@article {1496760, title = {Advancing the state of the art in automatic extraction of adverse drug events from narratives}, journal = {Journal of the American Medical Informatics Association}, volume = {27}, number = {1}, year = {2020}, url = {https://doi.org/10.1093/jamia/ocz206}, author = {{\"O}zlem Uzuner and Amber Stubbs and Leslie Lenert} } @article {1490164, title = {2018 n2c2 shared task on adverse drug events and medication extraction in electronic health records}, journal = {Journal of the American Medical Informatics Association}, volume = {27}, number = {1}, year = {2020}, pages = {3-12}, url = {https://doi.org/10.1093/jamia/ocz166}, author = {Sam Henry and Buchan, Kevin and Michele Filannino and Amber Stubbs and {\"O}zlem Uzuner} } @article {1490182, title = {A study of deep learning approaches for medication and adverse drug event extraction from clinical text}, journal = {Journal of the American Medical Informatics Association}, volume = {27}, number = {1}, year = {2020}, pages = {13-21}, url = {https://doi.org/10.1093/jamia/ocz063}, author = {Qiang Wei and Zongcheng Ji and Zhiheng Li and Jingcheng Du and Jingqi Wang and Xu, Jun and Xiang, Yang and Firat Tiryaki and Wu, Stephen and Yaoyun Zhang and Cui Tao and Xu, Hua} } @article {1490185, title = {An ensemble of neural models for nested adverse drug events and medication extraction with subwords}, journal = {Journal of the American Medical Informatics Association}, volume = {27}, number = {1}, year = {2020}, pages = {22-30}, url = {https://doi.org/10.1093/jamia/ocz075}, author = {Meizhi Ju and Nhung T H Nguyen and Makoto Miwa and Sophia Ananiadou} } @article {1490184, title = {Ensemble method{\textendash}based extraction of medication and related information from clinical texts}, journal = {Journal of the American Medical Informatics Association}, volume = {27}, number = {1}, year = {2020}, pages = {31-38}, url = {https://doi.org/10.1093/jamia/ocz100}, author = {Youngjun Kim and St{\'e}phane M Meystre} } @article {1490186, title = {Adverse drug events and medication relation extraction in electronic health records with ensemble deep learning methods}, journal = {Journal of the American Medical Informatics Association}, volume = {27}, number = {1}, year = {2020}, pages = {39-46}, url = {https://doi.org/10.1093/jamia/ocz101}, author = {Fenia Christopoulou and Thy Thy Tran and Sunil Kumar Sahu and Makoto Miwa and Sophia Ananiadou} } @article {1496766, title = {Adverse drug event and medication extraction in electronic health records via a cascading architecture with different sequence labeling models and word embeddings}, journal = {Journal of the American Medical Informatics Association}, volume = {27}, number = {1}, year = {2020}, pages = {47-55}, url = {https://doi.org/10.1093/jamia/ocz120}, author = {Hong-Jie Dai and Chu-Hsien Su and Chi-Shin Wu} } @article {1496768, title = {Extracting medications and associated adverse drug events using a natural language processing system combining knowledge base and deep learning}, journal = {Journal of the American Medical Informatics Association}, volume = {27}, number = {1}, year = {2020}, pages = {56-64}, url = {https://doi.org/10.1093/jamia/ocz141}, author = {Chen, Long and Yu Gu and Xin Ji and Zhiyong Sun and Haodan Li and Gao, Yuan and Yang Huang} } @article {1490183, title = {Identifying relations of medications with adverse drug events using recurrent convolutional neural networks and gradient boosting}, journal = {Journal of the American Medical Informatics Association}, volume = {27}, number = {1}, year = {2020}, pages = {65-72}, url = {https://doi.org/10.1093/jamia/ocz144}, author = {Xi Yang and Jiang Bian and Ruogu Fang and Ragnhildur I Bjarnadottir and William R Hogan and Yonghui Wu} } @article {1490180, title = {Multiple features for clinical relation extraction: A machine learning approach}, journal = {Journal of Biomedical Informatics}, volume = {103}, year = {2020}, url = {https://doi.org/10.1016/j.jbi.2020.103382}, author = {Ilseyar Alimova and Elena Tutubalina} } @article {1499379, title = {Classifying relations in clinical narratives using segment graph convolutional and recurrent neural networks (Seg-GCRNs)}, journal = {Journal of the American Medical Informatics Association}, volume = {26}, number = {3}, year = {2019}, pages = {262-268}, url = {https://doi.org/10.1093/jamia/ocy157}, author = {Yifu Li and Ran Jin and Yuan Luo} } @article {1499318, title = {An investigation of single-domain and multidomain medication and adverse drug event relation extraction from electronic health record notes using advanced deep learning models }, journal = {Journal of the American Medical Informatics Association}, volume = {26}, number = {7}, year = {2019}, pages = {646-654}, url = {https://doi.org/10.1093/jamia/ocz018}, author = {Fei Li and Hong Yu} } @article {1499313, title = {Enhancing clinical concept extraction with contextual embeddings }, journal = {Journal of the American Medical Informatics Association}, volume = {26}, number = {11}, year = {2019}, pages = {1297-1304}, url = {https://doi.org/10.1093/jamia/ocz096}, author = {Yuqi Si and Jingqi Wang and Xu, Hua and Kirk Roberts} } @article {1496751, title = {New approaches to cohort selection}, journal = {Journal of the American Medical Informatics Association}, volume = {26}, number = {11}, year = {2019}, pages = {1161-1162}, url = {https://doi.org/10.1093/jamia/ocz174}, author = {Amber Stubbs and {\"O}zlem Uzuner} } @article {1490163, title = {Cohort selection for clinical trials: n2c2 2018 shared task track 1}, journal = {Journal of the American Medical Informatics Association}, volume = {26}, number = {11}, year = {2019}, pages = {1163{\textendash}1171}, url = {https://doi.org/10.1093/jamia/ocz163}, author = {Amber Stubbs and Michele Filannino and Ergin Soysal and Samuel Henry and {\"O}zlem Uzuner} } @article {1490174, title = {Hybrid bag of approaches to characterize selection criteria for cohort identification}, journal = {Journal of the American Medical Informatics Association}, volume = {26}, number = {11}, year = {2019}, pages = {1172-1180}, url = {https://doi.org/10.1093/jamia/ocz079}, author = {V.G. Vinod Vydiswaran and Asher Strayhorn and Xinyan Zhao and Phil Robinson and Mahesh Agarwal and Erin Bagazinski and Madia Essiet and Bradley E Iott and Hyeon Joo and PingJui Ko and Dahee Lee and Jin Xiu Lu and Jinghui Liu and Adharsh Murali and Koki Sasagawa and Tianshi Wang and Nalingna Yuan} } @article {1490181, title = {Cohort selection for clinical trials using deep learning models}, journal = {Journal of the American Medical Informatics Association}, volume = {26}, number = {11}, year = {2019}, pages = {1181{\textendash}1188}, url = {https://doi.org/10.1093/jamia/ocz139}, author = {Isabel Segura-Bedmar and Pablo Raez} } @article {1490177, title = {Cohort selection for clinical trials using hierarchical neural network}, journal = {Journal of the American Medical Informatics Association}, volume = {26}, number = {11}, year = {2019}, pages = {1203-1208}, url = {https://doi.org/10.1093/jamia/ocz099}, author = {Ying Xiong and Xue Shi and Shuai Chen and Dehuan Jiang and Buzhou Tang and Xiaolong Wang and Qingcai Chen and Jun Yan} } @article {1490173, title = {Clinical trial cohort selection based on multi-level rule-based natural language processing system}, journal = {Journal of the American Medical Informatics Association}, volume = {26}, number = {11}, year = {2019}, pages = {1218{\textendash}1226}, url = {https://doi.org/10.1093/jamia/ocz109}, author = {Chen, Long and Yu Gu and Xin Ji and Chao Lou and Zhiyong Sun and Haodan Li and Gao, Yuan and Yang Huang} } @article {1490175, title = {Medical knowledge infused convolutional neural networks for cohort selection in clinical trials}, journal = {Journal of the American Medical Informatics Association}, volume = {26}, number = {11}, year = {2019}, pages = {1227-1236}, url = {https://doi.org/10.1093/jamia/ocz128}, author = {Chen, Chi-Jen and Neha Warikoo and Yung-Chun Chang and Jin-Hua Chen and Wen-Lian Hsu} } @article {1490159, title = {Evaluating shallow and deep learning strategies for the 2018 n2c2 shared task on clinical text classification}, journal = {Journal of the American Medical Informatics Association}, volume = {26}, number = {11}, year = {2019}, pages = {1247-1254}, url = {https://doi.org/10.1093/jamia/ocz149}, author = {Michel Oleynik and Amila Kugic and Zdenko Kas{\'a}{\v c} and Markus Kreuzthaler} } @article {1499395, title = {CLAMP {\textendash} a toolkit for efficiently building customized clinical natural language processing pipelines}, journal = {Journal of the American Medical Informatics Association}, volume = {25}, number = {3}, year = {2018}, pages = {331-336}, url = {https://doi.org/10.1093/jamia/ocx132}, author = {Ergin Soysal and Jingqi Wang and Min Jiang and Yonghui Wu and Serguei Pakhomov and Hongfang Liu and Xu, Hua} } @article {1499316, title = {Segment convolutional neural networks (Seg-CNNs) for classifying relations in clinical notes}, journal = {Journal of the American Medical Informatics Association}, volume = {25}, number = {1}, year = {2018}, pages = {93-98}, url = {https://doi.org/10.1093/jamia/ocx090}, author = {Yuan Luo and Yu Cheng and {\"O}zlem Uzuner and Szolovits, Peter and Justin Starren} } @article {1490122, title = {A natural language processing challenge for clinical records: Research Domains Criteria (RDoC) for psychiatry}, journal = {Journal of Biomedical Informatics}, volume = {75}, number = {Supplement}, year = {2017}, pages = {S1-S3}, url = {https://doi.org/10.1016/j.jbi.2017.10.005}, author = {{\"O}zlem Uzuner and Amber Stubbs and Michele Filannino} } @article {1489905, title = {De-identification of psychiatric intake records: Overview of 2016 CEGS N-GRID shared tasks Track 1}, journal = {Journal of Biomedical Informatics}, volume = {75}, number = {Supplement}, year = {2017}, pages = {S4-S18}, url = {https://doi.org/10.1016/j.jbi.2017.06.011}, author = {Amber Stubbs and Michele Filannino and {\"O}zlem Uzuner} } @article {1490117, title = {A hybrid approach to automatic de-identification of psychiatric notes}, journal = {Journal of Biomedical Informatics}, volume = {75}, number = {Supplement}, year = {2017}, pages = {S19-S27}, url = {https://doi.org/10.1016/j.jbi.2017.06.006}, author = {Hee-Jin Lee and Yonghui Wu and Yaoyun Zhang and Xu, Jun and Xu, Hua and Kirk Roberts} } @article {1490118, title = {Learning to identify Protected Health Information by integrating knowledge- and data-driven algorithms: A case study on psychiatric evaluation notes}, journal = {Journal of Biomedical Informatics}, volume = {75}, number = {Supplement}, year = {2017}, pages = {S28-S33}, url = {https://doi.org/10.1016/j.jbi.2017.06.005}, author = {Azad Dehghan and Aleksandar Kovacevic and George Karystianis and John A Keane and Goran Nenadic} } @article {1490111, title = {De-identification of clinical notes via recurrent neural network and conditional random field}, journal = {Journal of Biomedical Informatics}, volume = {75}, number = {Supplement}, year = {2017}, pages = {S34-S42}, url = {https://doi.org/10.1016/j.jbi.2017.05.023}, author = {Zengjian Liu and Buzhou Tang and Xiaolong Wang and Qingcai Chen} } @article {1490114, title = {De-identification of medical records using conditional random fields and long short-term memory networks}, journal = {Journal of Biomedical Informatics}, volume = {75}, number = {Supplement}, year = {2017}, pages = {S43-S53}, url = {https://doi.org/10.1016/j.jbi.2017.10.003}, author = {Jiang, Zhipeng and Zhao, Chao and He, Bin and Guan, Yi and Jiang, Jingchi} } @article {1490132, title = {The UAB Informatics Institute and 2016 CEGS N-GRID de-identification shared task challenge}, journal = {Journal of Biomedical Informatics}, volume = {75}, number = {Supplement}, year = {2017}, pages = {S54-S61}, url = { https://doi.org/10.1016/j.jbi.2017.05.001}, author = {Bui, Duy Duc An and Wyatt, Mathew and Cimino, James J} } @article {1490131, title = {Symptom severity prediction from neuropsychiatric clinical records: Overview of 2016 CEGS N-GRID shared tasks Track 2}, journal = {Journal of Biomedical Informatics}, volume = {75}, number = {Supplement}, year = {2017}, pages = {S62-S70}, url = {https://doi.org/10.1016/j.jbi.2017.04.017}, author = {Michele Filannino and Amber Stubbs and {\"O}zlem Uzuner} } @article {1490109, title = {Automatic recognition of symptom severity from psychiatric evaluation records}, journal = {Journal of Biomedical Informatics}, volume = {75}, number = {Supplement}, year = {2017}, pages = {S71-S84}, url = {https://doi.org/10.1016/j.jbi.2017.05.020}, author = {Goodwin, Travis R and Ramon Maldonado and Harabagiu, Sanda M} } @article {1490123, title = {Ordinal convolutional neural networks for predicting RDoC positive valence psychiatric symptom severity scores}, journal = {Journal of Biomedical Informatics}, volume = {75}, number = {Supplement}, year = {2017}, pages = {S85-S93}, url = {https://doi.org/10.1016/j.jbi.2017.05.008}, author = {Rios, Anthony and Kavuluru, Ramakanth} } @article {1490126, title = {Predictive modeling for classification of positive valence system symptom severity from initial psychiatric evaluation records}, journal = {Journal of Biomedical Informatics}, volume = {75}, number = {Supplement}, year = {2017}, pages = {S94-S104}, url = {https://doi.org/10.1016/j.jbi.2017.05.019}, author = {Posada, Jose D and Barda, Amie J and Lingyun Shi and Diyang Xue and Victor Ruiz and Pei-Han Kuan and Ryan, Neal D and Tsui, Fuchiang Rich} } @article {1490129, title = {Symptom severity classification with gradient tree boosting}, journal = {Journal of Biomedical Informatics}, volume = {75}, number = {Supplement}, year = {2017}, pages = {S105-S111}, url = {https://doi.org/10.1016/j.jbi.2017.05.015}, author = {Liu, Yang and Yu Gu and John Chu Nguyen and Haodan Li and Jiawei Zhang and Gao, Yuan and Yang Huang} } @article {1490110, title = {Counting trees in Random Forests: Predicting symptom severity in psychiatric intake reports}, journal = {Journal of Biomedical Informatics}, volume = {75}, number = {Supplement}, year = {2017}, pages = {S112-S119}, url = {https://doi.org/10.1016/j.jbi.2017.06.007}, author = {Elyne Scheurwegs and Madhumita Sushil and St{\'e}phan Tulkens and Walter Daelemans and Kim Luyckx} } @article {1489907, title = {Automatic classification of RDoC positive valence severity with a neural network}, journal = {Journal of Biomedical Informatics}, volume = {75}, number = {Supplement}, year = {2017}, pages = {S120-S128}, url = {https://doi.org/10.1016/j.jbi.2017.07.005}, author = {Cheryl Clark and Ben Wellner and Rachel Davis and John Aberdeen and Lynette Hirschman} } @article {1490128, title = {Psychiatric symptom recognition without labeled data using distributional representations of phrases and on-line knowledge}, journal = {Journal of Biomedical Informatics}, volume = {75}, number = {Supplement}, year = {2017}, pages = {S129-S137}, url = {https://doi.org/10.1016/j.jbi.2017.06.014}, author = {Yaoyun Zhang and Zhang, Olivia and Yonghui Wu and Hee-Jin Lee and Xu, Jun and Xu, Hua and Kirk Roberts} } @article {1490125, title = {Predicting mental conditions based on "history of present illness" in psychiatric notes with deep neural networks}, journal = {Journal of Biomedical Informatics}, volume = {75}, number = {Supplement}, year = {2017}, pages = {S138-S148}, url = {https://doi.org/10.1016/j.jbi.2017.06.010}, author = {Tran, Tung and Kavuluru, Ramakanth} } @article {1490115, title = {Exploring associations of clinical and social parameters with violent behaviors among psychiatric patients}, journal = {Journal of Biomedical Informatics}, volume = {75}, number = {Supplement}, year = {2017}, pages = {S149-S159}, url = {https://doi.org/10.1016/j.jbi.2017.08.009}, author = {Hong-Jie Dai and Emily Chia-Yu Su and Mohy Uddin and Jitendra Jonnagaddala and Chi-Shin Wu and Shabbir Syed-Abdul} } @article {1499389, title = {Active learning: a step towards automating medical concept extraction}, journal = {Journal of the American Medical Informatics Association}, volume = {23}, number = {2}, year = {2016}, pages = {289-296}, url = {https://doi.org/10.1093/jamia/ocv069}, author = {Mahnoosh Kholghi and Laurianne Sitbon and Guido Zuccon and Anthony Nguyen} } @article {1499314, title = {Multilayered temporal modeling for the clinical domain}, journal = {Journal of the American Medical Informatics Association}, volume = {23}, number = {2}, year = {2016}, pages = {387-395}, url = {https://doi.org/10.1093/jamia/ocv113}, author = {Lin, Chen and Dligach, Dmitriy and Miller, Timothy A and Bethard, Steven and Savova, Guergana K} } @article {1499438, title = {Practical applications for natural language processing in clinical research: The 2014 i2b2/UTHealth shared tasks}, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S1-S5}, url = {https://doi.org/10.1016/j.jbi.2015.10.007}, author = {{\"O}zlem Uzuner and Amber Stubbs} } @article {1499437, title = {Creation of a new longitudinal corpus of clinical narratives}, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S6-S10}, url = {https://doi.org/10.1016/j.jbi.2015.09.018}, author = {Vishesh Kumar and Amber Stubbs and Stanley Shaw and {\"O}zlem Uzuner} } @article {1499436, title = {Automated systems for the de-identification of longitudinal clinical narratives: Overview of 2014 i2b2/UTHealth shared task Track 1 }, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S11-S19}, url = {https://doi.org/10.1016/j.jbi.2015.06.007}, author = {Amber Stubbs and Christopher Kotfila and {\"O}zlem Uzuner} } @article {1499435, title = {Annotating longitudinal clinical narratives for de-identification: The 2014 i2b2/UTHealth corpus}, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S20-S29}, url = {https://doi.org/10.1016/j.jbi.2015.07.020}, author = {Amber Stubbs and {\"O}zlem Uzuner} } @article {1499434, title = {Automatic detection of protected health information from clinic narratives}, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S30-S38}, url = {https://doi.org/10.1016/j.jbi.2015.06.015}, author = {Yang, Hui and Jonathan M. Garibaldi} } @article {1499433, title = {CRFs based de-identification of medical records }, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S39-S46}, url = {https://doi.org/10.1016/j.jbi.2015.08.012}, author = {He, Bin and Jianyi Cheng and Keting Cen and Wenlan Hua} } @article {1499432, title = {Automatic de-identification of electronic medical records using token-level and character-level conditional random fields }, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S47-S52}, url = {https://doi.org/10.1016/j.jbi.2015.06.009}, author = {Zengjian Liu and Yangxin Chen and Buzhou Tang and Xiaolong Wang and Qingcai Chen and Haodi Li and Wang, Jingfeng and Qiwen Deng and Suisong Zhu} } @article {1499431, title = {Combining knowledge- and data-driven methods for de-identification of clinical narratives }, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S53-S59}, url = {https://doi.org/10.1016/j.jbi.2015.06.029}, author = {Azad Dehghan and Aleksandar Kovacevic and George Karystianis and John A. Keane and Goran Nenadic} } @article {1499430, title = {Hidden Markov model using Dirichlet process for de-identification }, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S60-S66}, url = {https://doi.org/10.1016/j.jbi.2015.09.004}, author = {Chen, Tao and Richard M. Cullen and Marshall Godwin} } @article {1499402, title = {Identifying risk factors for heart disease over time: Overview of 2014 i2b2/UTHealth shared task Track 2}, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S67-S77}, url = {https://doi.org/10.1016/j.jbi.2015.07.001}, author = {Amber Stubbs and Christopher Kotfila and Xu, Hua and {\"O}zlem Uzuner} } @article {1499428, title = {Annotating risk factors for heart disease in clinical narratives for diabetic patients }, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S78-S91}, url = {https://doi.org/10.1016/j.jbi.2015.05.009}, author = {Amber Stubbs and {\"O}zlem Uzuner} } @article {1499427, title = {A systematic comparison of feature space effects on disease classifier performance for phenotype identification of five diseases }, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S92-S102}, url = {https://doi.org/10.1016/j.jbi.2015.07.016}, author = {Christopher Kotfila and {\"O}zlem Uzuner} } @article {1499426, title = {Comparison of UMLS terminologies to identify risk of heart disease using clinical notes }, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S103-S110}, url = {https://doi.org/10.1016/j.jbi.2015.08.025}, author = {Chaitanya Shivade and Pranav Malewadkar and Eric Fosler-Lussier and Albert M. Lai} } @article {1499425, title = {The role of fine-grained annotations in supervised recognition of risk factors for heart disease from EHRs }, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S111-S119}, url = {https://doi.org/10.1016/j.jbi.2015.06.010}, author = {Kirk Roberts and Sonya E. Shooshan and Laritza Rodriguez and Swapna Abhyankar and Halil Kilicoglu and Dina Demner-Fushman} } @article {1499424, title = {Agile text mining for the 2014 i2b2/UTHealth Cardiac risk factors challenge }, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S120-S127}, url = {https://doi.org/10.1016/j.jbi.2015.06.030}, author = {James Cormack and Chinmoy Nath and David Milward and Kalpana Raja and Siddhartha R. Jonnalagadda} } @article {1499423, title = {Adapting existing natural language processing resources for cardiovascular risk factors identification in clinical notes }, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S128-S132}, url = {https://doi.org/10.1016/j.jbi.2015.08.002}, author = {Abdulrahman Khalifa and St{\'e}phane Meystre} } @article {1499422, title = {Combining glass box and black box evaluations in the identification of heart disease risk factors and their temporal relations from clinical records }, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S133-S142}, url = {https://doi.org/10.1016/j.jbi.2015.06.014}, author = {Cyril Grouin and V{\'e}ronique Moriceau and Pierre Zweigenbaum} } @article {1499420, title = {Mining heart disease risk factors in clinical text with named entity recognition and distributional semantic models}, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S143-149}, url = {https://doi.org/10.1016/j.jbi.2015.08.009}, author = {Jay Urbain} } @article {1499419, title = {A context-aware approach for progression tracking of medical concepts in electronic medical records}, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S150-S157}, url = {https://doi.org/10.1016/j.jbi.2015.09.013}, author = {Nai-Wen Chang and Hong-Jie Dai and Jitendra Jonnagaddala and Chih-Wei Chen and Richard Tzong-Han Tsai and Wen-Lian Hsu} } @article {1499418, title = {An automatic system to identify heart disease risk factors in clinical texts over time }, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S158-S163}, url = {https://doi.org/10.1016/j.jbi.2015.09.002}, author = {Qingcai Chen and Haodi Li and Buzhou Tang and Xiaolong Wang and Liu, Xin and Zengjian Liu and Shu Liu and Weida Wang and Qiwen Deng and Suisong Zhu and Yangxin Chen and Wang, Jingfeng} } @article {1499417, title = {Risk factor detection for heart disease by applying text analytics in electronic medical records }, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S164-S170}, url = {https://doi.org/10.1016/j.jbi.2015.08.011}, author = {Manabu Torii and Jung-wei Fan and Wei-li Yang and Theodore Lee and Matthew T. Wiley and Daniel S. Zisook and Yang Huang} } @article {1499416, title = {A hybrid model for automatic identification of risk factors for heart disease}, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S171-182}, url = {https://doi.org/10.1016/j.jbi.2015.09.006}, author = {Yang, Hui and Jonathan M. Garibaldi} } @article {1499415, title = {Using local lexicalized rules to identify heart disease risk factors in clinical notes}, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S183-S188}, url = {https://doi.org/10.1016/j.jbi.2015.06.013}, author = {George Karystianis and Azad Dehghan and Aleksandar Kovacevic and John A. Keane and Goran Nenadic} } @article {1499414, title = {Ease of adoption of clinical natural language processing software: An evaluation of five systems}, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S189-S196}, url = {https://doi.org/10.1016/j.jbi.2015.07.008}, author = {Kai Zheng and V.G. Vinod Vydiswaran and Liu, Yang and Wang, Yue and Amber Stubbs and {\"O}zlem Uzuner and Anupama E. Gururaj and Samuel Bayer and John Aberdeen and Anna Rumshisky and Serguei Pakhomov and Hongfang Liu and Xu, Hua} } @article {1499413, title = {Predicting changes in systolic blood pressure using longitudinal patient records}, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S197-S202}, url = {https://doi.org/10.1016/j.jbi.2015.06.024}, author = {John Wes Solomon and Rodney D. Nielsen} } @article {1499412, title = {Coronary artery disease risk assessment from unstructured electronic health records using text mining}, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S203-S210}, url = {https://doi.org/10.1016/j.jbi.2015.08.003}, author = {Jitendra Jonnagaddala and Siaw-Teng Liaw and Pradeep Ray and Manish Kumar and Nai-Wen Chang and Hong-Jie Dai} } @article {1499411, title = {Textual inference for eligibility criteria resolution in clinical trials}, journal = {Journal of Biomedical Informatics}, volume = {58}, number = {Supplement}, year = {2015}, pages = {S211-S218}, url = {https://doi.org/10.1016/j.jbi.2015.09.008}, author = {Chaitanya Shivade and Courtney Hebert and Marcelo Lopetegui and Marie-Catherine de Marneffe and Eric Fosler-Lussier and Albert M. Lai} } @article {1499391, title = {Evaluating the state of the art in disorder recognition and normalization of the clinical narrative}, journal = {Journal of the American Medical Informatics Association}, volume = {22}, number = {1}, year = {2015}, pages = {143-154}, url = {https://doi.org/10.1136/amiajnl-2013-002544}, author = {Pradhan, Sameer and No{\'e}mie Elhadad and Brett R South and David Martinez and Lee Christensen and Amy Vogel and Hanna Suominen and Chapman, Wendy W and Savova, Guergana} } @article {1499387, title = {Functional evaluation of out-of-the-box text-mining tools for data-mining tasks}, journal = {Journal of the American Medical Informatics Association}, volume = {22}, number = {1}, year = {2015}, pages = {121-131}, url = {https://doi.org/10.1136/amiajnl-2014-002902}, author = {Kenneth Jung and Paea LePendu and Srinivasan Iyer and Bauer-Mehren, Anna and Bethany Percha and Nigam H Shah} } @article {1499383, title = {Comparison of a semi-automatic annotation tool and a natural language processing application for the generation of clinical statement entries}, journal = {Journal of the American Medical Informatics Association}, volume = {22}, number = {1}, year = {2015}, pages = {132-142}, url = {https://doi.org/10.1136/amiajnl-2014-002991}, author = {Ching-Heng Lin and Nai-Yuan Wu and Wei-Shao Lai and Der-Ming Liou} } @article {1499380, title = {Normalization of relative and incomplete temporal expressions in clinical narratives }, journal = {Journal of the American Medical Informatics Association}, volume = {22}, number = {5}, year = {2015}, pages = {1001-1008}, url = {https://doi.org/10.1093/jamia/ocu004}, author = {Weiyi Sun and Anna Rumshisky and {\"O}zlem Uzuner} } @article {1498862, title = {Evaluating temporal relations in clinical text: 2012 i2b2 Challenge}, journal = {Journal of the American Medical Informatics Association}, volume = {20}, number = {5}, year = {2013}, pages = {806-813}, url = {https://doi.org/10.1136/amiajnl-2013-001628}, author = {Weiyi Sun and Anna Rumshisky and {\"O}zlem Uzuner} } @article {1498861, title = {Temporal reasoning over clinical text: the state of the art}, journal = {Journal of the American Medical Informatics Association}, volume = {20}, number = {5}, year = {2013}, pages = {814-819}, url = {https://doi.org/10.1136/amiajnl-2013-001760}, author = {Weiyi Sun and Anna Rumshisky and {\"O}zlem Uzuner} } @article {1498860, title = {Eventual situations for timeline extraction from clinical reports}, journal = {Journal of the American Medical Informatics Association}, volume = {20}, number = {5}, year = {2013}, pages = {820-827}, url = {https://doi.org/10.1136/amiajnl-2013-001627}, author = {Cyril Grouin and Natalia Grabar and Thierry Hamon and Sophie Rosset and Xavier Tannier and Pierre Zweigenbaum} } @article {1498859, title = {A hybrid system for temporal information extraction from clinical text}, journal = {Journal of the American Medical Informatics Association}, volume = {20}, number = {5}, year = {2013}, pages = {828-835}, url = {https://doi.org/10.1136/amiajnl-2013-001635}, author = {Buzhou Tang and Yonghui Wu and Min Jiang and Chen, Yukun and Denny, Joshua C and Xu, Hua} } @article {1498857, title = {Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification}, journal = {Journal of the American Medical Informatics Association}, volume = {20}, number = {5}, year = {2013}, pages = {836-842}, url = {https://doi.org/10.1136/amiajnl-2013-001622}, author = {Sunghwan Sohn and Kavishwar Wagholikar and Li, Dingcheng and Siddhartha R Jonnalagadda and Cui Tao and Ravikumar Komandur Elayavilli and Hongfang Liu} } @article {1498856, title = {{\`A} la Recherche du Temps Perdu: extracting temporal relations from medical text in the 2012 i2b2 NLP challenge}, journal = {Journal of the American Medical Informatics Association}, volume = {20}, number = {5}, year = {2013}, pages = {843-848}, url = {https://doi.org/10.1136/amiajnl-2013-001624}, author = {Colin Cherry and Xiaodan Zhu and Joel Martin and Berry de Bruijn} } @article {1498855, title = {An end-to-end system to identify temporal relation in discharge summaries: 2012 i2b2 challenge}, journal = {Journal of the American Medical Informatics Association}, volume = {20}, number = {5}, year = {2013}, pages = {849-858}, url = {https://doi.org/10.1136/amiajnl-2012-001607}, author = {Xu, Yan and Yining Wang and Tianren Liu and Junichi Tsujii and Eric I-Chao Chang} } @article {1498853, title = {Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives }, journal = {Journal of the American Medical Informatics Association}, volume = {20}, number = {5}, year = {2013}, pages = {859-866}, author = {Aleksandar Kova{\v c}evi{\'c} and Azad Dehghan and Michele Filannino and John A Keane and Goran Nenadic} } @article {1498852, title = {A flexible framework for recognizing events, temporal expressions, and temporal relations in clinical text }, journal = {Journal of the American Medical Informatics Association}, volume = {20}, number = {5}, year = {2013}, pages = {867-875}, url = {https://doi.org/10.1136/amiajnl-2013-001619}, author = {Kirk Roberts and Bryan Rink and Harabagiu, Sanda M} } @article {1504147, title = {Chronology of your health events: Approaches to extracting temporal relations from medical narratives}, journal = {Journal of Biomedical Informatics}, volume = {46}, number = {Supplement}, year = {2013}, pages = {S1-S4}, url = {https://doi.org/10.1016/j.jbi.2013.11.005}, author = {{\"O}zlem Uzuner and Amber Stubbs and Weiyi Sun} } @article {1504146, title = {Annotating temporal information in clinical narratives}, journal = {Journal of Biomedical Informatics}, volume = {6}, number = {Supplement}, year = {2013}, pages = {S5-S12}, url = {https://doi.org/10.1016/j.jbi.2013.07.004}, author = {Weiyi Sun and Anna Rumshisky and {\"O}zlem Uzuner} } @article {1504150, title = {Extraction of events and temporal expressions from clinical narratives}, journal = {Journal of Biomedical Informatics}, volume = {46}, number = {Supplement}, year = {2013}, pages = {S13-S19}, url = {https://doi.org/10.1016/j.jbi.2013.08.010}, author = {Prateek Jindal and Dan Roth} } @article {1504151, title = {MedTime: A temporal information extraction system for clinical narratives}, journal = {Journal of Biomedical Informatics}, volume = {46}, number = {Supplement}, year = {2013}, pages = {S20-S28}, url = {https://doi.org/10.1016/j.jbi.2013.07.012}, author = {Yu-Kai Lin and Hsinchun Chen and Randall A. Brown} } @article {1504152, title = {Classifying temporal relations in clinical data: A hybrid, knowledge-rich approach}, journal = {Journal of Biomedical Informatics}, volume = {46}, number = {Supplement}, year = {2013}, pages = {S29-S39}, url = {https://doi.org/10.1016/j.jbi.2013.08.003}, author = {Jennifer D{\textquoteright}Souza and Vincent Ng} } @article {1504153, title = {Towards generating a patient{\textquoteright}s timeline: Extracting temporal relationships from clinical notes}, journal = {Journal of Biomedical Informatics}, volume = {46}, number = {Supplement}, year = {2013}, pages = {S40-S47}, url = {https://doi.org/10.1016/j.jbi.2013.11.001}, author = {Azadeh Nikfarjam and Ehsan Emadzadeh and Graciela Gonzalez} } @article {1504154, title = {Temporal relation discovery between events and temporal expressions identified in clinical narrative}, journal = {Journal of Biomedical Informatics}, volume = {46}, number = {Supplement}, year = {2013}, pages = {S48-S53}, url = {https://doi.org/10.1016/j.jbi.2013.09.010}, author = {Yao Cheng and Anick, Peter and Hong, Pengyu and Xue, Nianwen} } @article {1504155, title = {TEMPTING system: A hybrid method of rule and machine learning for temporal relation extraction in patient discharge summaries}, journal = {Journal of Biomedical Informatics}, volume = {46}, number = {Supplement}, year = {2013}, pages = {S54-S62}, url = {https://doi.org/10.1016/j.jbi.2013.09.007}, author = {Yung-Chun Chang and Hong-Jie Dai and Johnny Chi-Yang Wu and Jian-Ming Chen and Richard Tzong-Han Tsai and Wen-Lian Hsu} } @article {1498808, title = {Using domain knowledge and domain-inspired discourse model for coreference resolution for clinical narratives}, journal = {Journal of the American Medical Informatics Association}, volume = {20}, number = {2}, year = {2013}, pages = {356-362}, url = {https://doi.org/10.1136/amiajnl-2011-000767}, author = {Prateek Jindal and Dan Roth} } @article {1499184, title = {Lexical patterns, features and knowledge resources for coreference resolution in clinical notes }, journal = {Journal of Biomedical Informatics}, volume = {45}, number = {5}, year = {2012}, pages = {901-912}, url = {https://doi.org/10.1016/j.jbi.2012.02.012}, author = {Phil Gooch and Abdul Roudsari} } @article {1498819, title = {Evaluating the state of the art in coreference resolution for electronic medical records}, journal = {Journal of the American Medical Informatics Association}, volume = {19}, number = {5}, year = {2012}, pages = {786-791}, url = {https://doi.org/10.1136/amiajnl-2011-000784}, author = {{\"O}zlem Uzuner and Andreea Bodnari and Shuying Shen and Tyler Forbush and John Pestian and Brett R South} } @article {1498820, title = {Feature engineering combined with machine learning and rule-based methods for structured information extraction from narrative clinical discharge summaries}, journal = {Journal of the American Medical Informatics Association}, volume = {19}, number = {5}, year = {2012}, pages = {824-832}, url = {https://doi.org/10.1136/amiajnl-2011-000776}, author = {Xu, Yan and Kai Hong and Junichi Tsujii and Eric I-Chao Chang} } @article {1498818, title = {Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules}, journal = {Journal of the American Medical Informatics Association}, volume = {19}, number = {5}, year = {2012}, pages = {867-874}, url = {https://doi.org/10.1136/amiajnl-2011-000766}, author = {Siddhartha Reddy Jonnalagadda and Li, Dingcheng and Sunghwan Sohn and Wu, Stephen and Kavishwar Wagholikar and Manabu Torii and Hongfang Liu} } @article {1498816, title = {A supervised framework for resolving coreference in clinical records}, journal = {Journal of the American Medical Informatics Association}, volume = {19}, number = {5}, year = {2012}, pages = {875-882}, url = {https://doi.org/10.1136/amiajnl-2012-000810}, author = {Bryan Rink and Kirk Roberts and Harabagiu, Sanda M} } @article {1498815, title = {Machine learning-based coreference resolution of concepts in clinical documents}, journal = {Journal of the American Medical Informatics Association}, volume = {19}, number = {5}, year = {2012}, pages = {883-887}, author = {Henry Ware and Charles J Mullett and Vasudevan Jagannathan and Oussama El-Rawas} } @article {1498812, title = {Coreference resolution of medical concepts in discharge summaries by exploiting contextual information}, journal = {Journal of the American Medical Informatics Association}, volume = {19}, number = {5}, year = {2012}, pages = {888-896}, url = {https://doi.org/10.1136/amiajnl-2012-000808}, author = {Hong-Jie Dai and Chun-Yu Chen and Chi-Yang Wu and Po-Ting Lai and Richard Tzong-Han Tsai and Wen-Lian Hsu} } @article {1498810, title = {A classification approach to coreference in discharge summaries: 2011 i2b2 challenge}, journal = {Journal of the American Medical Informatics Association}, volume = {19}, number = {5}, year = {2012}, pages = {897-905}, url = {https://doi.org/10.1136/amiajnl-2011-000734}, author = {Xu, Yan and Jiahua Liu and Jiajun Wu and Wang, Yue and Zhuowen Tu and Jian-Tao Sun and Junichi Tsujii and Eric I-Chao Chang} } @article {1498809, title = {MCORES: a system for noun phrase coreference resolution for clinical records }, journal = {Journal of the American Medical Informatics Association}, volume = {19}, number = {5}, year = {2012}, pages = {906-912}, url = {https://doi.org/10.1136/amiajnl-2011-000591}, author = {Andreea Bodnari and Szolovits, Peter and {\"O}zlem Uzuner} } @article {1498790, title = {Overcoming barriers to NLP for clinical text: the role of shared tasks and the need for additional creative solutions }, journal = {Journal of the American Medical Informatics Association}, volume = {18}, number = {5}, year = {2011}, pages = {540-543}, url = {https://doi.org/10.1136/amiajnl-2011-000465}, author = {Chapman, Wendy W and Prakash M Nadkarni and Lynette Hirschman and Leonard W D{\textquoteright}Avolio and Savova, Guergana K and {\"O}zlem Uzuner} } @article {1498789, title = {2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text}, journal = {Journal of the American Medical Informatics Association}, volume = {18}, number = {5}, year = {2011}, pages = {552-556}, url = {https://doi.org/10.1136/amiajnl-2011-000203}, author = {{\"O}zlem Uzuner and Brett R South and Shuying Shen and Scott L DuVall} } @article {1498788, title = {Machine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010 }, journal = {Journal of the American Medical Informatics Association}, volume = {18}, number = {5}, year = {2011}, pages = {557-562}, url = {https://doi.org/10.1136/amiajnl-2011-000150}, author = {Berry de Bruijn and Colin Cherry and Svetlana Kiritchenko and Joel Martin and Xiaodan Zhu} } @article {1498787, title = {MITRE system for clinical assertion status classification }, journal = {Journal of the American Medical Informatics Association}, volume = {18}, number = {5}, year = {2011}, pages = {563-567}, url = {https://doi.org/10.1136/amiajnl-2011-000164}, author = {Cheryl Clark and John Aberdeen and Matt Coarr and David Tresner-Kirsch and Ben Wellner and Alexander Yeh and Lynette Hirschman} } @article {1498786, title = {A flexible framework for deriving assertions from electronic medical records }, journal = {Journal of the American Medical Informatics Association}, volume = {18}, number = {5}, year = {2011}, pages = {568-573}, url = {https://doi.org/10.1136/amiajnl-2011-000152}, author = {Kirk Roberts and Harabagiu, Sanda M} } @article {1498785, title = {A knowledge discovery and reuse pipeline for information extraction in clinical notes }, journal = {Journal of the American Medical Informatics Association}, volume = {18}, number = {5}, year = {2011}, pages = {574-579}, url = {https://doi.org/10.1136/amiajnl-2011-000302}, author = {Jon D Patrick and Dung H M Nguyen and Yefeng Wang and Li, Min} } @article {1498692, title = {Using machine learning for concept extraction on clinical documents from multiple data sources}, journal = {Journal of the American Medical Informatics Association}, volume = {18}, number = {5}, year = {2011}, pages = {580-587}, url = {https://doi.org/10.1136/amiajnl-2011-000155}, author = {Manabu Torii and Kavishwar Wagholikar and Hongfang Liu} } @article {1498691, title = {Hybrid methods for improving information access in clinical documents: concept, assertion, and relation identification}, journal = {Journal of the American Medical Informatics Association}, volume = {18}, number = {5}, year = {2011}, pages = {588-593}, url = {https://doi.org/10.1136/amiajnl-2011-000154}, author = {Anne-Lyse Minard and Anne-Laure Ligozat and Asma Ben Abacha and Delphine Bernhard and Bruno Cartoni and Louise Del{\'e}ger and Brigitte Grau and Sophie Rosset and Pierre Zweigenbaum and Cyril Grouin} } @article {1498690, title = {Automatic extraction of relations between medical concepts in clinical texts }, journal = {Journal of the American Medical Informatics Association}, volume = {18}, number = {5}, year = {2011}, pages = {594-600}, url = {https://doi.org/10.1136/amiajnl-2011-000153}, author = {Bryan Rink and Sanda Harabagiu and Kirk Roberts} } @article {1498689, title = {A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries}, journal = {Journal of the American Medical Informatics Association}, volume = {18}, number = {5}, year = {2011}, pages = {601-606}, url = {https://doi.org/10.1136/amiajnl-2011-000163}, author = {Min Jiang and Chen, Yukun and Mei Liu and S Trent Rosenbloom and Subramani Mani and Denny, Joshua C and Xu, Hua} } @article {1498688, title = {Automated concept-level information extraction to reduce the need for custom software and rules development }, journal = {Journal of the American Medical Informatics Association}, volume = {18}, number = {5}, year = {2011}, pages = {607-613}, url = {https://doi.org/10.1136/amiajnl-2011-000183}, author = {Leonard W D{\textquoteright}Avolio and Thien M Nguyen and Goryachev, Sergey and Louis D Fiore} } @article {1498666, title = {Extracting medication information from clinical text}, journal = {Journal of the American Medical Informatics Association}, volume = {17}, number = {5}, year = {2010}, pages = {514-518}, url = {https://doi.org/10.1136/jamia.2010.003947}, author = {{\"O}zlem Uzuner and Imre Solti and Eithon Cadag} } @article {1498667, title = {Community annotation experiment for ground truth generation for the i2b2 medication challenge}, journal = {Journal of the American Medical Informatics Association}, volume = {17}, number = {5}, year = {2010}, pages = {519-523}, url = {https://doi.org/10.1136/jamia.2010.004200}, author = {{\"O}zlem Uzuner and Imre Solti and Fei Xia and Eithon Cadag} } @article {1498685, title = {High accuracy information extraction of medication information from clinical notes: 2009 i2b2 medication extraction challenge}, journal = {Journal of the American Medical Informatics Association}, volume = {17}, number = {5}, year = {2010}, pages = {524-527}, url = {https://doi.org/10.1136/jamia.2010.003939}, author = {Jon Patrick and Li, Min} } @article {1498684, title = {Integrating existing natural language processing tools for medication extraction from discharge summaries}, journal = {Journal of the American Medical Informatics Association}, volume = {17}, number = {5}, year = {2010}, pages = {528-531}, url = {https://doi.org/10.1136/jamia.2010.003855}, author = {Son Doan and Bastarache, Lisa and Sergio Klimkowski and Denny, Joshua C and Xu, Hua} } @article {1498683, title = {Medication information extraction with linguistic pattern matching and semantic rules}, journal = {Journal of the American Medical Informatics Association}, volume = {17}, number = {5}, year = {2010}, pages = {532-535}, url = {https://doi.org/10.1136/jamia.2010.003657}, author = {Irena Spasi{\'c} and Farzaneh Sarafraz and John A Keane and Goran Nenadi{\'c}} } @article {1498682, title = {Extracting Rx information from clinical narrative}, journal = {Journal of the American Medical Informatics Association}, volume = {17}, number = {5}, year = {2010}, pages = {536-539}, url = {https://doi.org/10.1136/jamia.2010.003970}, author = {James G Mork and Olivier Bodenreider and Dina Demner-Fushman and Rezarta Islamaj Do{\u g}an and Fran{\c c}ois-Michel Lang and Zhiyong Lu and Aur{\'e}lie N{\'e}v{\'e}ol and Lee Peters and Sonya E Shooshan and Alan R Aronson} } @article {1498678, title = {Improving textual medication extraction using combined conditional random fields and rule-based systems}, journal = {Journal of the American Medical Informatics Association}, volume = {17}, number = {5}, year = {2010}, pages = {540-544}, url = {https://doi.org/10.1136/jamia.2010.004119}, author = {Domonkos Tikk and Ill{\'e}s Solt} } @article {1498676, title = {Automatic extraction of medication information from medical discharge summaries}, journal = {Journal of the American Medical Informatics Association}, volume = {17}, number = {5}, year = {2010}, pages = {545-548}, url = {https://doi.org/10.1136/jamia.2010.003863}, author = {Yang, Hui} } @article {1498673, title = {Linguistic approach for identification of medication names and related information in clinical narratives }, journal = {Journal of the American Medical Informatics Association}, volume = {17}, number = {5}, year = {2010}, pages = {549-554}, url = {https://doi.org/10.1136/jamia.2010.004036}, author = {Thierry Hamon and Natalia Grabar} } @article {1498672, title = {Extracting medical information from narrative patient records: the case of medication-related information}, journal = {Journal of the American Medical Informatics Association}, volume = {17}, number = {5}, year = {2010}, pages = {555-558}, url = {https://doi.org/10.1136/jamia.2010.003962}, author = {Louise Del{\'e}ger and Cyril Grouin and Pierre Zweigenbaum} } @article {1498671, title = {Textractor: a hybrid system for medications and reason for their prescription extraction from clinical text documents}, journal = {Journal of the American Medical Informatics Association}, volume = {17}, number = {5}, year = {2010}, pages = {559-562}, url = {https://doi.org/10.1136/jamia.2010.004028}, author = {St{\'e}phane M Meystre and Julien Thibault and Shuying Shen and John F Hurdle and Brett R South} } @article {1498670, title = {Lancet: a high precision medication event extraction system for clinical text }, journal = {Journal of the American Medical Informatics Association}, volume = {17}, number = {5}, year = {2010}, pages = {563-567}, url = {https://doi.org/10.1136/jamia.2010.004077}, author = {Zuofeng Li and Feifan Liu and Lamont Antieau and Yonggang Cao and Hong Yu} } @article {1498659, title = {Recognizing Obesity and Comorbidities in Sparse Data}, journal = {Journal of the American Medical Informatics Association}, volume = {16}, number = {4}, year = {2009}, pages = {561-570}, url = {https://doi.org/10.1197/jamia.M3115}, author = {{\"O}zlem Uzuner} } @article {1498660, title = {Description of a Rule-based System for the i2b2 Challenge in Natural Language Processing for Clinical Data}, journal = {Journal of the American Medical Informatics Association}, volume = {16}, number = {4}, year = {2009}, pages = {571-575}, url = {https://doi.org/10.1197/jamia.M3083}, author = {Lois C. Childs and Robert Enelow and Lone Simonsen and Norris H. Heintzelman and Kimberly M. Kowalski and Robert J. Taylor} } @article {1498661, title = {A Rule-based Approach for Identifying Obesity and Its Comorbidities in Medical Discharge Summaries}, journal = {Journal of the American Medical Informatics Association}, volume = {16}, number = {4}, year = {2009}, pages = {576-579}, url = {https://doi.org/10.1197/jamia.M3086}, author = {Ninad K. Mishra and David M. Cummo and James J. Arnzen and Jason Bonander} } @article {1498664, title = {Semantic Classification of Diseases in Discharge Summaries Using a Context-aware Rule-based Classifier}, journal = {Journal of the American Medical Informatics Association}, volume = {16}, number = {4}, year = {2009}, pages = {580-584}, url = {https://doi.org/10.1197/jamia.M3087}, author = {Ill{\'e}s Solt and Domonkos Tikk and Viktor G{\'a}l and Zsolt T. Kardkov{\'a}cs} } @article {1498663, title = {Natural Language Processing Framework to Assess Clinical Conditions}, journal = {Journal of the American Medical Informatics Association}, volume = {16}, number = {4}, year = {2009}, pages = {585-589}, url = {https://doi.org/10.1197/jamia.M3091}, author = {Henry Ware and Charles J. Mullett and V. Jagannathan} } @article {1498658, title = {A System for Classifying Disease Comorbidity Status from Medical Discharge Summaries Using Automated Hotspot and Negated Concept Detection}, journal = {Journal of the American Medical Informatics Association}, volume = {16}, number = {4}, year = {2009}, pages = {590-595}, url = {https://doi.org/10.1197/jamia.M3095}, author = {Kyle H. Ambert and Aaron M. Cohen} } @article {1498665, title = {A Text Mining Approach to the Prediction of Disease Status from Clinical Discharge Summaries}, journal = {Journal of the American Medical Informatics Association}, volume = {16}, number = {4}, year = {2009}, pages = {596-600}, url = {https://doi.org/10.1197/jamia.M3096}, author = {Yang, Hui and Irena Spasic and John A. Keane and Goran Nenadic} } @article {1498662, title = {Semi-automated Construction of Decision Rules to Predict Morbidities from Clinical Texts}, journal = {Journal of the American Medical Informatics Association}, volume = {16}, number = {4}, year = {2009}, pages = {601-605}, url = {https://doi.org/10.1197/jamia.M3097}, author = {Rich{\'a}rd Farkas and Gy{\"o}rgy Szarvas and Istv{\'a}n Heged{\H u}s and Attila Alm{\'a}si and Veronika Vincze and R{\'o}bert Orm{\'a}ndi and R{\'o}bert Busa-Fekete} } @article {1498656, title = {A Software Tool for Removing Patient Identifying Information from Clinical Documents}, journal = {Journal of the American Medical Informatics Association}, volume = {15}, number = {5}, year = {2008}, pages = {601-610}, url = {https://doi.org/10.1197/jamia.M2702}, author = {F. Jeff Friedlin and Clement J. McDonald} } @article {1498642, title = {Identifying Patient Smoking Status from Medical Discharge Records}, journal = {Journal of the American Medical Informatics Association}, volume = {15}, number = {1}, year = {2008}, pages = {14-24}, url = {https://doi.org/10.1197/jamia.M2408}, author = {{\"O}zlem Uzuner and Ira Goldstein and Yuan Luo and Kohane, Isaac} } @article {1498643, title = {Mayo Clinic NLP System for Patient Smoking Status Identification}, journal = { Journal of the American Medical Informatics Association}, volume = {15}, number = {1}, year = {2008}, pages = {25-28}, url = {https://doi.org/10.1197/jamia.M2437}, author = {Savova, Guergana K. and Philip V. Ogren and Patrick H. Duffy and James D. Buntrock and Chute, Christopher G.} } @article {1498644, title = {Using Implicit Information to Identify Smoking Status in Smoke-blind Medical Discharge Summaries}, journal = {Journal of the American Medical Informatics Association}, volume = {15}, number = {1}, year = {2008}, pages = {29-31}, url = {https://doi.org/10.1197/jamia.M2440}, author = {Richard Wicentowski and Matthew R. Sydes} } @article {1498646, title = {Five-way Smoking Status Classification Using Text Hot-Spot Identification and Error-correcting Output Codes}, journal = {Journal of the American Medical Informatics Association}, volume = {15}, number = {1}, year = {2008}, pages = {32-35}, url = {https://doi.org/10.1197/jamia.M2434}, author = {Aaron M. Cohen} } @article {1498650, title = {Identifying Smokers with a Medical Extraction System}, journal = {Journal of the American Medical Informatics Association}, volume = {15}, number = {1}, year = {2008}, pages = {36-39}, url = {https://doi.org/10.1197/jamia.M2442}, author = {Cheryl Clark and Kathleen Good and Lesley Jezierny and Melissa Macpherson and Brian Wilson and Urszula Chajewska} } @article {1498645, title = {Medical i2b2 NLP Smoking Challenge: The A-Life System Architecture and Methodology}, journal = {Journal of the American Medical Informatics Association}, volume = {15}, number = {1}, year = {2008}, pages = {40-43}, url = {https://doi.org/10.1197/jamia.M2438}, author = {Daniel T. Heinze and Mark L. Morsch and Brian C. Potter and Ronald E Sheffer} } @article {1498651, title = {Evaluating the State-of-the-Art in Automatic De-identification}, journal = {Journal of the American Medical Informatics Association}, volume = {14}, number = {5}, year = {2007}, pages = {550-563}, url = {https://doi.org/10.1197/jamia.M2444}, author = {{\"O}zlem Uzuner and Yuan Luo and Szolovits, Peter} } @article {1498655, title = {Rapidly Retargetable Approaches to De-identification in Medical Records}, journal = {Journal of the American Medical Informatics Association}, volume = {14}, number = {5}, year = {2007}, pages = {564-573}, url = {https://doi.org/10.1197/jamia.M2435}, author = {Ben Wellner and Matt Huyck and Scott Mardis and John Aberdeen and Alex Morgan and Peshkin, Leonid and Alexander Yeh and Janet Hitzeman and Lynette Hirschman} } @article {1498652, title = {State-of-the-art Anonymization of Medical Records Using an Iterative Machine Learning Framework}, journal = {Journal of the American Medical Informatics Association}, volume = {14}, number = {5}, year = {2007}, pages = {574-580}, url = {https://doi.org/10.1197/j.jamia.M2441}, author = {Gy{\"o}rgy Szarvas and Rich{\'a}rd Farkas and R{\'o}bert Busa-Fekete} }