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ORCIDHua Xu 0001
Person information
- affiliation: Yale University, USA
- affiliation (former): University of Texas Health Science Center at Houston, School of Biomedical Informatics, TX, USA
- affiliation (former): Vanderbilt University, School of Medicine, Department of Biomedical Informatics, Nashville, TN, USA
Other persons with the same name
- Hua Xu — disambiguation page
- Hua Xu 0002
![[0000-0001-5478-6879]](https://dblp.dagstuhl.de/img/orcid-mark.12x12.png "0000-0001-5478-6879")
— The University of Tsukuba, Graduate School of Business Sciences, Japan (and 1 more) - Hua Xu 0003 — Tsinghua University, Department of Computer Science and Technology, Beijing, China
- Hua Xu 0004 (aka: Hua Xue 0001) — Nanjing University of Aeronautics and Astronautics, Center for More Electric Aircraft Power System (CMEAPS), China
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2020 – today
- 2025
[j148]Mingchen Li, Halil Kilicoglu, Hua Xu, Rui Zhang:
BiomedRAG: A retrieval augmented large language model for biomedicine. J. Biomed. Informatics 162: 104769 (2025)- [j147]Naimin Jing, Yiwen Lu, Jiayi Tong, James Weaver, Patrick B. Ryan, Hua Xu, Yong Chen:
Evaluating the Bias, type I error and statistical power of the prior Knowledge-Guided integrated likelihood estimation (PIE) for bias reduction in EHR based association studies. J. Biomed. Informatics 163: 104787 (2025) - [j146]Qianqian Xie, Qingyu Chen, Aokun Chen, Cheng Peng, Yan Hu, Fongci Lin, Xueqing Peng, Jimin Huang, Jeffrey Zhang, Vipina Kuttichi Keloth, Xinyu Zhou, Lingfei Qian, Huan He, Dennis Shung, Lucila Ohno-Machado, Yonghui Wu, Hua Xu, Jiang Bian:
Medical foundation large language models for comprehensive text analysis and beyond. npj Digit. Medicine 8(1) (2025) - [i37]Rachael L. Fleurence, Dalia Dawoud, Jiang Bian, Mitch Higashi, Xiaoyan Wang, Hua Xu, Jagpreet Chhatwal, Turgay Ayer:
The ELEVATE-AI LLMs Framework: An Evaluation Framework for Use of Large Language Models in HEOR: an ISPOR Working Group Report. CoRR abs/2501.12394 (2025) - 2024
- [j145]Huixue Zhou, Robin Austin, Sheng-Chieh Lu, Greg M. Silverman, Yuqi Zhou, Halil Kilicoglu, Hua Xu, Rui Zhang:
Complementary and Integrative Health Information in the literature: its lexicon and named entity recognition. J. Am. Medical Informatics Assoc. 31(2): 426-434 (2024) - [j144]Jiayi Tong, Chongliang Luo, Yifei Sun, Rui Duan, M. Elle Saine, Lifeng Lin, Yifan Peng, Yiwen Lu, Anchita Batra, Anni Pan, Olivia Wang, Ruowang Li, Arielle Marks-Anglin, Yuchen Yang, Xu Zuo, Yulun Liu, Jiang Bian, Stephen E. Kimmel, Keith Hamilton, Adam Cuker, Rebecca A. Hubbard, Hua Xu, Yong Chen:
Confidence score: a data-driven measure for inclusive systematic reviews considering unpublished preprints. J. Am. Medical Informatics Assoc. 31(4): 809-819 (2024) - [j143]Gongbo Zhang, Yiliang Zhou, Yan Hu, Hua Xu, Chunhua Weng, Yifan Peng:
A span-based model for extracting overlapping PICO entities from randomized controlled trial publications. J. Am. Medical Informatics Assoc. 31(5): 1163-1171 (2024) - [j142]Yan Hu, Qingyu Chen, Jingcheng Du, Xueqing Peng, Vipina Kuttichi Keloth, Xu Zuo, Yujia Zhou, Zehan Li, Xiaoqian Jiang, Zhiyong Lu, Kirk Roberts, Hua Xu:
Improving large language models for clinical named entity recognition via prompt engineering. J. Am. Medical Informatics Assoc. 31(9): 1812-1820 (2024) - [j141]Zhao Li, Qiang Wei, Liang-Chin Huang, Jianfu Li, Yan Hu, Yao-Shun Chuang, Jianping He, Avisha Das, Vipina Kuttichi Keloth, Yuntao Yang, Chiamaka S. Diala, Kirk E. Roberts, Cui Tao, Xiaoqian Jiang, W. Jim Zheng, Hua Xu:
Ensemble pretrained language models to extract biomedical knowledge from literature. J. Am. Medical Informatics Assoc. 31(9): 1904-1911 (2024) - [j140]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) - [j139]Yiming Li, Xueqing Peng, Jianfu Li, Xu Zuo, Suyuan Peng, Donghong Pei, Cui Tao, Hua Xu, Na Hong:
Relation extraction using large language models: a case study on acupuncture point locations. J. Am. Medical Informatics Assoc. 31(11): 2622-2631 (2024) - [j138]Yu Huang, Jingchuan Guo, Wei-Han William Chen, Hsin-Yueh Lin, Huilin Tang, Fei Wang, Hua Xu, Jiang Bian:
A scoping review of fair machine learning techniques when using real-world data. J. Biomed. Informatics 151: 104622 (2024) - [j137]Yiming Li, Wei Tao, Zehan Li, Zenan Sun, Fang Li, Susan H. Fenton, Hua Xu, Cui Tao:
Artificial intelligence-powered pharmacovigilance: A review of machine and deep learning in clinical text-based adverse drug event detection for benchmark datasets. J. Biomed. Informatics 152: 104621 (2024) - [j136]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) - [j135]Zhao Li, Lan Lan, Yujia Zhou, Ruoxing Li, Kenneth D. Chavin, Hua Xu, Liang Li, David J. H. Shih, W. Jim Zheng:
Developing deep learning-based strategies to predict the risk of hepatocellular carcinoma among patients with nonalcoholic fatty liver disease from electronic health records. J. Biomed. Informatics 152: 104626 (2024) - [j134]Yiwen Lu, Jiayi Tong, Jessica Chubak, Thomas Lumley, Rebecca A. Hubbard, Hua Xu, Yong Chen:
Leveraging error-prone algorithm-derived phenotypes: Enhancing association studies for risk factors in EHR data. J. Biomed. Informatics 157: 104690 (2024) - [j133]Jiang Bian, Yifan Peng, Eneida A. Mendonça, Imon Banerjee, Hua Xu, Hong Sun, Ye Ye, Casey Overby Taylor, Anália Maria Garcia Lourenço, Alejandro Rodríguez González, Elena Tutubalina:
Call for papers: Special issue on biomedical multimodal large language models - novel approaches and applications. J. Biomed. Informatics 157: 104703 (2024) - [j132]Yu Yin, Hyunjae Kim, Xiao Xiao, Chih-Hsuan Wei, Jaewoo Kang, Zhiyong Lu, Hua Xu, Meng Fang, Qingyu Chen:
Augmenting biomedical named entity recognition with general-domain resources. J. Biomed. Informatics 159: 104731 (2024) - [j131]Yiming Li, Qiang Wei, Xinghan Chen, Jianfu Li, Cui Tao, Hua Xu:
Improving tabular data extraction in scanned laboratory reports using deep learning models. J. Biomed. Informatics 159: 104735 (2024) - [j130]Jianping He, Fang Li, Jianfu Li, Xinyue Hu, Yi Nian, Yang Xiang, Jingqi Wang, Qiang Wei, Yiming Li, Hua Xu, Cui Tao:
Prompt Tuning in Biomedical Relation Extraction. J. Heal. Informatics Res. 8(2): 206-224 (2024) - [j129]Cathy Shyr, Yan Hu, Lisa Bastarache, Alex Cheng, Rizwan Hamid, Paul A. Harris, Hua Xu:
Identifying and Extracting Rare Diseases and Their Phenotypes with Large Language Models. J. Heal. Informatics Res. 8(2): 438-461 (2024) - [c153]Tianyu Liu, Yijia Xiao, Xiao Luo, Hua Xu, Wenjin Jim Zheng, Hongyu Zhao:
Geneverse: A Collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research. EMNLP (Findings) 2024: 4819-4836 - [c152]Pritham Ram, Na Hong, Hua Xu, Xiaoqian Jiang:
Mapping Study Variables to Common Data Elements Using GPT for Sheets: Towards Standardized Data Collection and Sharing. ICHI 2024: 320-325 - [c151]Fongci Lin, Hobart Patrick Young, Huan He, Jimin Huang, Roger Gagne, Daniel Rice, Nathan Price, William Byron, Yan Hu, Donn K. Felker, Will Button, Deniella Meeker, Allen L. Hsiao, Hua Xu, Charles J. Torre Jr., Wade L. Schulz:
Kamino: A Scalable Architecture to Support Medical AI Research Using Large Real World Data. ICHI 2024: 500-504 - [c150]Bin Choi, Brian Ondov, Huan He, Hua Xu:
Towards Enhanced Topic Discovery on Semantic Maps for Biomedical Literature Exploration. VAHC 2024: 25-27 - [i36]Gongbo Zhang, Yiliang Zhou, Yan Hu, Hua Xu, Chunhua Weng, Yifan Peng:
A Span-based Model for Extracting Overlapping PICO Entities from RCT Publications. CoRR abs/2401.06791 (2024) - [i35]Qianqian Xie, Qingyu Chen, Aokun Chen, Cheng Peng, Yan Hu, Fongci Lin, Xueqing Peng, Jimin Huang, Jeffrey Zhang, Vipina Kuttichi Keloth, Xingyu Zhou, Huan He, Lucila Ohno-Machado, Yonghui Wu, Hua Xu, Jiang Bian:
Me LLaMA: Foundation Large Language Models for Medical Applications. CoRR abs/2402.12749 (2024) - [i34]Yiming Li, Xueqing Peng, Jianfu Li, Xu Zuo, Suyuan Peng, Donghong Pei, Cui Tao, Hua Xu, Na Hong:
Relation Extraction Using Large Language Models: A Case Study on Acupuncture Point Locations. CoRR abs/2404.05415 (2024) - [i33]Mingchen Li, Halil Kilicoglu, Hua Xu, Rui Zhang:
BiomedRAG: A Retrieval Augmented Large Language Model for Biomedicine. CoRR abs/2405.00465 (2024) - [i32]Hanlei Zhang, Hua Xu, Fei Long, Xin Wang, Kai Gao:
Unsupervised Multimodal Clustering for Semantics Discovery in Multimodal Utterances. CoRR abs/2405.12775 (2024) - [i31]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) - [i30]Yu Yin, Hyunjae Kim, Xiao Xiao, Chih-Hsuan Wei, Jaewoo Kang, Zhiyong Lu, Hua Xu, Meng Fang, Qingyu Chen:
Augmenting Biomedical Named Entity Recognition with General-domain Resources. CoRR abs/2406.10671 (2024) - [i29]Tianyu Liu, Yijia Xiao, Xiao Luo, Hua Xu, W. Jim Zheng, Hongyu Zhao:
Geneverse: A collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research. CoRR abs/2406.15534 (2024) - [i28]Yiming Li, Deepthi Viswaroopan, William He, Jianfu Li, Xu Zuo, Hua Xu, Cui Tao:
Improving Entity Recognition Using Ensembles of Deep Learning and Fine-tuned Large Language Models: A Case Study on Adverse Event Extraction from Multiple Sources. CoRR abs/2406.18049 (2024) - [i27]Rachael L. Fleurence, Jiang Bian, Xiaoyan Wang, Hua Xu, Dalia Dawoud, Mitch Higashi, Jagpreet Chhatwal:
Generative AI for Health Technology Assessment: Opportunities, Challenges, and Policy Considerations. CoRR abs/2407.11054 (2024) - [i26]Jiasheng Zhang, Jialin Chen, Ali Maatouk, Ngoc Bui, Qianqian Xie, Leandros Tassiulas, Jie Shao, Hua Xu, Rex Ying:
LitFM: A Retrieval Augmented Structure-aware Foundation Model For Citation Graphs. CoRR abs/2409.12177 (2024) - [i25]Aidan Gilson, Xuguang Ai, Thilaka Arunachalam, Ziyou Chen, Ki Xiong Cheong, Amisha D. Dave, Cameron Duic, Mercy Kibe, Annette Kaminaka, Minali Prasad, Fares Siddig, Maxwell B. Singer, Wendy Wong, Qiao Jin, Tiarnan D. L. Keenan, Xia Hu, Emily Y. Chew, Zhiyong Lu, Hua Xu, Ron A. Adelman, Yih-Chung Tham, Qingyu Chen:
Enhancing Large Language Models with Domain-specific Retrieval Augment Generation: A Case Study on Long-form Consumer Health Question Answering in Ophthalmology. CoRR abs/2409.13902 (2024) - [i24]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) - [i23]Aidan Gilson, Xuguang Ai, Qianqian Xie, Sahana Srinivasan, Krithi Pushpanathan, Maxwell B. Singer, Jimin Huang, Hyunjae Kim, Erping Long, Peixing Wan, Luciano V. Del Priore, Lucila Ohno-Machado, Hua Xu, Dianbo Liu, Ron A. Adelman, Yih-Chung Tham, Qingyu Chen:
Language Enhanced Model for Eye (LEME): An Open-Source Ophthalmology-Specific Large Language Model. CoRR abs/2410.03740 (2024) - [i22]Rongbin Li, Wenbo Chen, Jinbo Li, Hanwen Xing, Hua Xu, Zhao Li, W. Jim Zheng:
GPTON: Generative Pre-trained Transformers enhanced with Ontology Narration for accurate annotation of biological data. CoRR abs/2410.10899 (2024) - [i21]Betina Idnay, Zihan Xu, William G. Adams, Mohammad Adibuzzaman, Nicholas R. Anderson, Neil Bahroos, Douglas S. Bell, Cody Bumgardner, Thomas R. Campion Jr., Victor M. Castro, James J. Cimino, I. Glenn Cohen, David A. Dorr, Peter L. Elkin, Jungwei W. Fan, Todd Ferris, David J. Foran, David A. Hanauer, Mike Hogarth, Kun Huang, Jayashree Kalpathy-Cramer, Manoj Kandpal, Niranjan S. Karnik, Avnish Katoch, Albert M. Lai, Christophe G. Lambert, Lang Li, Christopher Lindsell, Jinze Liu, Zhiyong Lu, Yuan Luo, Peter McGarvey, Eneida A. Mendonça, Parsa Mirhaji, Shawn N. Murphy, John D. Osborne, Ioannis Ch. Paschalidis, Paul A. Harris, Fred W. Prior, Nicholas J. Shaheen, Nawar Shara, Ida Sim, Umberto Tachinardi, Lemuel R. Waitman, Rosalind J. Wright, Adrian H. Zai, Kai Zheng, Sandra Soo-Jin Lee, Bradley A. Malin, Karthik Natarajan, W. Nicholson Price, Rui Zhang, Yiye Zhang, Hua Xu, Jiang Bian, Chunhua Weng, Yifan Peng:
Environment Scan of Generative AI Infrastructure for Clinical and Translational Science. CoRR abs/2410.12793 (2024) - [i20]Rachael L. Fleurence, Xiaoyan Wang, Jiang Bian, Mitch Higashi, Turgay Ayer, Hua Xu, Dalia Dawoud, Jagpreet Chhatwal:
Generative AI in Health Economics and Outcomes Research: A Taxonomy of Key Definitions and Emerging Applications, an ISPOR Working Group Report. CoRR abs/2410.20204 (2024) - [i19]Yiming Li, Fang Li, Kirk Roberts, Licong Cui, Cui Tao, Hua Xu:
A Comparative Study of Recent Large Language Models on Generating Hospital Discharge Summaries for Lung Cancer Patients. CoRR abs/2411.03805 (2024) - [i18]Yan Hu, Xu Zuo, Yujia Zhou, Xueqing Peng, Jimin Huang, Vipina Kuttichi Keloth, Vincent J. Zhang, Ruey-Ling Weng, Qingyu Chen, Xiaoqian Jiang, Kirk E. Roberts, Hua Xu:
Information Extraction from Clinical Notes: Are We Ready to Switch to Large Language Models? CoRR abs/2411.10020 (2024) - [i17]Yan Wang, Jimin Huang, Huan He, Vincent J. Zhang, Yujia Zhou, Xubing Hao, Pritham Ram, Lingfei Qian, Qianqian Xie, Ruey-Ling Weng, Fongci Lin, Yan Hu, Licong Cui, Xiaoqian Jiang, Hua Xu, Na Hong:
CDEMapper: Enhancing NIH Common Data Element Normalization using Large Language Models. CoRR abs/2412.00491 (2024) - [i16]Yutong Xie, Yijun Pan, Hua Xu, Qiaozhu Mei:
Bridging AI and Science: Implications from a Large-Scale Literature Analysis of AI4Science. CoRR abs/2412.09628 (2024) - [i15]Xingjian Zhang, Ziyang Xiong, Shixuan Liu, Yutong Xie, Tolga Ergen, Dongsub Shim, Hua Xu, Honglak Lee, Qiaozhu Mei:
Map2Text: New Content Generation from Low-Dimensional Visualizations. CoRR abs/2412.18673 (2024) - 2023
- [j128]Yan Hu, Vipina Kuttichi Keloth, Kalpana Raja, Yong Chen, Hua Xu:
Towards precise PICO extraction from abstracts of randomized controlled trials using a section-specific learning approach. Bioinform. 39(9) (2023) - [j127]Zhaoyi Chen, Hansi Zhang, Xi Yang, Songzi Wu, Xing He, Jie Xu, Jingchuan Guo, Mattia Prosperi, Fei Wang, Hua Xu, Yong Chen, Hui Hu, Steven DeKosky, Matthew Farrer, Yi Guo, Yonghui Wu, Jiang Bian:
Assess the documentation of cognitive tests and biomarkers in electronic health records via natural language processing for Alzheimer's disease and related dementias. Int. J. Medical Informatics 170: 104973 (2023) - [j126]Tsung-Ting Kuo, Anh Pham, Maxim E. Edelson, Jihoon Kim, Jason Chan, Yash Gupta, Lucila Ohno-Machado, David M. Anderson, Chandrasekar Balacha, Tyler Bath, Sally L. Baxter, Andrea Becker-Pennrich, Douglas S. Bell, Elmer V. Bernstam, Ngan Chau, Michele E. Day, Jason N. Doctor, Scott L. DuVall, Robert El-Kareh, Renato Florian, Robert W. Follett, Benjamin P. Geisler, Alessandro Ghigi, Assaf Gottlieb, Ludwig Christian G. Hinske, Zhaoxian Hu, Diana Ir, Xiaoqian Jiang, Katherine K. Kim, Tara K. Knight, Jejo D. Koola, Nelson Lee, Ulrich Mansmann, Michael E. Matheny, Daniella Meeker, Zongyang Mou, Larissa Neumann, Nghia H. Nguyen, Nick Anderson, Eunice Park, Paulina Paul, Mark J. Pletcher, Kai W. Post, Clemens Rieder, Clemens Scherer, Lisa M. Schilling, Andrey Soares, Spencer L. SooHoo, Ekin Soysal, Steven Covington, Brian Tep, Brian Toy, Baocheng Wang, Zhen R. Wu, Hua Xu, Yong K. Choi, Kai Zheng, Yujia Zhou, Rachel A Zucker:
Blockchain-enabled immutable, distributed, and highly available clinical research activity logging system for federated COVID-19 data analysis from multiple institutions. J. Am. Medical Informatics Assoc. 30(6): 1167-1178 (2023) - [j125]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) - [j124]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) - [j123]Lucila Ohno-Machado, Xiaoqian Jiang, Tsung-Ting Kuo, Shiqiang Tao, Luyao Chen, Pritham Ram, Guo-Qiang Zhang, Hua Xu:
A hierarchical strategy to minimize privacy risk when linking "De-identified" data in biomedical research consortia. J. Biomed. Informatics 139: 104322 (2023) - [j122]Vipina Kuttichi Keloth, Juan M. Banda, Michael J. Gurley, Paul M. Heider, Georgina Kennedy, Hongfang Liu, Feifan Liu, Timothy 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) - [j121]Yan Hu, Yong Chen, Hua Xu:
Towards More Generalizable and Accurate Sentence Classification in Medical Abstracts with Less Data. J. Heal. Informatics Res. 7(4): 542-556 (2023) - [c149]Omer Anjum, Luyao Chen, Ryan Denlinger, Ejaz Anam, Dongsheng Yuan, Connie Wooldridge, Martin J. Citardi, Jiajie Zhang, Hua Xu, Xiaoqian Jiang:
FinFax: Fast Interpretation of Fax with NLP. BCB 2023: 73:1-73:2 - [c148]Yiming Li, Xueqing Peng, Jianfu Li, Suyuan Peng, Donghong Pei, Cui Tao, Hua Xu, Na Hong:
Development of a Natural Language Processing Tool to Extract Acupuncture Point Location Terms. ICHI 2023: 344-351 - [c147]Zehan Li, Iqra Ameer, Yan Hu, Ahmed Abdelhameed, Cui Tao, Salih Selek, Hua Xu:
Suicide Tendency Prediction from Psychiatric Notes Using Transformer Models. ICHI 2023: 481-483 - [c146]Yongkang Xiao, Yu Hou, Huixue Zhou, Gayo Diallo, Marcelo Fiszman, Julian Wolfson, Halil Kilicoglu, You Chen, Hua Xu, William G. Mantyh, Rui Zhang:
Repurposing Drugs for Alzheimer's Diseases through Link Prediction on Biomedical Literature. ICHI 2023: 750-752 - [c145]Avisha Das, Zhao Li, Qiang Wei, Jianfu Li, Liang-Chin Huang, Yan Hu, Rongbin Li, Wenjin Jim Zheng, Hua Xu:
Extracting Drug-Protein Relation from Literature Using Ensembles of Biomedical Transformers. MedInfo 2023: 639-643 - [i14]Yan Hu, Iqra Ameer, Xu Zuo, Xueqing Peng, Yujia Zhou, Zehan Li, Yiming Li, Jianfu Li, Xiaoqian Jiang, Hua Xu:
Zero-shot Clinical Entity Recognition using ChatGPT. CoRR abs/2303.16416 (2023) - [i13]Qingyu Chen, Jingcheng Du, Yan Hu, Vipina Kuttichi Keloth, Xueqing Peng, Kalpana Raja, Rui Zhang, Zhiyong Lu, Hua Xu:
Large language models in biomedical natural language processing: benchmarks, baselines, and recommendations. CoRR abs/2305.16326 (2023) - [i12]Cathy Shyr, Yan Hu, Paul A. Harris, Hua Xu:
Identifying and Extracting Rare Disease Phenotypes with Large Language Models. CoRR abs/2306.12656 (2023) - [i11]Rui Yang, Qingcheng Zeng, Keen You, Yujie Qiao, Lucas Huang, Chiachun Hsieh, Benjamin Rosand, Jeremy Goldwasser, Amisha D. Dave, Tiarnan D. L. Keenan, Emily Y. Chew, Dragomir Radev, Zhiyong Lu, Hua Xu, Qingyu Chen, Irene Li:
MedGen: A Python Natural Language Processing Toolkit for Medical Text Processing. CoRR abs/2311.16588 (2023) - 2022
- [j120]Yilu Fang, Betina Ross S. Idnay, Yingcheng Sun, Hao Liu, Zhehuan Chen, Karen Marder, Hua Xu, Rebecca Schnall, Chunhua Weng:
Combining human and machine intelligence for clinical trial eligibility querying. J. Am. Medical Informatics Assoc. 29(7): 1161-1171 (2022) - [j119]Hua Xu, David L. Buckeridge, Fei Wang, Peter Tarczy-Hornoch:
Novel informatics approaches to COVID-19 Research: From methods to applications. J. Biomed. Informatics 129: 104028 (2022) - [j118]Dalton Schutte, Jake Vasilakes, Anusha Bompelli, Yuqi Zhou, Marcelo Fiszman, Hua Xu, Halil Kilicoglu, Jeffrey R. Bishop, Terrence Adam, Rui Zhang:
Discovering novel drug-supplement interactions using SuppKG generated from the biomedical literature. J. Biomed. Informatics 131: 104120 (2022) - [j117]Hua Xu, Ziqi Yuan, Kang Zhao, Yunfeng Xu, Jiyun Zou, Kai Gao:
GAR-Net: A Graph Attention Reasoning Network for conversation understanding. Knowl. Based Syst. 240: 108055 (2022) - [j116]Jianfu Li, Qiang Wei, Omid Ghiasvand, Miao Chen, Victor S. Lobanov, Chunhua Weng, Hua Xu:
A comparative study of pre-trained language models for named entity recognition in clinical trial eligibility criteria from multiple corpora. BMC Medical Informatics Decis. Mak. 22(3): 235 (2022) - [j115]Andrea H. Ramirez, Lina M. Sulieman, David J. Schlueter, Alese E. Halvorson, Jun Qian, Francis Ratsimbazafy, Roxana Loperena-Cortes, Kelsey R. Mayo, Melissa A. Basford, Nicole Deflaux, Karthik Muthuraman, Karthik Natarajan, Abel N. Kho, Hua Xu, Consuelo H. Wilkins, Hoda Anton-Culver, Eric Boerwinkle, Mine Cicek, Cheryl R. Clark, Elizabeth Cohn, Lucila Ohno-Machado, Sheri D. Schully, Brian K. Ahmedani, Maria Argos, Robert M. Cronin, Christopher J. O'Donnell, Mona Fouad, David B. Goldstein, Philip Greenland, Scott J. Hebbring, Elizabeth W. Karlson, Parinda Khatri, Bruce Korf, Jordan W. Smoller, Stephen Sodeke, John Wilbanks, Justin Hentges, Stephen Mockrin, Christopher Lunt, Stephanie A. Devaney, Kelly Gebo, Joshua C. Denny, Robert J. Carroll, David Glazer, Paul A. Harris, George Hripcsak, Anthony A. Philippakis, Dan M. Roden:
The All of Us Research Program: Data quality, utility, and diversity. Patterns 3(8): 100570 (2022) - [c144]Yan Hu, Vipina Kuttichi Keloth, Hua Xu:
Section-specific Annotation of PICO for Medical Evidence Extraction: Applications to Articles of Randomized Controlled Trials for Alzheimer's Disease and COVID-19. AMIA 2022 - [c143]Tsung-Ting Kuo, Xiaoqian Jiang, Hua Xu, Li Xiong, Lucila Ohno-Machado:
Existing and emerging privacy challenges and solutions for federated data coordination. AMIA 2022 - [c142]Yiming Li, Qiang Wei, Yujia Zhou, Hua Xu:
Fast Textual Corpus Retrieval from Electronic Health Records using PDF Parser and TxtSplit Tools. AMIA 2022 - [c141]Maryamsadat Mohtashamian, Ran Hu, Rashmie Abeysinghe, Xubing Hao, Hua Xu, Licong Cui:
Automated Identification of Missing IS-A Relations in the Human Phenotype Ontology. AMIA 2022 - [c140]Qiang Wei, Xu Zuo, Omer Anjum, Yan Hu, Ryan Denlinger, Elmer V. Bernstam, Martin J. Citardi, Hua Xu:
ClinicalLayoutLM: A Pre-trained Multi-modal Model for Understanding Scanned Document in Electronic Health Records. IEEE Big Data 2022: 2821-2827 - [c139]Avisha Das, Salih Selek, Alia R. Warner, Xu Zuo, Yan Hu, Vipina Kuttichi Keloth, Jianfu Li, W. Jim Zheng, Hua Xu:
Conversational Bots for Psychotherapy: A Study of Generative Transformer Models Using Domain-specific Dialogues. BioNLP@ACL 2022: 285-297 - [c138]Shiqiang Tao, Wei-Chun Chou, Jianfu Li, Jingcheng Du, Pritham Ram, Rashmie Abeysinghe, Hua Xu, Xiaoqian Jiang, Peter W. Rose, Lucila Ohno-Machado, Guo-Qiang Zhang:
IMI-CDE: an interactive interface for collaborative mapping of study variables to common data elements. ICHI 2022: 465-468 - [c137]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 - [c136]Yan Hu, Yong Chen, Hua Xu:
Improving Sentence Classification in Abstracts of Randomized Controlled Trial using Prompt Learning. ICHI 2022: 606-607 - [c135]Jianping He, Fang Li, Xinyue Hu, Jianfu Li, Yi Nian, Jingqi Wang, Yang Xiang, Qiang Wei, Hua Xu, Cui Tao:
Chemical-Protein Relation Extraction with Pre-trained Prompt Tuning. ICHI 2022: 608-609 - [i10]Yihe Liu, Ziqi Yuan, Huisheng Mao, Zhiyun Liang, Wanqiuyue Yang, Yuanzhe Qiu, Tie Cheng, Xiaoteng Li, Hua Xu, Kai Gao:
Make Acoustic and Visual Cues Matter: CH-SIMS v2.0 Dataset and AV-Mixup Consistent Module. CoRR abs/2209.02604 (2022) - [i9]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) - 2021
- [j114]Xu Zuo, Yong Chen, Lucila Ohno-Machado, Hua Xu:
How do we share data in COVID-19 research? A systematic review of COVID-19 datasets in PubMed Central Articles. Briefings Bioinform. 22(2): 800-811 (2021) - [j113]Jingqi Wang, Yuankai Ren, Zhi Zhang, Hua Xu, Yaoyun Zhang:
From Tokenization to Self-Supervision: Building a High-Performance Information Extraction System for Chemical Reactions in Patents. Frontiers Res. Metrics Anal. 6: 691105 (2021) - [j112]Jingqi Wang, Noor Abu-El-Rub, Josh Gray, Huy Anh Pham, Yujia Zhou, Frank J. Manion, Mei Liu, Xing Song, Hua Xu, Masoud Rouhizadeh, Yaoyun Zhang:
COVID-19 SignSym: a fast adaptation of a general clinical NLP tool to identify and normalize COVID-19 signs and symptoms to OMOP common data model. J. Am. Medical Informatics Assoc. 28(6): 1275-1283 (2021) - [j111]Jingcheng Du, Yang Xiang, Madhuri Sankaranarayanapillai, Meng Zhang, Jingqi Wang, Yuqi Si, Huy Anh Pham, Hua Xu, Yong Chen, Cui Tao:
Extracting postmarketing adverse events from safety reports in the vaccine adverse event reporting system (VAERS) using deep learning. J. Am. Medical Informatics Assoc. 28(7): 1393-1400 (2021) - [j110]Jihoon Kim, Larissa Neumann, Paulina Paul, Michele E. Day, Michael Aratow, Douglas S. Bell, Jason N. Doctor, Ludwig Christian G. Hinske, Xiaoqian Jiang, Katherine K. Kim, Michael E. Matheny, Daniella Meeker, Mark J. Pletcher, Lisa M. Schilling, Spencer L. SooHoo, Hua Xu, Kai Zheng, Lucila Ohno-Machado:
Privacy-protecting, reliable response data discovery using COVID-19 patient observations. J. Am. Medical Informatics Assoc. 28(8): 1765-1776 (2021) - [j109]Yi Guo, Yahan Zhang, Tianchen Lyu, Mattia Prosperi, Fei Wang, Hua Xu, Jiang Bian:
The application of artificial intelligence and data integration in COVID-19 studies: a scoping review. J. Am. Medical Informatics Assoc. 28(9): 2050-2067 (2021) - [j108]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) - [j107]Kang Zhao, Hua Xu, Yue Cheng, Xiaoteng Li, Kai Gao:
Representation iterative fusion based on heterogeneous graph neural network for joint entity and relation extraction. Knowl. Based Syst. 219: 106888 (2021) - [c134]Hanlei Zhang, Xiaoteng Li, Hua Xu, Panpan Zhang, Kang Zhao, Kai Gao:
TEXTOIR: An Integrated and Visualized Platform for Text Open Intent Recognition. ACL (demo) 2021: 167-174 - [c133]Laila Rasmy, Bijun S. Kannadath, Masayuki Nigo, Ziqian Xie, Bingyu Mao, Khush A. Patel, Yujia Zhou, Xiao Dong, Hua Xu, Degui Zhi:
Generalizable Gated Recurrent Neural Network based model to predict COVID-19 patient outcomes on admission. AMIA 2021 - [c132]Laila Rasmy, Masayuki Nigo, Bijun S. Kannadath, Ziqian Xie, Bingyu Mao, Khush A. Patel, Wanheng Zhang, Yujia Zhou, Angela Ross, Hua Xu, Degui Zhi:
CovRNN: predicting outcomes of COVID-19 patients on admission using their electronic health records with minimal data processing. AMIA 2021 - [c131]Hong Guan, Jianfu Li, Hua Xu, Murthy V. Devarakonda:
Robustly Pre-Trained Neural Model for Direct Temporal Relation Extraction. ICHI 2021: 501-502 - [c130]Jianfu Li, Qiang Wei, Omid Ghiasvand, Miao Chen, Victor S. Lobanov, Chunhua Weng, Hua Xu:
Study of Pre-trained Language Models for Named Entity Recognition in Clinical Trial Eligibility Criteria from Multiple Corpora. ICHI 2021: 511-512 - [i8]Dalton Schutte, Jake Vasilakes, Anusha Bompelli, Yuqi Zhou, Marcelo Fiszman, Hua Xu, Halil Kilicoglu, Jeffrey R. Bishop, Terrence Adam, Rui Zhang:
Discovering novel drug-supplement interactions using a dietary supplements knowledge graph generated from the biomedical literature. CoRR abs/2106.12741 (2021) - [i7]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) - [i6]Laila Rasmy, Jie Zhu, Zhiheng Li, Xin Hao, Hong Thoai Tran, Yujia Zhou, Firat Tiryaki, Yang Xiang, Hua Xu, Degui Zhi:
Simple Recurrent Neural Networks is all we need for clinical events predictions using EHR data. CoRR abs/2110.00998 (2021) - [i5]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
- [j106]Qiang Wei, Yaoyun Zhang, Muhammad Amith, Rebecca Lin, Jenay Lapeyrolerie, Cui Tao, Hua Xu:
Recognizing software names in biomedical literature using machine learning. Health Informatics J. 26(1) (2020) - [j105]Fang Li, Guozheng Rao, Jingcheng Du, Yang Xiang, Yaoyun Zhang, Salih Selek, Jane Elizabeth Hamilton, Hua Xu, Cui Tao:
Ontological representation-oriented term normalization and standardization of the Research Domain Criteria. Health Informatics J. 26(2): 726-737 (2020) - [j104]Jianhong Luo, Jingcheng Du, Cui Tao, Hua Xu, Yaoyun Zhang:
Exploring temporal suicidal behavior patterns on social media: Insight from Twitter analytics. Health Informatics J. 26(2): 738-752 (2020) - [j103]Qiang Wei, Zongcheng Ji, Zhiheng Li, Jingcheng Du, Jingqi Wang, Jun Xu, Yang Xiang, Firat Tiryaki, Stephen Wu, Yaoyun Zhang, Cui Tao, Hua Xu:
A study of deep learning approaches for medication and adverse drug event extraction from clinical text. J. Am. Medical Informatics Assoc. 27(1): 13-21 (2020) - [j102]Rui Duan, Mary Regina Boland, Zixuan Liu, Yue Liu, Howard H. Chang, Hua Xu, Haitao Chu, Christopher H. Schmid, Christopher B. Forrest, John H. Holmes, Martijn J. Schuemie, Jesse A. Berlin, Jason H. Moore, Yong Chen:
Learning from electronic health records across multiple sites: A communication-efficient and privacy-preserving distributed algorithm. J. Am. Medical Informatics Assoc. 27(3): 376-385 (2020) - [j101]Stephen Wu, Kirk Roberts, Surabhi Datta, Jingcheng Du, Zongcheng Ji, Yuqi Si, Sarvesh Soni, Qiong Wang, Qiang Wei, Yang Xiang, Bo Zhao, Hua Xu:
Deep learning in clinical natural language processing: a methodical review. J. Am. Medical Informatics Assoc. 27(3): 457-470 (2020) - [j100]Rui Duan, Chongliang Luo, Martijn J. Schuemie, Jiayi Tong, C. Jason Liang, Howard H. Chang, Mary Regina Boland, Jiang Bian, Hua Xu, John H. Holmes, Christopher B. Forrest, Sally C. Morton, Jesse A. Berlin, Jason H. Moore, Kevin B. Mahoney, Yong Chen:
Learning from local to global: An efficient distributed algorithm for modeling time-to-event data. J. Am. Medical Informatics Assoc. 27(7): 1028-1036 (2020) - [j99]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) - [j98]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) - [j97]Laila Rasmy, Firat Tiryaki, Yujia Zhou, Yang Xiang, Cui Tao, Hua Xu, Degui Zhi:
Representation of EHR data for predictive modeling: a comparison between UMLS and other terminologies. J. Am. Medical Informatics Assoc. 27(10): 1593-1599 (2020) - [j96]Jean Louis Raisaro, Francesco Marino, Juan Ramón Troncoso-Pastoriza, Raphaelle Beau-Lejdstrom, Riccardo Bellazzi, Robert Murphy, Elmer V. Bernstam, Henry Wang, Mauro Bucalo, Yong Chen, Assaf Gottlieb, Arif Ozgun Harmanci, Miran Kim, Yejin Kim, Jeffrey G. Klann, Catherine Klersy, Bradley A. Malin, Marie Méan, Fabian Prasser, Luigia Scudeller, Ali Torkamani, Julien Vaucher, Mamta Puppala, Stephen T. C. Wong, Milana Frenkel-Morgenstern, Hua Xu, Baba Maiyaki Musa, Abdulrazaq G. Habib, Trevor Cohen, Adam B. Wilcox, Hamisu M. Salihu, Heidi Sofia, Xiaoqian Jiang, Jean-Pierre Hubaux:
SCOR: A secure international informatics infrastructure to investigate COVID-19. J. Am. Medical Informatics Assoc. 27(11): 1721-1726 (2020) - [j95]Qiong Wang, Zongcheng Ji, Jingqi Wang, Stephen Wu, Weiyan Lin, Wenzhen Li, Li Ke, Guohong Xiao, Qing Jiang, Hua Xu, Yi Zhou:
A study of entity-linking methods for normalizing Chinese diagnosis and procedure terms to ICD codes. J. Biomed. Informatics 105: 103418 (2020) - [j94]Muhammad Amith, Rebecca Lin, Licong Cui, Dennis Wang, Anna Zhu, Grace Xiong, Hua Xu, Kirk Roberts, Cui Tao:
Conversational ontology operator: patient-centric vaccine dialogue management engine for spoken conversational agents. BMC Medical Informatics Decis. Mak. 20-S(4): 259 (2020) - [c129]Hongfang Liu, Xiaoqian Jiang, Serguei V. S. Pakhomov, Chunhua Weng, Hua Xu:
The Open Health Natural Language Processing Collaboratory. AMIA 2020 - [c128]Yaoyun Zhang, Jingqi Wang, Hua Xu:
LANN: An integrated online annotation tool for information extraction. AMIA 2020 - [c127]Xu Zuo, Jianfu Li, Bo Zhao, Yujia Zhou, Xiao Dong, Jon D. Duke, Karthik Natarajan, George Hripcsak, Nigam Shah, Juan M. Banda, Ruth M. Reeves, Hua Xu:
Normalizing Clinical Document Titles to LOINC Document Ontology: an Initial Study. AMIA 2020 - [c126]Jingqi Wang, William Christopher Mathews, Huy Anh Pham, Hua Xu, Yaoyun Zhang:
Opioid2FHIR: A system for extracting FHIR-compatible opioid prescriptions from clinical text. BIBM 2020: 1748-1751 - [c125]Xi Yang, Hanyuan Yang, Tianchen Lyu, Shuang Yang, Yi Guo, Jiang Bian, Hua Xu, Yonghui Wu:
A Natural Language Processing Tool to Extract Quantitative Smoking Status from Clinical Narratives. ICHI 2020: 1-2 - [c124]Qiang Wei, Yujia Zhou, Bo Zhao, Xinyue Hu, Qiaozhu Mei, Cui Tao, Hua Xu:
Named Entity Recognition from Table Headers in Randomized Controlled Trial Articles. ICHI 2020: 1-2 - [i4]Hong Guan, Jianfu Li, Hua Xu, Murthy V. Devarakonda:
Robustly Pre-trained Neural Model for Direct Temporal Relation Extraction. CoRR abs/2004.06216 (2020)
2010 – 2019
- 2019
- [j93]Yaoyun Zhang, Olivia R. Zhang, Rui Li, Aaron Flores, Salih Selek, Xiang Y. Zhang, Hua Xu:
Psychiatric stressor recognition from clinical notes to reveal association with suicide. Health Informatics J. 25(4) (2019) - [j92]Yuqi Si, Jingqi Wang, Hua Xu, Kirk E. Roberts:
Enhancing clinical concept extraction with contextual embeddings. J. Am. Medical Informatics Assoc. 26(11): 1297-1304 (2019) - [j91]Qiang Wei, Yukun Chen, Mandana Salimi, Joshua C. Denny, Qiaozhu Mei, Thomas A. Lasko, Qingxia Chen, Stephen Wu, Amy Franklin, Trevor Cohen, Hua Xu:
Cost-aware active learning for named entity recognition in clinical text. J. Am. Medical Informatics Assoc. 26(11): 1314-1322 (2019) - [j90]Xue Shi, Yingping Yi, Ying Xiong, Buzhou Tang, Qingcai Chen, Xiaolong Wang, Zongcheng Ji, Yaoyun Zhang, Hua Xu:
Extracting entities with attributes in clinical text via joint deep learning. J. Am. Medical Informatics Assoc. 26(12): 1584-1591 (2019) - [j89]Zengjian Liu, Xiaolong Wang, Qingcai Chen, Buzhou Tang, Hua Xu:
Temporal indexing of medical entity in Chinese clinical notes. BMC Medical Informatics Decis. Mak. 19-S(1): 17:1-17:11 (2019) - [j88]Zhiheng Li, Zhihao Yang, Chen Shen, Jun Xu, Yaoyun Zhang, Hua Xu:
Integrating shortest dependency path and sentence sequence into a deep learning framework for relation extraction in clinical text. BMC Medical Informatics Decis. Mak. 19-S(1): 22:1-22:8 (2019) - [j87]Yang Xiang, Jun Xu, Yuqi Si, Zhiheng Li, Laila Rasmy, Yujia Zhou, Firat Tiryaki, Fang Li, Yaoyun Zhang, Yonghui Wu, Xiaoqian Jiang, W. Jim Zheng, Degui Zhi, Cui Tao, Hua Xu:
Time-sensitive clinical concept embeddings learned from large electronic health records. BMC Medical Informatics Decis. Mak. 19-S(2): 139-148 (2019) - [j86]Ying Xiong, Zhongmin Wang, Dehuan Jiang, Xiaolong Wang, Qingcai Chen, Hua Xu, Jun Yan, Buzhou Tang:
A fine-grained Chinese word segmentation and part-of-speech tagging corpus for clinical text. BMC Medical Informatics Decis. Mak. 19-S(2): 179-184 (2019) - [j85]Yaoyun Zhang, Firat Tiryaki, Min Jiang, Hua Xu:
Parsing clinical text using the state-of-the-art deep learning based parsers: a systematic comparison. BMC Medical Informatics Decis. Mak. 19-S(3): 51-58 (2019) - [j84]V. G. Vinod Vydiswaran, Yaoyun Zhang, Yanshan Wang, Hua Xu:
Special issue of BMC medical informatics and decision making on health natural language processing. BMC Medical Informatics Decis. Mak. 19-S(3): 76:1-76:3 (2019) - [j83]Yanshan Wang, Hua Xu, Özlem Uzuner:
Editorial: The second international workshop on health natural language processing (HealthNLP 2019). BMC Medical Informatics Decis. Mak. 19-S(5): 1 (2019) - [j82]Jun Xu, Zhiheng Li, Qiang Wei, Yonghui Wu, Yang Xiang, Hee-Jin Lee, Yaoyun Zhang, Stephen Wu, Hua Xu:
Applying a deep learning-based sequence labeling approach to detect attributes of medical concepts in clinical text. BMC Medical Informatics Decis. Mak. 19-S(5): 8 (2019) - [c123]Liwei Wang, Jason A. Wampfler, Angela Dispenzieri, Hua Xu, Ping Yang, Hongfang Liu:
Achievability to Extract Specific Date Information for Cancer Research. AMIA 2019 - [c122]Jingqi Wang, Yaoyun Zhang, Hua Xu:
CLAMP-ATR: A deep learning pipeline for attribute recognition of clinical concepts. AMIA 2019 - [c121]Qiang Wei, Zongcheng Ji, Yuqi Si, Jingcheng Du, Jingqi Wang, Firat Tiryaki, Stephen Wu, Cui Tao, Kirk Roberts, Hua Xu:
Relation Extraction from Clinical Narratives Using Pre-trained Language Models. AMIA 2019 - [c120]Muhammad Amith, Licong Cui, Kirk Roberts, Hua Xu, Cui Tao:
Ontology of Consumer Health Vocabulary: providing a formal and interoperable semantic resource for linking lay language and medical terminology. BIBM 2019: 1177-1178 - [c119]Jun Xu, Zhiheng Li, Qiang Wei, Yonghui Wu, Yang Xiang, Hee-Jin Lee, Yaoyun Zhang, Stephen Wu, Hua Xu:
Detect Attributes of Medical Concepts via Sequence Labeling. ICHI 2019: 1-2 - [c118]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 - [c117]Jiatong Li, Kai Zheng, Hua Xu, Qiaozhu Mei, Yue Wang:
The Strength of the Weakest Supervision: Topic Classification Using Class Labels. NAACL-HLT (Student Research Workshop) 2019: 22-28 - [c116]Muhammad Amith, Rebecca Lin, Licong Cui, Dennis Wang, Anna Zhu, Grace Xiong, Hua Xu, Kirk Roberts, Cui Tao:
An Ontology-Powered Dialogue Engine For Patient Communication of Vaccines. SEPDA@ISWC 2019: 24-30 - [i3]Yuqi Si, Jingqi Wang, Hua Xu, Kirk Roberts:
Enhancing Clinical Concept Extraction with Contextual Embedding. CoRR abs/1902.08691 (2019) - [i2]Zongcheng Ji, Qiang Wei, Hua Xu:
BERT-based Ranking for Biomedical Entity Normalization. CoRR abs/1908.03548 (2019) - 2018
- [j81]Shumei Miao, Tingyu Xu, Yonghui Wu, Hui Xie, Jingqi Wang, Shenqi Jing, Yaoyun Zhang, Xiaoliang Zhang, Yinshuang Yang, Xin Zhang, Tao Shan, Li Wang, Hua Xu, Shui Wang, Yun Liu:
Extraction of BI-RADS findings from breast ultrasound reports in Chinese using deep learning approaches. Int. J. Medical Informatics 119: 17-21 (2018) - [j80]Xiaoling Chen, Anupama E. Gururaj, Ibrahim Burak Özyurt, Ruiling Liu, Ergin Soysal, Trevor Cohen, Firat Tiryaki, Yueling Li, Nansu Zong, Min Jiang, Deevakar Rogith, Mandana Salimi, Hyeon-Eui Kim, Philippe Rocca-Serra, Alejandra N. González-Beltrán, Claudiu Farcas, Todd Johnson, Ronald Margolis, George Alter, Susanna-Assunta Sansone, Ian Fore, Lucila Ohno-Machado, Jeffrey S. Grethe, Hua Xu:
DataMed - an open source discovery index for finding biomedical datasets. J. Am. Medical Informatics Assoc. 25(3): 300-308 (2018) - [j79]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) - [j78]Ram Dixit, Deevakar Rogith, Vidya Narayana, Mandana Salimi, Anupama E. Gururaj, Lucila Ohno-Machado, Hua Xu, Todd R. Johnson:
User needs analysis and usability assessment of DataMed - a biomedical data discovery index. J. Am. Medical Informatics Assoc. 25(3): 337-344 (2018) - [j77]Jing Huang, Rui Duan, Rebecca A. Hubbard, Yonghui Wu, Jason H. Moore, Hua Xu, Yong Chen:
PIE: A prior knowledge guided integrated likelihood estimation method for bias reduction in association studies using electronic health records data. J. Am. Medical Informatics Assoc. 25(3): 345-352 (2018) - [j76]Yue Wang, Kai Zheng, Hua Xu, Qiaozhu Mei:
Interactive medical word sense disambiguation through informed learning. J. Am. Medical Informatics Assoc. 25(7): 800-808 (2018) - [j75]Li Wang, Yaoyun Zhang, Min Jiang, Jingqi Wang, Jiancheng Dong, Yun Liu, Cui Tao, Guoqian Jiang, Yi Zhou, Hua Xu:
Toward a normalized clinical drug knowledge base in China - applying the RxNorm model to Chinese clinical drugs. J. Am. Medical Informatics Assoc. 25(7): 809-818 (2018) - [j74]Laila Rasmy, Yonghui Wu, Ningtao Wang, Xin Geng, W. Jim Zheng, Fei Wang, Hulin Wu, Hua Xu, Degui Zhi:
A study of generalizability of recurrent neural network-based predictive models for heart failure onset risk using a large and heterogeneous EHR data set. J. Biomed. Informatics 84: 11-16 (2018) - [j73]Guocai Chen, Alex Tsoi, Hua Xu, W. Jim Zheng:
Predict effective drug combination by deep belief network and ontology fingerprints. J. Biomed. Informatics 85: 149-154 (2018) - [j72]Xin Zhang, Li Wang, Shumei Miao, Hua Xu, Yuechuchu Yin, Yueshi Zhu, Zuolei Dai, Tao Shan, Shenqi Jing, Jian Wang, Xiaoliang Zhang, Zhongqiu Huang, Zhongmin Wang, Jianjun Guo, Yun Liu:
Analysis of treatment pathways for three chronic diseases using OMOP CDM. J. Medical Syst. 42(12): 260:1-260:12 (2018) - [j71]Hee-Jin Lee, Yaoyun Zhang, Min Jiang, Jun Xu, Cui Tao, Hua Xu:
Identifying direct temporal relations between time and events from clinical notes. BMC Medical Informatics Decis. Mak. 18(S-2): 23-34 (2018) - [j70]Jingcheng Du, Yaoyun Zhang, Jianhong Luo, Yuxi Jia, Qiang Wei, Cui Tao, Hua Xu:
Extracting psychiatric stressors for suicide from social media using deep learning. BMC Medical Informatics Decis. Mak. 18(S-2): 77-87 (2018) - [c115]Jing An, Mandana Salimi, Anupama E. Gururaj, Cui Tao, Degui Zhi, Hua Xu:
Development of HeartData, a Data Discovery Index Prototype for Cardiovascular data. AMIA 2018 - [c114]Halil Kilicoglu, Aurélie Névéol, Timothy Clark, Hua Xu, Neil R. Smalheiser:
Methods and Tools to Enhance Rigor and Reproducibility of Biomedical Research. AMIA 2018 - [c113]Lingyi Tang, Yaoyun Zhang, Hua Xu:
Building a Biomedical Bilingual Parallel Corpus between Chinese and English from PubMed. AMIA 2018 - [c112]Qiang Wei, Amy Franklin, Trevor Cohen, Hua Xu:
Clinical text annotation - what factors are associated with the cost of time? AMIA 2018 - [c111]Yonghui Wu, Xi Yang, Jiang Bian, Yi Guo, Hua Xu, William R. Hogan:
Combine Factual Medical Knowledge and Distributed Word Representation to Improve Clinical Named Entity Recognition. AMIA 2018 - [c110]Jun Xu, Yaoyun Zhang, Jingcheng Du, Jingqi Wang, Firat Tiryaki, Hua Xu:
Detecting Anatomical Entities in Clinical Text. AMIA 2018 - [c109]Yaoyun Zhang, Qiang Wei, Jingqi Wang, Hua Xu:
CLAMP-PA: A machine learning based pre-annotation pipeline for corpus construction of clinical concepts. AMIA 2018 - [c108]Xiao Dong, Yaoyun Zhang, Hua Xu, Chunhua Weng:
Guideline-driven data quality assessment- A case study of warfarin management. AMIA 2018 - [c107]Jianhong Luo, Jingcheng Du, Cui Tao, Hua Xu, Yaoyun Zhang:
Exploring Temporal Patterns of Suicidal Behavior on Twitter. ICHI Workshops 2018: 55-56 - [c106]Fang Li, Guozheng Rao, Jingcheng Du, Yang Xiang, Yaoyun Zhang, Salih Selek, Jane Elizabeth Hamilton, Hua Xu, Cui Tao:
Term Standardization and Normalization for Research Domain Criteria (RDoC). ICHI Workshops 2018: 60-61 - [c105]Yaoyun Zhang, Firat Tiryaki, Min Jiang, Hua Xu:
Parsing Clinical Text: How Good are the state-of-the-art Deep Learning Based Parsers? ICHI Workshops 2018: 80-81 - 2017
- [j69]Ruichu Cai, Mei Liu, Yong Hu, Brittany Melton, Michael E. Matheny, Hua Xu, Lian Duan, Lemuel R. Waitman:
Identification of adverse drug-drug interactions through causal association rule discovery from spontaneous adverse event reports. Artif. Intell. Medicine 76: 7-15 (2017) - [j68]Trevor Cohen, Kirk Roberts, Anupama E. Gururaj, Xiaoling Chen, Saeid Pournejati, George Alter, William R. Hersh, Dina Demner-Fushman, Lucila Ohno-Machado, Hua Xu:
A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge. Database J. Biol. Databases Curation 2017: bax061 (2017) - [j67]Kirk Roberts, Anupama E. Gururaj, Xiaoling Chen, Saeid Pournejati, William R. Hersh, Dina Demner-Fushman, Lucila Ohno-Machado, Trevor Cohen, Hua Xu:
Information retrieval for biomedical datasets: the 2016 bioCADDIE dataset retrieval challenge. Database J. Biol. Databases Curation 2017: bax068 (2017) - [j66]Hao Wang, Jiamao Luo, Chun Liu, Huilin Niu, Jing Wang, Qi Liu, Zhongming Zhao, Hua Xu, Yanqing Ding, Jingchun Sun, Qingling Zhang:
Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer. BMC Bioinform. 18(1): 388 (2017) - [j65]Haodi Li, Qingcai Chen, Buzhou Tang, Xiaolong Wang, Hua Xu, Baohua Wang, Dong Huang:
CNN-based ranking for biomedical entity normalization. BMC Bioinform. 18(S-11): 79-86 (2017) - [j64]Jingchun Sun, Qiang Wei, Yubo Zhou, Jingqi Wang, Qi Liu, Hua Xu:
A systematic analysis of FDA-approved anticancer drugs. BMC Syst. Biol. 11(S-5): 87:1-87:17 (2017) - [j63]W. Jim Zheng, Jianhua Ruan, Hua Xu, Zhongming Zhao, Zhangdong Liu:
The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work. BMC Syst. Biol. 11(S-5): 88:1-88:3 (2017) - [j62]Yonghui Wu, Joshua C. Denny, S. Trent Rosenbloom, Randolph A. Miller, Dario A. Giuse, Lulu Wang, Carmelo Blanquicett, Ergin Soysal, Jun Xu, Hua Xu:
A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD). J. Am. Medical Informatics Assoc. 24(e1): e79-e86 (2017) - [j61]Muhammad Amith, Hsing-yi Song, Yaoyun Zhang, Hua Xu, Cui Tao:
Lightweight predicate extraction for patient-level cancer information and ontology development. BMC Medical Informatics Decis. Mak. 17(2): 23-34 (2017) - [j60]Yukun Chen, Thomas A. Lasko, Qiaozhu Mei, Qingxia Chen, Sungrim Moon, Jingqi Wang, Ky Nguyen, Tolulola Dawodu, Trevor Cohen, Joshua C. Denny, Hua Xu:
An active learning-enabled annotation system for clinical named entity recognition. BMC Medical Informatics Decis. Mak. 17(2): 35-44 (2017) - [j59]Zengjian Liu, Ming Yang, Xiaolong Wang, Qingcai Chen, Buzhou Tang, Zhe Wang, Hua Xu:
Entity recognition from clinical texts via recurrent neural network. BMC Medical Informatics Decis. Mak. 17(2): 53-61 (2017) - [j58]Cui Tao, Yang Gong, Hua Xu, Zhongming Zhao:
Introduction: the International Conference on Intelligent Biology and Medicine (ICIBM) 2016: special focus on medical informatics and big data. BMC Medical Informatics Decis. Mak. 17(2): 77:1-77:3 (2017) - [c104]Xiaoling Chen, Jun Xu, Jingqi Wang, Anupama E. Gururaj, Lucila Ohno-Machado, Hua Xu:
A Natural Language Processing System for Biomedical Dataset Retrieval. AMIA 2017 - [c103]Ram Dixit, Deevakar Rogith, Vidya Narayana, Mandana Salimi, Anupama E. Gururaj, Lucila Ohno-Machado, Hua Xu, Todd R. Johnson:
Meeting User Needs for a Data Discovery Index of Biomedical Big Data. AMIA 2017 - [c102]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 - [c101]Hee-Jin Lee, Yaoyun Zhang, Kirk Roberts, Hua Xu:
Leveraging existing corpora for de-identification of psychiatric notes using domain adaptation. AMIA 2017 - [c100]Aurélie Névéol, Noémie Elhadad, Sumithra Velupillai, Hua Xu, Guergana Savova:
Clinical Natural Language Processing in Languages Other Than English. AMIA 2017 - [c99]Kirk Roberts, Anupama E. Gururaj, Xiaoling Chen, Saeid Pournejati, Trevor Cohen, William R. Hersh, Dina Demner-Fushman, Lucila Ohno-Machado, Hua Xu:
Information Retrieval for Biomedical Datasets: The 2016 bioCADDIE Challenge. AMIA 2017 - [c98]Lingyi Tang, Yaoyun Zhang, Hua Xu:
Identifying Disease Hierarchical Relation with Concept Embeddings and Distant Supervision. AMIA 2017 - [c97]Yue Wang, Kai Zheng, Hua Xu, Qiaozhu Mei:
Interactive Medical Word Sense Disambiguation with Instance and Feature Labeling. AMIA 2017 - [c96]Yue Wang, Jian Tang, V. G. Vinod Vydiswaran, Kai Zheng, Hua Xu, Qiaozhu Mei:
Matching Consumer Health Vocabulary with Professional Medical Terms Through Concept Embedding. AMIA 2017 - [c95]Yonghui Wu, Min Jiang, Jun Xu, Degui Zhi, Hua Xu:
Clinical Named Entity Recognition Using Deep Learning Models. AMIA 2017 - [c94]Hua Xu, Ergin Soysal, Jingqi Wang, Min Jiang, Yonghui Wu:
CLAMP - A User-Centric Clinical Natural Language Processing Toolkit. AMIA 2017 - [c93]Jun Xu, Yonghui Wu, Yaoyun Zhang, Qiang Wei, Hua Xu:
Detecting Contradictory and Consistent Citations in Biomedical Literature. AMIA 2017 - [c92]Jun Xu, Yonghui Wu, Yaoyun Zhang, Hua Xu:
Detecting Body Location Modifiers of Disorders in Clinical Texts via Sequence Labeling. AMIA 2017 - [c91]Yaoyun Zhang, Hee-Jin Lee, Yonghui Wu, Hua Xu:
Evaluating Word Embeddings from Multiple Domains for Symptom Recognition in Psychiatric Notes. AMIA 2017 - [c90]Jingcheng Du, Yaoyun Zhang, Cui Tao, Hua Xu:
A pilot study of mining association between psychiatric stressors and symptoms in tweets. BIBM 2017: 1254-1257 - [c89]Hee-Jin Lee, Yaoyun Zhang, Jun Xu, Cui Tao, Hua Xu, Min Jiang:
Towards practical temporal relation extraction from clinical notes: An analysis of direct temporal relations. BIBM 2017: 1272-1275 - [c88]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 - [c87]Hee-Jin Lee, Min Jiang, Yonghui Wu, Christian Shaffer, John H. Cleator, Eitan Friedman, Joshua P. Lewis, Dan M. Roden, Joshua C. Denny, Hua Xu:
A comparative study of different methods for automatic identification of clopidogrel-induced bleedings in electronic health records. CRI 2017 - [c86]Ergin Soysal, Jeremy L. Warner, Joshua C. Denny, Hua Xu:
Identifying Metastases related Information from Pathology Reports of Lung Cancer Patients. CRI 2017 - [c85]Muhammad Amith, Yaoyun Zhang, Hua Xu, Cui Tao:
Knowledge-Based Approach for Named Entity Recognition in Biomedical Literature: A Use Case in Biomedical Software Identification. IEA/AIE (2) 2017: 386-395 - [c84]Olivia R. Zhang, Yaoyun Zhang, Jun Xu, Kirk Roberts, Xiang Y. Zhang, Hua Xu:
Interweaving Domain Knowledge and Unsupervised Learning for Psychiatric Stressor Extraction from Clinical Notes. IEA/AIE (2) 2017: 396-406 - [c83]Zongcheng Ji, Yaoyun Zhang, Jun Xu, Xiaoling Chen, Yonghui Wu, Hua Xu:
Comparing Cancer Information Needs for Consumers in the US and China. MedInfo 2017: 126-130 - [c82]Muhammad Amith, Frank J. Manion, Marcelline R. Harris, Yaoyun Zhang, Hua Xu, Cui Tao:
Expressing Biomedical Ontologies in Natural Language for Expert Evaluation. MedInfo 2017: 838-842 - [i1]Jun Xu, Hee-Jin Lee, Zongcheng Ji, Jingqi Wang, Qiang Wei, Hua Xu:
UTH_CCB System for Adverse Drug Reaction Extraction from Drug Labels at TAC-ADR 2017. TAC 2017 - 2016
- [j57]Jun Xu, Yonghui Wu, Yaoyun Zhang, Jingqi Wang, Hee-Jin Lee, Hua Xu:
CD-REST: a system for extracting chemical-induced disease relation in literature. Database J. Biol. Databases Curation 2016 (2016) - [j56]Yaoyun Zhang, Jun Xu, Hui Chen, Jingqi Wang, Yonghui Wu, Manu Prakasam, Hua Xu:
Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning. Database J. Biol. Databases Curation 2016 (2016) - [j55]Yaoyun Zhang, Heng-Yi Wu, Jingcheng Du, Jun Xu, Jingqi Wang, Cui Tao, Lang Li, Hua Xu:
Extracting drug-enzyme relation from literature as evidence for drug drug interaction. J. Biomed. Semant. 7: 11 (2016) - [j54]Yaoyun Zhang, Heng-Yi Wu, Jingcheng Du, Jun Xu, Jingqi Wang, Cui Tao, Lang Li, Hua Xu:
Erratum to: Extracting drug-enzyme relation from literature as evidence for drug drug interaction. J. Biomed. Semant. 7: 21 (2016) - [j53]Yaoyun Zhang, Heng-Yi Wu, Jun Xu, Jingqi Wang, Ergin Soysal, Lang Li, Hua Xu:
Leveraging syntactic and semantic graph kernels to extract pharmacokinetic drug drug interactions from biomedical literature. BMC Syst. Biol. 10(S-3): 67 (2016) - [j52]Jun Xu, Hee-Jin Lee, Jia Zeng, Yonghui Wu, Yaoyun Zhang, Liang-Chin Huang, Amber M. Johnson, Vijaykumar Holla, Ann M. Bailey, Trevor Cohen, Funda Meric-Bernstam, Elmer V. Bernstam, Hua Xu:
Extracting genetic alteration information for personalized cancer therapy from ClinicalTrials.gov. J. Am. Medical Informatics Assoc. 23(4): 750-757 (2016) - [j51]Safa Fathiamini, Amber M. Johnson, Jia Zeng, Alejandro Araya, Vijaykumar Holla, Ann M. Bailey, Beate Litzenburger, Nora S. Sanchez, Yekaterina Khotskaya, Hua Xu, Funda Meric-Bernstam, Elmer V. Bernstam, Trevor Cohen:
Automated identification of molecular effects of drugs (AIMED). J. Am. Medical Informatics Assoc. 23(4): 758-765 (2016) - [c81]Xiao Dong, Yaoyun Zhang, Hua Xu:
GWAS Finder: Search Engine for GWAS Datasets in Biomedical Literature. AMIA 2016 - [c80]Rui Duan, Ming Cao, Yonghui Wu, Jing Huang, Joshua C. Denny, Hua Xu, Yong Chen:
An Empirical Study for Impacts of Measurement Errors on EHR based Association Studies. AMIA 2016 - [c79]Jeffrey S. Grethe, Ibrahim Burak Özyurt, Hua Xu, Xiaoling Chen, Ruiling Liu, Ergin Soysal, Anupama E. Gururaj, Hyeon-Eui Kim, Trevor Cohen, Todd R. Johnson, Mandana Salimi, Saeid Pournejati, Min Jiang, Claudiu Farcas, Alejandra N. González-Beltrán, Philippe Rocca-Serra, Muhamamd F. Amith, Cui Tao, Ian Fore, Ronald Margolis, George Alter, Susanna-Assunta Sansone, Lucila Ohno-Machado:
A Scalable Dataset Indexing Infrastructure for the bioCADDIE Data Discovery System. AMIA 2016 - [c78]Yang Huang, Hua Xu, Joshua C. Denny:
Building Successful Natural Language Processing Applications in Clinical Research and Healthcare Operations. AMIA 2016 - [c77]Scott A. Malec, Peng Wei, Hua Xu, Elmer V. Bernstam, Sahiti Myneni, Trevor Cohen:
Literature-Based Discovery of Confounding in Observational Clinical Data. AMIA 2016 - [c76]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 - [c75]Sungrim Moon, Yukun Chen, Jingqi Wang, Joshua C. Denny, S. Trent Rosenbloom, Ky Nguyen, Tolulola Dawodu, Hua Xu:
Applying Active Learning to Clinical Abbreviation Disambiguation in Real Time. AMIA 2016 - [c74]Sungrim Moon, Trevor Cohen, Hua Xu:
Semantic Relatedness and Similarity between Biomedical Concepts. AMIA 2016 - [c73]Yue Wang, Kai Zheng, Hua Xu, Qiaozhu Mei:
Clinical Word Sense Disambiguation with Interactive Search and Classification. AMIA 2016 - [c72]Qiang Wei, Yukun Chen, Sungrim Moon, Trevor Cohen, Hua Xu:
A Study of Active Learning for Document Selection in Clinical Named Entity Recognition. AMIA 2016 - [c71]Yonghui Wu, Jun Xu, Yaoyun Zhang, Hua Xu:
What Can Neural Networks Learn from Unlabeled Clinical Narratives? AMIA 2016 - [c70]Hua Xu, Jeffrey S. Grethe, Xiaoling Chen, Ruiling Liu, Ergin Soysal, Anupama E. Gururaj, Yueling Li, Ibrahim Burak Özyurt, Hyeon-Eui Kim, Trevor Cohen, Todd R. Johnson, Mandana Salimi, Saeid Pournejati, Min Jiang, Claudiu Farcas, Alejandra N. González-Beltrán, Philippe Rocca-Serra, Muhamamd F. Amith, Cui Tao, Ian Fore, Ronald Margolis, George Alter, Susanna-Assunta Sansone, Lucila Ohno-Machado:
Development of DataMed, a Data Discovery Index Prototype by bioCADDIE: Laying the Groundwork for Biomedical Data Discovery. AMIA 2016 - [c69]Yaoyun Zhang, Min Jiang, Jingqi Wang, Hua Xu:
Semantic Role Labeling of Clinical Text: Comparing Syntactic Parsers and Features. AMIA 2016 - [c68]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 - [c67]W. Jim Zheng, Guocai Chen, Lam C. Tsoi, Tingting Qin, Chia-Hua Chang, Geoffrey Bartholomeusz, Hua Xu:
Developing Combination Cancer Therapy from Ontology Fingerprint Derived Gene Network. CRI 2016 - [c66]Hee-Jin Lee, Hua Xu, Jingqi Wang, Yaoyun Zhang, Sungrim Moon, Jun Xu, Yonghui Wu:
UTHealth at SemEval-2016 Task 12: an End-to-End System for Temporal Information Extraction from Clinical Notes. SemEval@NAACL-HLT 2016: 1292-1297 - 2015
- [j50]Guocai Chen, Jieyi Zhao, Trevor Cohen, Cui Tao, Jingchun Sun, Hua Xu, Elmer V. Bernstam, Andrew Lawson, Jia Zeng, Amber M. Johnson, Vijaykumar Holla, Ann M. Bailey, Humberto Lara-Guerra, Beate Litzenburger, Funda Meric-Bernstam, W. Jim Zheng:
Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature. Database J. Biol. Databases Curation 2015 (2015) - [j49]Cui Tao, Jingchun Sun, W. Jim Zheng, Junjie Chen, Hua Xu:
Colorectal cancer drug target prediction using ontology-based inference and network analysis. Database J. Biol. Databases Curation 2015 (2015) - [j48]Jingchun Sun, Kevin W. Zhu, W. Jim Zheng, Hua Xu:
A comparative study of disease genes and drug targets in the human protein interactome. BMC Bioinform. 16(S-5): S1 (2015) - [j47]Liang-Chin Huang, Ergin Soysal, W. Jim Zheng, Zhongming Zhao, Hua Xu, Jingchun Sun:
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. BMC Syst. Biol. 9(S-4): S2 (2015) - [j46]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) - [j45]Yaoyun Zhang, Buzhou Tang, Min Jiang, Jingqi Wang, Hua Xu:
Domain adaptation for semantic role labeling of clinical text. J. Am. Medical Informatics Assoc. 22(5): 967-979 (2015) - [j44]Yukun Chen, Thomas A. Lasko, Qiaozhu Mei, Joshua C. Denny, Hua Xu:
A study of active learning methods for named entity recognition in clinical text. J. Biomed. Informatics 58: 11-18 (2015) - [j43]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) - [j42]Amber Stubbs, Christopher Kotfila, Hua Xu, Özlem Uzuner:
Identifying risk factors for heart disease over time: Overview of 2014 i2b2/UTHealth shared task Track 2. J. Biomed. Informatics 58: S67-S77 (2015) - [j41]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) - [j40]Buzhou Tang, Yudong Feng, Xiaolong Wang, Yonghui Wu, Yaoyun Zhang, Min Jiang, Jingqi Wang, Hua Xu:
A comparison of conditional random fields and structured support vector machines for chemical entity recognition in biomedical literature. J. Cheminformatics 7(S-1): S8 (2015) - [j39]Min Jiang, Yang Huang, Jungwei Fan, Buzhou Tang, Joshua C. Denny, Hua Xu:
Parsing clinical text: how good are the state-of-the-art parsers? BMC Medical Informatics Decis. Mak. 15-S(S-1): S2 (2015) - [j38]Jingchun Sun, Min Zhao, Peilin Jia, Lily Wang, Yonghui Wu, Carissa Iverson, Yubo Zhou, Erica A. Bowton, Dan M. Roden, Joshua C. Denny, Melinda C. Aldrich, Hua Xu, Zhongming Zhao:
Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action. PLoS Comput. Biol. 11(6) (2015) - [c65]Jun Xu, Yaoyun Zhang, Yonghui Wu, Jingqi Wang, Xiao Dong, Hua Xu:
Citation Sentiment Analysis in Clinical Trial Papers. AMIA 2015 - [c64]Atul J. Butte, Nigam Shah, Nicholas P. Tatonetti, Hua Xu, Ping Zhang:
Recent Advances in Computational Drug Repositioning. AMIA 2015 - [c63]Yukun Chen, Sungrim Moon, Thomas A. Lasko, Qiaozhu Mei, Jingqi Wang, Trevor Cohen, Qingxia Chen, Joshua C. Denny, Hua Xu:
Real Time Active Learning Study for Clinical Named Entity Recognition. AMIA 2015 - [c62]Ergin Soysal, Jingqi Wang, Min Jiang, Yonghui Wu, Hua Xu:
Clinical Language Annotation, Modeling, and Processing Toolkit (CLAMP) - a user-centric NLP system. AMIA 2015 - [c61]Buzhou Tang, Qingcai Chen, Xiaolong Wang, Yonghui Wu, Yaoyun Zhang, Jingqi Wang, Hua Xu:
Recognizing Disjoint Clinical Concepts in Clinical Text Using Machine Learning-based Methods. AMIA 2015 - [c60]Yonghui Wu, Jun Xu, Min Jiang, Yaoyun Zhang, Hua Xu:
A Study of Neural Word Embeddings for Named Entity Recognition in Clinical Text. AMIA 2015 - [c59]Yonghui Wu, Jun Xu, Yaoyun Zhang, Hua Xu:
Clinical Abbreviation Disambiguation Using Neural Word Embeddings. BioNLP@IJCNLP 2015: 171-176 - [c58]Yonghui Wu, Min Jiang, Jianbo Lei, Hua Xu:
Named Entity Recognition in Chinese Clinical Text Using Deep Neural Network. MedInfo 2015: 624-628 - [c57]Jun Xu, Yaoyun Zhang, Jingqi Wang, Yonghui Wu, Min Jiang, Ergin Soysal, Hua Xu:
UTH-CCB: The Participation of the SemEval 2015 Challenge - Task 14. SemEval@NAACL-HLT 2015: 311-314 - 2014
- [j37]Son Doan, Ko-Wei Lin, Mike Conway, Lucila Ohno-Machado, Alexander Hsieh, Stephanie Feudjio Feupe, Asher Garland, Mindy K. Ross, Xiaoqian Jiang, Seena Farzaneh, Rebecca Walker, Neda Alipanah, Jing Zhang, Hua Xu, Hyeoneui Kim:
PhenDisco: phenotype discovery system for the database of genotypes and phenotypes. J. Am. Medical Informatics Assoc. 21(1): 31-36 (2014) - [j36]Mei Liu, Ruichu Cai, Yong Hu, Michael E. Matheny, Jingchun Sun, Jun Hu, Hua Xu:
Determining molecular predictors of adverse drug reactions with causality analysis based on structure learning. J. Am. Medical Informatics Assoc. 21(2): 245-251 (2014) - [j35]Jianbo Lei, Buzhou Tang, Xueqin Lu, Kaihua Gao, Min Jiang, Hua Xu:
Research and applications: A comprehensive study of named entity recognition in Chinese clinical text. J. Am. Medical Informatics Assoc. 21(5): 808-814 (2014) - [j34]Glenn T. Gobbel, Jennifer H. Garvin, Ruth M. Reeves, Robert M. Cronin, Julia Heavirland, Jenifer Williams, Allison Weaver, Shrimalini Jayaramaraja, Dario A. Giuse, Theodore Speroff, Steven H. Brown, Hua Xu, Michael E. Matheny:
Research and applications: Assisted annotation of medical free text using RapTAT. J. Am. Medical Informatics Assoc. 21(5): 833-841 (2014) - [j33]Ning Shang, Hua Xu, Thomas C. Rindflesch, Trevor Cohen:
Identifying plausible adverse drug reactions using knowledge extracted from the literature. J. Biomed. Informatics 52: 293-310 (2014) - [c56]Yukun Chen, Jesse O. Wrenn, Hua Xu, Anderson Spickard III, Ralf Habermann, James S. Powers, Joshua C. Denny:
Automated Assessment of Medical Students' Clinical Exposures according to AAMC Geriatric Competencies. AMIA 2014 - [c55]Yukun Chen, Yaoyun Zhang, Qiaozhu Mei, Dead Account, Joshua C. Denny, Hua Xu:
A Preliminary Study of Coupling Transfer Learning with Active Learning for Clinical Named Entity Recognition between Two Institutions. AMIA 2014 - [c54]Yang Huang, Jungwei Fan, Elly W. Yang, Hua Xu:
Building a Treebank of hospital discharge summaries. AMIA 2014 - [c53]Sungrim Moon, Yukun Chen, Jingqi Wang, Joshua C. Denny, Hua Xu:
Applying Active Learning to Word Sense Disambiguation in a Real-Time Setting. AMIA 2014 - [c52]Sungrim Moon, Trevor Cohen, Hua Xu:
A study of synonym extraction from clinical texts using semantic vector models. AMIA 2014 - [c51]Ning Shang, Hua Xu, Thomas C. Rindflesch, Trevor Cohen:
Identifying Plausible Adverse Drug Reactions Using Knowledge Extracted from the Literature. AMIA 2014 - [c50]Ergin Soysal, Jeremy L. Warner, Joshua C. Denny, Hua Xu:
Identifying Metastases from Pathology Reports in Lung Cancer Patients. AMIA 2014 - [c49]Jingchun Sun, Cui Tao, Kevin W. Zhu, W. Jim Zheng, Junjie Chen, Hua Xu:
An Integrative Framework for Drug Target Prediction and Repurposing. AMIA 2014 - [c48]Yonghui Wu, Adam Wright, Hua Xu, Allison B. McCoy, Dean F. Sittig:
Development of a Unified Computable Problem-Medication Knowledge base. AMIA 2014 - [c47]Hua Xu, Qingxia Chen, Jeremy L. Warner, Han Xue, Min Jiang, Anushi Shah, Melinda Aldrich, Qi Dai, Joshua C. Denny:
Mining electronic health record data to detect drug-repurposing signals for cancers. AMIA 2014 - [c46]Yaoyun Zhang, Buzhou Tang, Min Jiang, Jingqi Wang, Yonghui Wu, Hua Xu:
Domain Adaptation for Semantic Role Labeling of Clinical Text. AMIA 2014 - [c45]Min Jiang, Yang Huang, Jungwei Fan, Buzhou Tang, Joshua C. Denny, Hua Xu:
Parsing Clinical Text: How Good are the State-of-the-Art Parsers? DTMBIO@CIKM 2014: 1 - [c44]Luonan Chen, Doheon Lee, Hua Xu, Min Song:
DTMBIO 2014: International Workshop on Data and Text Mining in Biomedical Informatics. CIKM 2014: 2090-2091 - [c43]Sina Madani, Reza Alemy, Dean F. Sittig, Hua Xu:
Quality of Care Metric Reporting from Clinical Narratives: Assessing Ontology Components. ICBO 2014: 47-51 - [c42]Guocai Chen, Jieyi Zhao, Trevor Cohen, Cui Tao, Jingchun Sun, Hua Xu, Elmer V. Bernstam, Jia Zeng, Amber M. Johnson, Vijaykumar Holla, Ann Balley, Funda Meric-Bernstam, W. Jim Zheng:
Using Ontology Fingerprints to Disambiguate Gene Name Entities in the Biomedical Literature. ICBO 2014: 66 - [c41]Cui Tao, Jingchun Sun, W. Jim Zheng, Junjie Chen, Hua Xu:
Drug Target Prediction for Colorectal Cancer by Combining Ontology and Network Approaches. ICBO 2014: 67 - [c40]Yaoyun Zhang, Jingqi Wang, Cui Tao, Hua Xu:
Ontology-based Normalization for Disease-Lab test Relation Extraction. ICBO 2014: 87-89 - [c39]Yaoyun Zhang, Jingqi Wang, Buzhou Tang, Yonghui Wu, Min Jiang, Yukun Chen, Hua Xu:
UTH_CCB: A report for SemEval 2014 - Task 7 Analysis of Clinical Text. SemEval@COLING 2014: 802-806 - [e3]Doheon Lee, Luonan Chen, Min Song, Hua Xu:
Proceedings of the ACM 8th International Workshop on Data and Text Mining in Bioinformatics, DTMBIO@CIKM 2014, Shanghai, China, November 7, 2014. ACM 2014, ISBN 978-1-4503-1275-2 [contents] - 2013
- [j32]Mei Liu, Eugenia Renne McPeek Hinz, Michael Edwin Matheny, Joshua C. Denny, Jonathan Scott Schildcrout, Randolph A. Miller, Hua Xu:
Comparative analysis of pharmacovigilance methods in the detection of adverse drug reactions using electronic medical records. J. Am. Medical Informatics Assoc. 20(3): 420-426 (2013) - [j31]Laura K. Wiley, Anushi Shah, Hua Xu, William S. Bush:
Research and applications: ICD-9 tobacco use codes are effective identifiers of smoking status. J. Am. Medical Informatics Assoc. 20(4): 652-658 (2013) - [j30]Subramani Mani, Yukun Chen, Xia Li, Lori R. Arlinghaus, A. Bapsi Chakravarthy, Vandana G. Abramson, Sandeep R. Bhave, Mia A. Levy, Hua Xu, Thomas E. Yankeelov:
Research and applications: Machine learning for predicting the response of breast cancer to neoadjuvant chemotherapy. J. Am. Medical Informatics Assoc. 20(4): 688-695 (2013) - [j29]Buzhou Tang, Yonghui Wu, Min Jiang, Yukun Chen, Joshua C. Denny, Hua Xu:
A hybrid system for temporal information extraction from clinical text. J. Am. Medical Informatics Assoc. 20(5): 828-835 (2013) - [j28]Wei-Qi Wei, Robert M. Cronin, Hua Xu, Thomas A. Lasko, Lisa Bastarache, Joshua C. Denny:
Development and evaluation of an ensemble resource linking medications to their indications. J. Am. Medical Informatics Assoc. 20(5): 954-961 (2013) - [j27]Yukun Chen, Hongxin Cao, Qiaozhu Mei, Kai Zheng, Hua Xu:
Applying active learning to supervised word sense disambiguation in MEDLINE. J. Am. Medical Informatics Assoc. 20(5): 1001-1006 (2013) - [j26]Jungwei Fan, Elly W. Yang, Min Jiang, Rashmi Prasad, Richard M. Loomis, Daniel Zisook, Joshua C. Denny, Hua Xu, Yang Huang:
Research and applications: Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences. J. Am. Medical Informatics Assoc. 20(6): 1168-1177 (2013) - [j25]Buzhou Tang, Hongxin Cao, Yonghui Wu, Min Jiang, Hua Xu:
Recognizing clinical entities in hospital discharge summaries using Structural Support Vector Machines with word representation features. BMC Medical Informatics Decis. Mak. 13(S-1): S1 (2013) - [c38]Elmer V. Bernstam, Ken Chen, Hua Xu, Funda Meric-Bernstam:
Informatics Infrastructure for Routine Personalized Medicine. AMIA 2013 - [c37]Yukun Chen, Thomas A. Lasko, Qiaozhu Mei, Joshua C. Denny, Hua Xu:
A Study of Active Learning Methods for Clinical Entities Recognition. AMIA 2013 - [c36]Sina Madani, Dean F. Sittig, Hua Xu, Parsa Mirhaji, Kim Dunn, Reza Alemy:
Ontology-Based Entity Extraction of Quality Metrics from Narrative Texts. AMIA 2013 - [c35]Sungrim Moon, Bjoern-Toby Berster, Hua Xu, Trevor Cohen:
Word Sense Disambiguation of Clinical Abbreviations with Hyperdimensional Computing. AMIA 2013 - [c34]Yonghui Wu, S. Trent Rosenbloom, Joshua C. Denny, Randolph A. Miller, Dario A. Giuse, Hua Xu:
Building a Large Clinical Abbreviation Sense Inventory from Discharge Summaries. AMIA 2013 - [c33]Yaoyun Zhang, Hua Xu:
Understanding Consumers' Information Needs about Breast Cancer by Analyzing Online Questions. AMIA 2013 - [c32]Huiru Zheng, Haiying Wang, Hua Xu, Zhongming Zhao, Francisco Azuaje:
Correlating adverse drug reactions with biological pathways in humans. BIBM 2013: 197-200 - [c31]Si Sun, Xiaomu Zhou, Joshua C. Denny, S. Trent Rosenbloom, Hua Xu:
Messaging to your doctors: understanding patient-provider communications via a portal system. CHI 2013: 1739-1748 - [c30]Yonghui Wu, Joshua C. Denny, S. Trent Rosenbloom, Randolph A. Miller, Dario A. Giuse, Min Song, Hua Xu:
A prototype application for real-time recognition and disambiguation of clinical abbreviations. DTMBIO 2013: 7-8 - [c29]Atul J. Butte, Doheon Lee, Hua Xu, Min Song:
DTMBIO 2013: international workshop on data and text mining in biomedical informatics. CIKM 2013: 2555-2556 - [c28]Buzhou Tang, Yonghui Wu, Min Jiang, Joshua C. Denny, Hua Xu:
Recognizing and Encoding Discorder Concepts in Clinical Text using Machine Learning and Vector Space Model. CLEF (Working Notes) 2013 - [c27]Yonghui Wu, Buzhou Tang, Min Jiang, Sungrim Moon, Joshua C. Denny, Hua Xu:
Clinical Acronym/Abbreviation Normalization using a Hybrid Approach. CLEF (Working Notes) 2013 - [c26]Yaoyun Zhang, Trevor Cohen, Min Jiang, Buzhou Tang, Hua Xu:
Evaluation of Vector Space Models for Medical Disorders Information Retrieval. CLEF (Working Notes) 2013 - [c25]Yonghui Wu, Jianbo Lei, Wei-Qi Wei, Buzhou Tang, Joshua C. Denny, S. Trent Rosenbloom, Randolph A. Miller, Dario A. Giuse, Kai Zheng, Hua Xu:
Analyzing Differences between Chinese and English Clinical Text: A Cross-Institution Comparison of Discharge Summaries in Two Languages. MedInfo 2013: 662-666 - [e2]Atul J. Butte, Doheon Kim, Min Song, Hua Xu:
Proceeding of the 7rd International Workshop on Data and Text Mining in Bioinformatics, DTMBIO 2013, San Francisco, CA, USA, November 1, 2013. ACM 2013, ISBN 978-1-4503-2419-9 [contents] - 2012
- [j24]Jingchun Sun, Yonghui Wu, Hua Xu, Zhongming Zhao:
DTome: a web-based tool for drug-target interactome construction. BMC Bioinform. 13(S-9): S7 (2012) - [j23]Yufei Huang, Zhongming Zhao, Hua Xu, Yu Shyr, Bing Zhang:
Advances in systems biology: computational algorithms and applications. BMC Syst. Biol. 6(S-3): S1 (2012) - [j22]Bing Han, Xue-wen Chen, Zohreh Talebizadeh, Hua Xu:
Genetic studies of complex human diseases: Characterizing SNP-disease associations using Bayesian networks. BMC Syst. Biol. 6(S-3): S14 (2012) - [j21]Yanxin Lu, Hua Xu, Neeraja B. Peterson, Qi Dai, Min Jiang, Joshua C. Denny, Mei Liu:
Extracting epidemiologic exposure and outcome terms from literature using machine learning approaches. Int. J. Data Min. Bioinform. 6(4): 447-459 (2012) - [j20]Robert J. Carroll, William K. Thompson, Anne E. Eyler, Arthur M. Mandelin, Tianxi Cai, Raquel M. Zink, Jennifer A. Pacheco, Chad S. Boomershine, Thomas A. Lasko, Hua Xu, Elizabeth W. Karlson, Raúl G. Pérez, Vivian S. Gainer, Shawn N. Murphy, Eric M. Ruderman, Richard M. Pope, Robert M. Plenge, Abel N. Kho, Katherine P. Liao, Joshua C. Denny:
Portability of an algorithm to identify rheumatoid arthritis in electronic health records. J. Am. Medical Informatics Assoc. 19(e1) (2012) - [j19]Mei Liu, Yonghui Wu, Yukun Chen, Jingchun Sun, Zhongming Zhao, Xue-wen Chen, Michael E. Matheny, Hua Xu:
Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs. J. Am. Medical Informatics Assoc. 19(e1) (2012) - [j18]Yukun Chen, Subramani Mani, Hua Xu:
Applying active learning to assertion classification of concepts in clinical text. J. Biomed. Informatics 45(2): 265-272 (2012) - [j17]Hua Xu, Yonghui Wu, Noemie Elhadad, Peter D. Stetson, Carol Friedman:
A new clustering method for detecting rare senses of abbreviations in clinical notes. J. Biomed. Informatics 45(6): 1075-1083 (2012) - [j16]Son Doan, Nigel Collier, Hua Xu, Pham Duy, Tu Minh Phuong:
Recognition of medication information from discharge summaries using ensembles of classifiers. BMC Medical Informatics Decis. Mak. 12: 36 (2012) - [j15]Mei Liu, Michael E. Matheny, Yong Hu, Hua Xu:
Data mining methodologies for pharmacovigilance. SIGKDD Explor. 14(1): 35-42 (2012) - [c24]Min Jiang, Joshua C. Denny, Buzhou Tang, Hongxin Cao, Hua Xu:
Extracting Semantic Lexicons from Discharge Summaries using Machine Learning and the C-Value Method. AMIA 2012 - [c23]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 - [c22]Anushi Shah, Min Jiang, Yonghui Wu, Joshua C. Denny, Hua Xu:
MedEx-UIMA - An Open-Source System for Medication Information Extraction from Clinical Text. AMIA 2012 - [c21]Si Sun, Xiaomu Zhou, Hua Xu, Joshua C. Denny:
Understanding Patient-Provider Communication via a Patient Portal. AMIA 2012 - [c20]Buzhou Tang, Yonghui Wu, Min Jiang, Hua Xu:
Clinical Entity Recognition Using Structural Support Vector Machines. AMIA 2012 - [c19]Yonghui Wu, Joshua C. Denny, Samuel Rosenbloom, Randolph A. Miller, Dario A. Giuse, Hua Xu:
A comparative study of current clinical natural language processing systems on handling abbreviations in discharge summaries. AMIA 2012 - [c18]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 - [c17]Hua Xu, Peter D. Stetson, Carol Friedman:
Combining Corpus-derived Sense Profiles with Estimated Frequency Information to Disambiguate Clinical Abbreviations. AMIA 2012 - [c16]Si Sun, Xiaomu Zhou, Joshua C. Denny, S. Trent Rosenbloom, Hua Xu:
Understanding patient-provider communication entered via a patient portal system. ASIST 2012: 1-4 - [c15]Si Sun, Xiaomu Zhou, Joshua C. Denny, S. Trent Rosenbloom, Hua Xu:
Understanding patient-provider communication entered via a patient portal system. ASIST 2012: 1-4 - [c14]Buzhou Tang, Hongxin Cao, Yonghui Wu, Min Jiang, Hua Xu:
Clinical entity recognition using structural support vector machines with rich features. DTMBIO@CIKM 2012: 13-20 - [c13]Min Song, Doheon Lee, Hua Xu, Sophia Ananiadou:
DTMBIO 2012: international workshop on data and text mining in biomedical informatics. CIKM 2012: 2766-2767 - [c12]Mei Liu, Michael E. Matheny, Yonghui Wu, Eugenia R. McPeek Hinz, Joshua C. Denny, Jonathan S. Schildcrout, Randolph A. Miller, Hua Xu:
Detecting Adverse Drug Reactions Using Inpatient Medication Orders and Laboratory Tests Data. HISB 2012: 131 - [c11]Yonghui Wu, Mei Liu, W. Jim Zheng, Zhongming Zhao, Hua Xu:
Ranking Gene-Drug Relationships in Biomedical Literature Using Latent Dirichlet Allocation. Pacific Symposium on Biocomputing 2012: 422-433 - [e1]Doheon Kim, Sophia Ananiadou, Min Song, Hua Xu:
Proceedings of the ACM sixth international workshop on Data and text mining in biomedical informatics, DTMBIO@CIKM 2012, Maui, Hawaii, USA, October 29, 2012. ACM 2012, ISBN 978-1-4503-1716-0 [contents] - 2011
- [j14]S. Trent Rosenbloom, Joshua C. Denny, Hua Xu, Nancy M. Lorenzi, William W. Stead, Kevin B. Johnson:
Data from clinical notes: a perspective on the tension between structure and flexible documentation. J. Am. Medical Informatics Assoc. 18(2): 181-186 (2011) - [j13]Hua Xu, Min Jiang, Matthew Oetjens, Erica A. Bowton, Andrea H. Ramirez, Janina M. Jeff, Melissa A. Basford, Jill M. Pulley, James D. Cowan, Xiaoming Wang, Marylyn D. Ritchie, Daniel R. Masys, Dan M. Roden, Dana C. Crawford, Joshua C. Denny:
Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin. J. Am. Medical Informatics Assoc. 18(4): 387-391 (2011) - [j12]Min Jiang, Yukun Chen, Mei Liu, S. Trent Rosenbloom, Subramani Mani, Joshua C. Denny, Hua Xu:
A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. J. Am. Medical Informatics Assoc. 18(5): 601-606 (2011) - [j11]Hua Xu, Samir AbdelRahman, Yanxin Lu, Joshua C. Denny, Son Doan:
Applying semantic-based probabilistic context-free grammar to medical language processing - A preliminary study on parsing medication sentences. J. Biomed. Informatics 44(6): 1068-1075 (2011) - [c10]Hua Xu, Samir AbdelRahman, Min Jiang, Jungwei Fan, Yang Huang:
An initial study of full parsing of clinical text using the Stanford Parser. BIBM Workshops 2011: 607-614 - 2010
- [j10]Mei Liu, Joshua C. Denny, Subramani Mani, Yukun Chen, Yong Hu, Hua Xu:
Identifying potential drugs that induce QT prolongation using electronic medical records. BMC Bioinform. 11(S-4): P2 (2010) - [j9]Hua Xu, Shane P. Stenner, Son Doan, Kevin B. Johnson, Lemuel R. Waitman, Joshua C. Denny:
Application of information technology: MedEx: a medication information extraction system for clinical narratives. J. Am. Medical Informatics Assoc. 17(1): 19-24 (2010) - [j8]Joshua C. Denny, Josh F. Peterson, Neesha N. Choma, Hua Xu, Randolph A. Miller, Lisa Bastarache, Neeraja B. Peterson:
Extracting timing and status descriptors for colonoscopy testing from electronic medical records. J. Am. Medical Informatics Assoc. 17(4): 383-388 (2010) - [j7]Son Doan, Lisa Bastarache, Sergio Klimkowski, Joshua C. Denny, Hua Xu:
Integrating existing natural language processing tools for medication extraction from discharge summaries. J. Am. Medical Informatics Assoc. 17(5): 528-531 (2010) - [c9]Son Doan, Hua Xu:
Recognizing Medication related Entities in Hospital Discharge Summaries using Support Vector Machine. COLING (Posters) 2010: 259-266
2000 – 2009
- 2009
- [j6]Hua Xu, Peter D. Stetson, Carol Friedman:
Research Paper: Methods for Building Sense Inventories of Abbreviations in Clinical Notes. J. Am. Medical Informatics Assoc. 16(1): 103-108 (2009) - [c8]Joshua C. Denny, Josh F. Peterson, Neesha N. Choma, Hua Xu, Randolph A. Miller, Lisa Bastarache, Neeraja B. Peterson:
Development of a Natural Language Processing System to Identify Timing and Status of Colonoscopy Testing in Electronic Medical Records. AMIA 2009 - 2008
- [j5]Elizabeth S. Chen, George Hripcsak, Hua Xu, Marianthi Markatou, Carol Friedman:
Research Paper: Automated Acquisition of Disease-Drug Knowledge from Biomedical and Clinical Documents: An Initial Study. J. Am. Medical Informatics Assoc. 15(1): 87-98 (2008) - [c7]Hua Xu, Peter D. Stetson, Carol Friedman:
Methods for Building Sense Inventories of Abbreviations in Clinical Notes. AMIA 2008 - 2007
- [j4]Hua Xu, Jungwei Fan, George Hripcsak, Eneida A. Mendonça, Marianthi Markatou, Carol Friedman:
Gene symbol disambiguation using knowledge-based profiles. Bioinform. 23(8): 1015-1022 (2007) - [j3]Jungwei Fan, Hua Xu, Carol Friedman:
Using contextual and lexical features to restructure and validate the classification of biomedical concepts. BMC Bioinform. 8 (2007) - [j2]P. Karina Tulipano, Ying Tao, William S. Millar, Pat Zanzonico, Katherine Kolbert, Hua Xu, Hong Yu, Lifeng Chen, Yves A. Lussier, Carol Friedman:
Natural language processing and visualization in the molecular imaging domain. J. Biomed. Informatics 40(3): 270-281 (2007) - [c6]Hua Xu, Peter D. Stetson, Carol Friedman:
A Study of Abbreviations in Clinical Notes. AMIA 2007 - [c5]Hua Xu, Jungwei Fan, Carol Friedman:
Combining multiple evidence for gene symbol disambiguation. BioNLP@ACL 2007: 41-48 - [c4]Jungwei Fan, Hua Xu, Carol Friedman:
Using Distributional Analysis to Semantically Classify UMLS Concepts. MedInfo 2007: 519-523 - 2006
- [j1]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) - [c3]Hua Xu, Debra M. Krupke, Judith A. Blake, Carol Friedman:
A Natural Language Processing (NLP) Tool to Assist in the Curation Of the Laboratory Mouse Tumor Biology Database. AMIA 2006 - 2004
- [c2]Hua Xu, Kristin Anderson, Victor R. Grann, Carol Friedman:
Facilitating Cancer Research using Natural Language Processing of Pathology Reports. MedInfo 2004: 565-569 - 2003
- [c1]Hua Xu, Carol Friedman:
Facilitating Research in Pathology using Natural Language Processing. AMIA 2003
Coauthor Index
Joshua C. Denny
aka: Joshua Charles Denny
aka: Joshua Charles Denny
[j115] [j91] [c118] [j62] [j60] [c87] [c86] [c80] [c78] [c75] [j46] [j44] [j39] [j38] [c63] [c56] [c55] [c53] [c50] [c47] [c45] [j32] [j29] [j28] [j26] [c37] [c34] [c31] [c30] [c28] [c27] [c25] [j21] [j20] [c24] [c23] [c22] [c21] [c19] [c18] [c16] [c15] [c12] [j14] [j13] [j12] [j11] [j10] [j9] [j8] [j7] [c8]
Michael E. Matheny
aka: Michael Edwin Matheny
aka: Michael Edwin Matheny
Serguei V. S. Pakhomov
aka: Serguei Pakhomov
aka: Serguei Pakhomov
Kirk Roberts
aka: Kirk E. Roberts
aka: Kirk E. Roberts
S. Trent Rosenbloom
aka: Samuel Rosenbloom
aka: Samuel Rosenbloom
[j141] [j139] [j137] [j136] [j131] [j130] [i34] [i28] [i19] [j125] [c148] [c147] [c135] [i9] [j111] [j106] [j105] [j104] [j103] [j99] [j97] [j94] [c124] [j87] [c121] [c120] [c118] [c116] [j75] [j71] [j70] [c115] [c107] [c106] [j61] [j58] [c90] [c89] [c85] [c82] [j55] [j54] [c79] [c70] [j50] [j49] [c49] [c42] [c41] [c40]
[j146] [i35] [j127] [c125] [j87] [j82] [c119] [j81] [j79] [j77] [j74] [c111] [j62] [c95] [c94] [c93] [c92] [c91] [c87] [c83] [j57] [j56] [j52] [c80] [c71] [c66] [j40] [j38] [c65] [c62] [c61] [c60] [c59] [c58] [c57] [c48] [c46] [c39] [j29] [j25] [c34] [c30] [c28] [c27] [c25] [j24] [j19] [j17] [c22] [c20] [c19] [c14] [c12] [c11]
[j113] [j112] [j106] [j105] [j104] [j103] [c128] [c126] [j93] [j90] [j88] [j87] [j85] [j84] [j82] [c122] [c119] [j81] [j75] [j71] [j70] [c113] [c110] [c109] [c108] [c107] [c106] [c105] [j61] [c101] [c98] [c93] [c92] [c91] [c90] [c89] [c85] [c84] [c83] [c82] [j57] [j56] [j55] [j54] [j53] [j52] [c81] [c71] [c69] [c66] [j45] [j40] [c65] [c61] [c60] [c59] [c57] [c55] [c46] [c40] [c39] [c33] [c26]
W. Jim Zheng
aka: Wenjin Jim Zheng
aka: Wenjin Jim Zheng
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