, Kavishwar B. Wagholikar, Stephen T. Wu, Christopher G. Chute, Hongfang Liu, Scott R. Halgrim:
Systematic Analysis of Cross-Institutional Medication Description Patterns in Clinical Notes. HISB 2012: 118
[c40]
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Stephen T. Wu, James J. Masanz, K. E. Ravikumar, Hongfang Liu:
Three Questions About Clinical Information Retrieval. TREC 2012
2011
[j34]
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Barry Zeeberg, Hongfang Liu, Ari B. Kahn, Martin Ehler, Vinodh N. Rajapakse, Robert F. Bonner, Jacob D. Brown, Brian P. Brooks, Vladimir L. Larionov, William C. Reinhold, John N. Weinstein, Yves Pommier:
RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis. BMC Bioinform. 12: 52 (2011)
[j33]
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Jinlian Wang, Manabu Torii, Hongfang Liu, Gerald W. Hart, Zhang-Zhi Hu:
dbOGAP - An Integrated Bioinformatics Resource for Protein O-GlcNAcylation. BMC Bioinform. 12: 91 (2011)
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Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, Minlie Huang, Jingchen Liu, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tsai, Hong-Jie Dai, Naoaki Okazaki, Han-Cheol Cho, Martin Gerner, Illés Solt, Shashank Agarwal, Feifan Liu, Dina Vishnyakova, Patrick Ruch, Martin Romacker, Fabio Rinaldi, Sanmitra Bhattacharya, Padmini Srinivasan, Hongfang Liu, Manabu Torii, Sérgio Matos, David Campos, Karin Verspoor, Kevin M. Livingston, W. John Wilbur:
The gene normalization task in BioCreative III. BMC Bioinform. 12(S-8): S2 (2011)
[j31]
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Manabu Torii, Lanlan Yin, Thang Nguyen, Chand T. Mazumdar, Hongfang Liu, David M. Hartley, Noele P. Nelson:
An exploratory study of a text classification framework for Internet-based surveillance of emerging epidemics. Int. J. Medical Informatics 80(1): 56-66 (2011)
[j30]
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Manabu Torii, Kavishwar B. Wagholikar, Hongfang Liu:
Using machine learning for concept extraction on clinical documents from multiple data sources. J. Am. Medical Informatics Assoc. 18(5): 580-587 (2011)
[c39]
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Kavishwar B. Wagholikar, Manabu Torii, Hongfang Liu:
Human gene/protein synonym dictionary from WikiLinks. BCB 2011: 462-464
[c38]
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Yang Chen, Manabu Torii, Chang-Tien Lu, Hongfang Liu:
Learning from positive and unlabeled documents for automated detection of alternative splicing sentences in medline abstracts. BIBM Workshops 2011: 530-537
[c37]
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Hongfang Liu, Ruijuan Li, Nana Li:
Hamilton Non-holonomic Momentum Equation of the System and Conclusions. ICICA (1) 2011: 23-29
[c36]
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Stephen T. Wu, Kavishwar B. Wagholikar, Sunghwan Sohn, Vinod Kaggal, Hongfang Liu:
Empirical Ontologies for Cohort Identification. TREC 2011
2010
[j29]
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Lanlan Yin, Guixian Xu, Manabu Torii, Zhendong Niu, José M. Maisog, Cathy H. Wu, Zhang-Zhi Hu, Hongfang Liu:
Document classification for mining host pathogen protein-protein interactions. Artif. Intell. Medicine 49(3): 155-160 (2010)
[j28]
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Günes Koru, Hongfang Liu, Dongsong Zhang, Khaled El Emam:
Testing the theory of relative defect proneness for closed-source software. Empir. Softw. Eng. 15(6): 577-598 (2010)
[j27]
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Hongfang Liu, Manabu Torii, Guixian Xu, Johannes Goll:
Classification Systems for Bacterial Protein-Protein Interaction Document Retrieval. Int. J. Comput. Model. Algorithms Medicine 1(1): 34-44 (2010)
[j26]
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Min Song, Hongfang Liu:
LFXtractor: Text chunking for long form detection from biomedical text. Int. J. Funct. Informatics Pers. Medicine 3(2): 89-102 (2010)
[c35]
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Manabu Torii, Burt-Ujin Bayarsaikhan, Hongfang Liu, Thang Nguyen, Kevin Jones, Noele P. Nelson, David M. Hartley:
An exploratory study of news article clustering for web-based bio-surveillance. IHI 2010: 435-439
[c34]
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Chong Min Lee, Manabu Torii, Zhang-Zhi Hu, Yi-Ting Tsai, Jinesh Shah, Hongfang Liu:
Evaluating gene/protein name tagging and mapping for article retrieval. Semantic Mining in Biomedicine 2010

2000 – 2009

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2009
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Cecilia N. Arighi, Hongfang Liu, Darren A. Natale, Winona C. Barker, Harold J. Drabkin, Judith A. Blake, Barry Smith, Cathy H. Wu:
TGF-beta signaling proteins and the Protein Ontology. BMC Bioinform. 10(S-5) (2009)
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Manabu Torii, Zhang-Zhi Hu, Cathy H. Wu, Hongfang Liu:
Research Paper: BioTagger-GM: A Gene/Protein Name Recognition System. J. Am. Medical Informatics Assoc. 16(2): 247-255 (2009)
[j23]
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Akif Günes Koru, Dongsong Zhang, Khaled El Emam, Hongfang Liu:
An Investigation into the Functional Form of the Size-Defect Relationship for Software Modules. IEEE Trans. Software Eng. 35(2): 293-304 (2009)
[c33]
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Manabu Torii, Hongfang Liu, Zhang-Zhi Hu:
Support Vector Machine-Based Mucin-Type O-linked Glycosylation Site Prediction Using Enhanced Sequence Feature Encoding. AMIA 2009
[c32]
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Medha Umarji, Carolyn B. Seaman, Akif Günes Koru, Hongfang Liu:
Software Engineering Education for Bioinformatics. CSEE&T 2009: 216-223
[c31]
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Hongyong Jin, Xiuping Zhao, Hongfang Liu:
Testing of the Uniformity of Color Appearance Space. CSIE (6) 2009: 307-311
[c30]
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Guixian Xu, Zhendong Niu, Peter Uetz, Xu Gao, Xuping Qin, Hongfang Liu:
Semi-supervised Learning of Text Classification on Bacterial Protein-Protein Interaction Documents. IJCBS 2009: 263-270
2008
[j22]
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Hans A. Kestler, André Müller, Johann M. Kraus, Malte Buchholz, Thomas M. Gress, Hongfang Liu, David W. Kane, Barry Zeeberg, John N. Weinstein:
VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays. BMC Bioinform. 9 (2008)
[j21]
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Michael C. Ryan, Barry Zeeberg, Natasha J. Caplen, James A. Cleland, Ari B. Kahn, Hongfang Liu, John N. Weinstein:
SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies. BMC Bioinform. 9 (2008)
[j20]
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Akif Günes Koru, Khaled El Emam, Dongsong Zhang, Hongfang Liu, Divya Mathew:
Theory of relative defect proneness. Empir. Softw. Eng. 13(5): 473-498 (2008)
[c29]
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Hongfang Liu, Xin Li, Victoria Y. Yoon, Robert Clarke:
Annotating breast cancer microarray samples using ontologies. AMIA 2008
[c28]
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Guixian Xu, Lanlan Yin, Manabu Torii, Zhendong Niu, Cathy H. Wu, Zhang-Zhi Hu, Hongfang Liu:
Document Classification for Mining Host Pathogen Protein-Protein Interactions. BIBM 2008: 461-466
[c27]
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Zhang-Zhi Hu, K. Bretonnel Cohen, Lynette Hirschman, Alfonso Valencia, Hongfang Liu, Michelle G. Giglio, Cathy H. Wu:
iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology. BIBM 2008: 467-472
[c26]
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Ionut Bebu, Françoise Seillier-Moiseiwitsch, Hongfang Liu:
Analysis of Microarray Titration Experiments. BIOCOMP 2008: 942-946
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Medha Umarji, Mark Pohl, Carolyn Seaman, Akif Günes Koru, Hongfang Liu:
Teaching software engineering to end-users. WEUSE@ICSE 2008: 40-42
[c24]
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Hongfang Liu, Manabu Torii, Guixian Xu, Zhang-Zhi Hu, Johannes Goll:
Learning from Positive and Unlabeled Documents for Retrieval of Bacterial Protein-Protein Interaction Literature. BioLINK@ISMB/ECCB 2008: 62-70
2007
[j19]
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Hongfang Liu, Barry Zeeberg, Gang Qu, Akif Günes Koru, Alessandro Ferrucci, Ari B. Kahn, Michael C. Ryan, Antej Nuhanovic, Peter J. Munson, William C. Reinhold, David W. Kane, John N. Weinstein:
AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets. Bioinform. 23(18): 2385-2390 (2007)
[j18]
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Ari B. Kahn, Michael C. Ryan, Hongfang Liu, Barry Zeeberg, D. Curtis Jamison, John N. Weinstein:
SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis. BMC Bioinform. 8 (2007)
[j17]
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Darren A. Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Ti-Cheng Chang, Zhang-Zhi Hu, Hongfang Liu, Barry Smith, Cathy H. Wu:
Framework for a Protein Ontology. BMC Bioinform. 8(S-9) (2007)
[j16]
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Manabu Torii, Zhang-Zhi Hu, Min Song, Cathy H. Wu, Hongfang Liu:
A comparison study on algorithms of detecting long forms for short forms in biomedical text. BMC Bioinform. 8(S-9) (2007)
[j15]
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Akif Günes Koru, Hongfang Liu:
Identifying and characterizing change-prone classes in two large-scale open-source products. J. Syst. Softw. 80(1): 63-73 (2007)
[c23]
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Manabu Torii, Hongfang Liu:
Enhancing Acronym/Abbreviation Knowledge Bases with Semantic Information. AMIA 2007
[c22]
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Ionut Bebu, Françoise Seillier-Moiseiwitsch, Hongfang Liu:
Semiparametric RMA Background-Correction for Oligonucleotide Arrays. BIBE 2007: 1404-1408
[c21]
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Hongfang Liu, Manabu Torii, Zhang-Zhi Hu, Cathy H. Wu:
Mapping Gene/Protein Names in Free Text to Biomedical Databases. ICDM Workshops 2007: 101-106
[c20]
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Akif Günes Koru, Dongsong Zhang, Hongfang Liu:
Modeling the Effect of Size on Defect Proneness for Open-Source Software. ICSE Companion 2007: 115-124
[c19]
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Manabu Torii, Hongfang Liu:
Classifier Ensemble for Biomedical Document Retrieval. LBM (Short Papers) 2007
[c18]
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Akif Günes Koru, Dongsong Zhang, Hongfang Liu:
Effect of Coupling on Defect Proneness in Evolutionary Open-Source Software Development. OSS 2007: 271-276
[c17]
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Akif Günes Koru, Dongsong Zhang, Hongfang Liu:
Modeling the Effect of Size on Defect Proneness for Open-Source Software. PROMISE@ICSE 2007: 10
[c16]
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Miguel E. Ruiz, Ying Sun, Jianqiang Wang, Hongfang Liu:
Exploring Traits of Adjectives to Predict Polarity Opinion in Blogs and Semantic Filters in Genomics. TREC 2007
2006
[j14]
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Hongfang Liu, Zhang-Zhi Hu, Jian Zhang, Cathy H. Wu:
BioThesaurus: a web-based thesaurus of protein and gene names. Bioinform. 22(1): 103-105 (2006)
[j13]
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Hua Xu, Marianthi Markatou, Rositsa Dimova, Hongfang Liu, Carol Friedman:
Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues. BMC Bioinform. 7: 334 (2006)
[j12]
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Hongfang Liu, Zhang-Zhi Hu, Manabu Torii, Cathy H. Wu, Carol Friedman:
Research Paper: Quantitative Assessment of Dictionary-based Protein Named Entity Tagging. J. Am. Medical Informatics Assoc. 13(5): 497-507 (2006)
[j11]
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Li Zhou, Ying Tao, James J. Cimino, Elizabeth S. Chen, Hongfang Liu, Yves A. Lussier, George Hripcsak, Carol Friedman:
Terminology model discovery using natural language processing and visualization techniques. J. Biomed. Informatics 39(6): 626-636 (2006)
[c15]
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Manabu Torii, Hongfang Liu:
Headwords and Suffixes in Biomedical Names. KDLL 2006: 29-41
2005
[j10]
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Lifeng Chen, Hongfang Liu, Carol Friedman:
Gene name ambiguity of eukaryotic nomenclatures. Bioinform. 21(2): 248-256 (2005)
[j9]
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Hongfang Liu, Zhang-Zhi Hu, Cathy H. Wu:
DynGO: a tool for visualizing and mining of Gene Ontology and its associations. BMC Bioinform. 6: 201 (2005)
[j8]
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Akif Günes Koru, Hongfang Liu:
An investigation of the effect of module size on defect prediction using static measures. ACM SIGSOFT Softw. Eng. Notes 30(4): 1-5 (2005)
[j7]
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Akif Günes Koru, Hongfang Liu:
Building Effective Defect-Prediction Models in Practice. IEEE Softw. 22(6): 23-29 (2005)
[c14]
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Hongfang Liu, Zhang-Zhi Hu, Cathy H. Wu:
Dynamically Generating a Protein Entity Dictionary Using Online Resources. ACL 2005: 17-20
[c13]
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Akif Günes Koru, Hongfang Liu:
An investigation of the effect of module size on defect prediction using static measures. PROMISE@ICSE 2005: 7:1-7:5
[c12]
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Alan R. Aronson, Dina Demner-Fushman, Susanne M. Humphrey, Jimmy Lin, Patrick Ruch, Miguel E. Ruiz, Lawrence H. Smith, Lorraine K. Tanabe, W. John Wilbur, Hongfang Liu:
Fusion of Knowledge-Intensive and Statistical Approaches for Retrieving and Annotating Textual Genomics Documents. TREC 2005
2004
[j6]
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Zhang-Zhi Hu, Inderjeet Mani, Vincent Hermoso, Hongfang Liu, Cathy H. Wu:
iProLINK: an integrated protein resource for literature mining. Comput. Biol. Chem. 28(5-6): 409-416 (2004)
[j5]
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Hongfang Liu, Virginia Teller, Carol Friedman:
Research Paper: A Multi-aspect Comparison Study of Supervised Word Sense Disambiguation. J. Am. Medical Informatics Assoc. 11(4): 320-331 (2004)
[c11]
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Han-Yu Chuang, Hongfang Liu, Stuart M. Brown, Cameron McMunn-Coffran, Cheng-Yan Kao, D. Frank Hsu:
Identifying Significant Genes from Microarray Data. BIBE 2004: 358-365
[c10]
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Han-Yu Chuang, Hongfang Liu, Fang-An Chen, Cheng-Yan Kao, D. Frank Hsu:
Combination Methods in Microarray Analysis. ISPAN 2004: 625-630
[c9]
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Hongfang Liu, Carol Friedman:
CliniViewer: A Tool for Viewing Electronic Medical Records Based on Natural Language Processing and XML. MedInfo 2004: 639-643
[c8]
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Olivia Tuason, Lifeng Chen, Hongfang Liu, Judith A. Blake, Carol Friedman:
Biological Nomenclatures: A Source of Lexical Knowledge and Ambiguity. Pacific Symposium on Biocomputing 2004: 238-249
[c7]
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Alan R. Aronson, Susanne M. Humphrey, Nicholas C. Ide, Won Kim, Russell F. Loane, James G. Mork, Lawrence H. Smith, Lorraine K. Tanabe, W. John Wilbur, Natalie Xie, Dina Demner-Fushman, Hongfang Liu:
Knowledge-Intensive and Statistical Approaches to the Retrieval and Annotation of Genomics MEDLINE Citations. TREC 2004
2003
[j4]
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Carol Friedman, Hongfang Liu, Lyudmila Shagina:
A vocabulary development and visualization tool based on natural language processing and the mining of textual patient reports. J. Biomed. Informatics 36(3): 189-201 (2003)
[c6]
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Hongfang Liu, Carol Friedman:
Mining Terminological Knowledge in Large Biomedical Corpora. Pacific Symposium on Biocomputing 2003: 415-426
2002
[j3]
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Hongfang Liu, Stephen B. Johnson, Carol Friedman:
Research Paper: Automatic Resolution of Ambiguous Terms Based on Machine Learning and Conceptual Relations in the UMLS. J. Am. Medical Informatics Assoc. 9(6): 621-636 (2002)
[c5]
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Hongfang Liu, Alan R. Aronson, Carol Friedman:
A study of abbreviations in MEDLINE abstracts. AMIA 2002
2001
[j2]
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Hongfang Liu, Yves A. Lussier, Carol Friedman:
Disambiguating Ambiguous Biomedical Terms in Biomedical Narrative Text: An Unsupervised Method. J. Biomed. Informatics 34(4): 249-261 (2001)
[c4]
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Carol Friedman, Hongfang Liu, Lyudmila Shagina, Stephen B. Johnson, George Hripcsak:
Evaluating the UMLS as a source of lexical knowledge for medical language processing. AMIA 2001
[c3]
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Hongfang Liu, Yves A. Lussier, Carol Friedman:
A study of abbreviations in the UMLS. AMIA 2001
2000
[c2]
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Hongfang Liu, Carol Friedman:
A method for vocabulary development and visualization based on medical language processing and XML. AMIA 2000

1990 – 1999

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1999
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Carol Friedman, George Hripcsak, Lyudmila Shagina, Hongfang Liu:
Research Paper: Representing Information in Patient Reports Using Natural Language Processing and the Extensible Markup Language. J. Am. Medical Informatics Assoc. 6(1): 76-87 (1999)
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Hongfang Liu, D. Frank Hsu, S. Horiguchi:
Generalized shuffle-exchange digraphs: Hamiltonian properties. ISCAS (6) 1999: 157-160

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