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2020 – today
- 2025
[j115]Betina Idnay
, Gongbo Zhang, Fangyi Chen, Casey N. Ta, Matthew W. Schelke, Karen Marder, Chunhua Weng:
Mini-mental status examination phenotyping for Alzheimer's disease patients using both structured and narrative electronic health record features. J. Am. Medical Informatics Assoc. 32(1): 119-128 (2025)- 2024
- [j114]Aimiel Casillan, Michelle E. Florido, Jamie Galarza-Cornejo, Suzanne Bakken, John A Lynch, Wendy K. Chung, Kathleen F. Mittendorf, Eta S. Berner, John J. Connolly, Chunhua Weng, Ingrid A. Holm, Atlas Khan, Krzysztof Kiryluk, Nita A Limdi, Lynn Petukhova, Maya Sabatello, Julia Wynn:
Participant-guided development of bilingual genomic educational infographics for Electronic Medical Records and Genomics Phase IV study. J. Am. Medical Informatics Assoc. 31(2): 306-316 (2024) - [j113]Betina Ross S. Idnay, Jianfang Liu, Yilu Fang, Alex Hernandez, Shivani Kaw, Alicia Etwaru, Janeth Juarez Padilla, Sergio Ozoria Ramirez, Karen Marder, Chunhua Weng, Rebecca Schnall:
Sociotechnical feasibility of natural language processing-driven tools in clinical trial eligibility prescreening for Alzheimer's disease and related dementias. J. Am. Medical Informatics Assoc. 31(5): 1062-1073 (2024) - [j112]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) - [j111]Zhiyong Lu, Yifan Peng, Trevor Cohen, Marzyeh Ghassemi, Chunhua Weng, Shubo Tian:
Large language models in biomedicine and health: current research landscape and future directions. J. Am. Medical Informatics Assoc. 31(9): 1801-1811 (2024) - [j110]Yilu Fang, Patrick Ryan, Chunhua Weng:
Knowledge-guided generative artificial intelligence for automated taxonomy learning from drug labels. J. Am. Medical Informatics Assoc. 31(9): 2065-2075 (2024) - [j109]Andy Wang, Cong Liu, Jingye Yang, Chunhua Weng:
Fine-tuning large language models for rare disease concept normalization. J. Am. Medical Informatics Assoc. 31(9): 2076-2083 (2024) - [j108]Gongbo Zhang, Qiao Jin, Denis Jered McInerney, Yong Chen, Fei Wang, Curtis L. Cole, Qian Yang, Yanshan Wang, Bradley A. Malin, Mor Peleg, Byron C. Wallace, Zhiyong Lu, Chunhua Weng, Yifan Peng:
Leveraging generative AI for clinical evidence synthesis needs to ensure trustworthiness. J. Biomed. Informatics 153: 104640 (2024) - [j107]Jimyung Park, Yilu Fang, Casey N. Ta, Gongbo Zhang, Betina Idnay, Fangyi Chen, David Feng, Rebecca Shyu, Emily R. Gordon, Matthew E. Spotnitz, Chunhua Weng:
Criteria2Query 3.0: Leveraging generative large language models for clinical trial eligibility query generation. J. Biomed. Informatics 154: 104649 (2024) - [j106]Kayla Schiffer-Kane, Cong Liu, Tiffany J. Callahan, Casey N. Ta, Jordan G. Nestor, Chunhua Weng:
Converting OMOP CDM to phenopackets: A model alignment and patient data representation evaluation. J. Biomed. Informatics 155: 104659 (2024) - [j105]Betina Idnay, Yilu Fang, Edward Stanley, Brenda Ruotolo, Wendy K. Chung, Karen Marder, Chunhua Weng:
Promoting equity in clinical research: The role of social determinants of health. J. Biomed. Informatics 156: 104663 (2024) - [j104]Charlotte Zelin, Wendy K. Chung, Mederic Jeanne, Gongbo Zhang, Chunhua Weng:
Rare disease diagnosis using knowledge guided retrieval augmentation for ChatGPT. J. Biomed. Informatics 157: 104702 (2024) - [j103]Fangyi Chen, Priyanka Ahimaz, Quan M. Nguyen, Rachel Lewis, Wendy K. Chung, Casey N. Ta, Katherine M. Szigety, Sarah E. Sheppard, Ian M. Campbell, Kai Wang, Chunhua Weng, Cong Liu:
Phenotype driven molecular genetic test recommendation for diagnosing pediatric rare disorders. npj Digit. Medicine 7(1) (2024) - [j102]Gongbo Zhang, Qiao Jin, Yiliang Zhou, Song Wang, Betina Idnay, Yiming Luo, Elizabeth Park, Jordan G. Nestor, Matthew E. Spotnitz, Ali Soroush, Thomas Campion, Zhiyong Lu, Chunhua Weng, Yifan Peng:
Closing the gap between open source and commercial large language models for medical evidence summarization. npj Digit. Medicine 7(1) (2024) - [j101]Jingye Yang, Cong Liu, Wendy Deng, Da Wu, Chunhua Weng, Yunyun Zhou, Kai Wang:
Enhancing phenotype recognition in clinical notes using large language models: PhenoBCBERT and PhenoGPT. Patterns 5(1): 100887 (2024) - [i9]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) - [i8]Gongbo Zhang, Qiao Jin, Yiliang Zhou, Song Wang, Betina Ross S. Idnay, Yiming Luo, Elizabeth Park, Jordan G. Nestor, Matthew E. Spotnitz, Ali Soroush, Thomas Campion, Zhiyong Lu, Chunhua Weng, Yifan Peng:
Closing the gap between open-source and commercial large language models for medical evidence summarization. CoRR abs/2408.00588 (2024) - [i7]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) - [i6]Qiao Jin, Nicholas Wan, Robert Leaman, Shubo Tian, Zhizheng Wang, Yifan Yang, Zifeng Wang, Guangzhi Xiong, Po-Ting Lai, Qingqing Zhu, Benjamin Hou, Maame Sarfo-Gyamfi, Gongbo Zhang, Aidan Gilson, Balu Bhasuran, Zhe He, Aidong Zhang, Jimeng Sun, Chunhua Weng, Ronald M. Summers, Qingyu Chen, Yifan Peng, Zhiyong Lu:
Demystifying Large Language Models for Medicine: A Primer. CoRR abs/2410.18856 (2024) - 2023
- [j100]Betina Ross S. Idnay, Yilu Fang, Caitlin N. Dreisbach, Karen Marder, Chunhua Weng, Rebecca Schnall:
Clinical research staff perceptions on a natural language processing-driven tool for eligibility prescreening: An iterative usability assessment. Int. J. Medical Informatics 171: 104985 (2023) - [j99]Casey N. Ta, Jason E. Zucker, Po-Hsiang Chiu, Yilu Fang, Karthik Natarajan, Chunhua Weng:
Clinical and temporal characterization of COVID-19 subgroups using patient vector embeddings of electronic health records. J. Am. Medical Informatics Assoc. 30(2): 256-272 (2023) - [j98]Pascal S. Brandt, Abel N. Kho, Yuan Luo, Jennifer A. Pacheco, Theresa L. Walunas, Hakon Hakonarson, George Hripcsak, Cong Liu, Ning Shang, Chunhua Weng, Nephi Walton, David S. Carrell, Paul K. Crane, Eric B. Larson, Christopher G. Chute, Iftikhar J. Kullo, Robert J. Carroll, Joshua C. Denny, Andrea H. Ramirez, Wei-Qi Wei, Jyotishman Pathak, Laura K. Wiley, Rachel L. Richesson, Justin B. Starren, Luke V. Rasmussen:
Characterizing variability of electronic health record-driven phenotype definitions. J. Am. Medical Informatics Assoc. 30(3): 427-437 (2023) - [j97]Tian Kang, Yingcheng Sun, Jae Hyun Kim, Casey N. Ta, Adler J. Perotte, Kayla Schiffer, Mutong Wu, Yang Zhao, Nour Moustafa-Fahmy, Yifan Peng, Chunhua Weng:
EvidenceMap: a three-level knowledge representation for medical evidence computation and comprehension. J. Am. Medical Informatics Assoc. 30(6): 1022-1031 (2023) - [j96]Abigail Newbury, Hao Liu, Betina Ross S. Idnay, Chunhua Weng:
The suitability of UMLS and SNOMED-CT for encoding outcome concepts. J. Am. Medical Informatics Assoc. 30(12): 1895-1903 (2023) - [j95]Yilu Fang, Hao Liu, Betina Ross S. Idnay, Casey N. Ta, Karen Marder, Chunhua Weng:
A data-driven approach to optimizing clinical study eligibility criteria. J. Biomed. Informatics 142: 104375 (2023) - [j94]Liyan Tang, Zhaoyi Sun, Betina Ross S. Idnay, Jordan G. Nestor, Ali Soroush, Pierre A. Elias, Ziyang Xu, Ying Ding, Greg Durrett, Justin F. Rousseau, Chunhua Weng, Yifan Peng:
Evaluating large language models on medical evidence summarization. npj Digit. Medicine 6 (2023) - [c109]Karthik Natarajan, Chunhua Weng, Soumitra Sengupta:
A Model for Multi-Institutional Clinical Data Repository. MIE 2023: 312-316 - [c108]Hao Liu, Yifan Peng, Chunhua Weng:
How Good Is ChatGPT for Medication Evidence Synthesis? MIE 2023: 1062-1066 - [i5]Jingye Yang, Cong Liu, Wendy Deng, Da Wu, Chunhua Weng, Yunyun Zhou, Kai Wang:
Enhancing Phenotype Recognition in Clinical Notes Using Large Language Models: PhenoBCBERT and PhenoGPT. CoRR abs/2308.06294 (2023) - [i4]Jenna Kefeli, Ali Soroush, Courtney J. Diamond, Haley M. Zylberberg, Benjamin L. May, Julian A. Abrams, Chunhua Weng, Nicholas P. Tatonetti:
Large Language Models for Granularized Barrett's Esophagus Diagnosis Classification. CoRR abs/2308.08660 (2023) - [i3]Gongbo Zhang, Qiao Jin, Denis Jered McInerney, Yong Chen, Fei Wang, Curtis L. Cole, Qian Yang, Yanshan Wang, Bradley A. Malin, Mor Peleg, Byron C. Wallace, Zhiyong Lu, Chunhua Weng, Yifan Peng:
Leveraging Generative AI for Clinical Evidence Summarization Needs to Achieve Trustworthiness. CoRR abs/2311.11211 (2023) - [i2]Da Wu, Jingye Yang, Steven Klein, Cong Liu, Tzung-Chien Hsieh, Peter Krawitz, Chunhua Weng, Gholson J. Lyon, Jennifer M. Kalish, Kai Wang:
Multimodal Machine Learning Combining Facial Images and Clinical Texts Improves Diagnosis of Rare Genetic Diseases. CoRR abs/2312.15320 (2023) - 2022
- [j93]Sarah J. Nelson, Bethany Drury, Daniel Hood, Jeremy Harper, Tiffany Bernard, Chunhua Weng, Nan Kennedy, Bernard LaSalle, Ramkiran Gouripeddi, Consuelo H. Wilkins, Paul A. Harris:
EHR-based cohort assessment for multicenter RCTs: a fast and flexible model for identifying potential study sites. J. Am. Medical Informatics Assoc. 29(4): 652-659 (2022) - [j92]Young J. Juhn, Euijung Ryu, Chung-Il Wi, Katherine S. King, Momin M. Malik, Santiago Romero-Brufau, Chunhua Weng, Sunghwan Sohn, Richard R. Sharp, John D. Halamka:
Assessing socioeconomic bias in machine learning algorithms in health care: a case study of the HOUSES index. J. Am. Medical Informatics Assoc. 29(7): 1142-1151 (2022) - [j91]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) - [j90]Ken Wiley, Laura Findley, Madison Goldrich, Tejinder K. Rakhra-Burris, Ana Stevens, Pamela Williams, Carol J. Bult, Rex L. Chisholm, Patricia Deverka, Geoffrey S. Ginsburg, Eric D. Green, Gail P. Jarvik, George A. Mensah, Erin Ramos, Mary V. Relling, Dan M. Roden, Robb Rowley, Gil Alterovitz, Samuel J. Aronson, Lisa Bastarache, James J. Cimino, Erin L. Crowgey, Guilherme Del Fiol, Robert R. Freimuth, Mark A. Hoffman, Janina M. Jeff, Kevin B. Johnson, Kensaku Kawamoto, Subha Madhavan, Eneida A. Mendonça, Lucila Ohno-Machado, Siddharth Pratap, Casey Overby Taylor, Marylyn D. Ritchie, Nephi Walton, Chunhua Weng, Teresa Zayas-Cabán, Teri A. Manolio, Marc S. Williams:
A research agenda to support the development and implementation of genomics-based clinical informatics tools and resources. J. Am. Medical Informatics Assoc. 29(8): 1342-1349 (2022) - [j89]Sylvia Cho, Ipek Ensari, Noémie Elhadad, Chunhua Weng, Jennifer M. Radin, Brinnae Bent, Pooja M. Desai, Karthik Natarajan:
An interactive fitness-for-use data completeness tool to assess activity tracker data. J. Am. Medical Informatics Assoc. 29(12): 2032-2040 (2022) - [j88]James R. Rogers, Jovana Pavisic, Casey N. Ta, Cong Liu, Ali Soroush, Ying Kuen Cheung, George Hripcsak, Chunhua Weng:
Leveraging electronic health record data for clinical trial planning by assessing eligibility criteria's impact on patient count and safety. J. Biomed. Informatics 127: 104032 (2022) - [j87]Junghwan Lee, Cong Liu, Junyoung Kim, Zhehuan Chen, Yingcheng Sun, James R. Rogers, Wendy K. Chung, Chunhua Weng:
Deep learning for rare disease: A scoping review. J. Biomed. Informatics 135: 104227 (2022) - [j86]Hao Liu, Simona Carini, Zhehuan Chen, Spencer Phillips Hey, Ida Sim, Chunhua Weng:
Ontology-based categorization of clinical studies by their conditions. J. Biomed. Informatics 135: 104235 (2022) - [j85]Jingzhi Yu, Jennifer A. Pacheco, Anika S. Ghosh, Yuan Luo, Chunhua Weng, Ning Shang, Barbara Benoit, David S. Carrell, Robert J. Carroll, Ozan Dikilitas, Robert R. Freimuth, Vivian S. Gainer, Hakon Hakonarson, George Hripcsak, Iftikhar J. Kullo, Frank D. Mentch, Shawn N. Murphy, Peggy L. Peissig, Andrea H. Ramirez, Nephi Walton, Wei-Qi Wei, Luke V. Rasmussen:
Under-specification as the source of ambiguity and vagueness in narrative phenotype algorithm definitions. BMC Medical Informatics Decis. Mak. 22(1): 23 (2022) - [j84]Yu Deng, Jennifer A. Pacheco, Anika S. Ghosh, Anh H. Chung, Chengsheng Mao, Joshua C. Smith, Juan Zhao, Wei-Qi Wei, April Barnado, Chad Dorn, Chunhua Weng, Cong Liu, Adam Cordon, Jingzhi Yu, Yacob Tedla, Abel Kho, Rosalind Ramsey-Goldman, Theresa Walunas, Yuan Luo:
Natural language processing to identify lupus nephritis phenotype in electronic health records. BMC Medical Informatics Decis. Mak. 22-S(2): 348 (2022) - [j83]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) - [c107]Betina Ross S. Idnay, Yilu Fang, Caitlin N. Dreisbach, Karen Marder, Chunhua Weng, Rebecca Schnall:
Optimizing Clinical Research Eligibility Prescreening: An Iterative Usability Evaluation of an NLP-driven Cohort Identification Tool. AMIA 2022 - [c106]Betina Ross S. Idnay, Yilu Fang, Yingcheng Sun, Hao Liu, Zhehuan Chen, Rebecca Schnall, Chunhua Weng:
Criteria2Query 2.0: Combining Machine Efficiency and Human Intelligence to Define a More Accurate and Feasible Cohort for Clinical Trial Recruitment. AMIA 2022 - [c105]Kayla Schiffer, Chunhua Weng, Yoolim A. Choi:
Leveraging Hierarchical Concept Relations to Improve Automatic Detection of Off-Label Drug Use in Electronic Health Records Data. AMIA 2022 - [c104]Ali Soroush, Courtney J. Diamond, Haley Zylberberg, Julian Abrams, Chunhua Weng:
A Clinical Data Summarization Pipeline for Patients at Risk for Esophageal Adenocarcinoma Undergoing Endoscopic Surveillance. AMIA 2022 - [c103]Zhehuan Chen, Yilu Fang, Hao Liu, Chunhua Weng:
Data-Driven Modeling of Randomized Controlled Trial Outcomes. MIE 2022: 392-396 - 2021
- [j82]Melissa Beauchemin, Chunhua Weng, Lillian Sung, Adrienne Pichon, Maura Abbott, Dawn L. Hershman, Rebecca Schnall:
Data Quality of Chemotherapy-Induced Nausea and Vomiting Documentation. Appl. Clin. Inform. 12(02): 320-328 (2021) - [j81]Yingcheng Sun, Alex M. Butler, Ibrahim Diallo, Jae Hyun Kim, Casey N. Ta, James R. Rogers, Hao Liu, Chunhua Weng:
A Framework for Systematic Assessment of Clinical Trial Population Representativeness Using Electronic Health Records Data. Appl. Clin. Inform. 12(4): 816-825 (2021) - [j80]Jae Hyun Kim, Alex M. Butler, Casey N. Ta, Yingcheng Sun, Mathew S. Maurer, Chunhua Weng:
The potential role of EHR data in optimizing eligibility criteria definition for cardiovascular outcome trials. Int. J. Medical Informatics 156: 104587 (2021) - [j79]Jae Hyun Kim, Casey N. Ta, Cong Liu, Cynthia Sung, Alex M. Butler, Latoya A. Stewart, Lyudmila Ena, James R. Rogers, Junghwan Lee, Anna Ostropolets, Patrick B. Ryan, Hao Liu, Shing M. Lee, Mitchell S. V. Elkind, Chunhua Weng:
Towards clinical data-driven eligibility criteria optimization for interventional COVID-19 clinical trials. J. Am. Medical Informatics Assoc. 28(1): 14-22 (2021) - [j78]James R. Rogers, Junghwan Lee, Ziheng Zhou, Ying Kuen Cheung, George Hripcsak, Chunhua Weng:
Contemporary use of real-world data for clinical trial conduct in the United States: a scoping review. J. Am. Medical Informatics Assoc. 28(1): 144-154 (2021) - [j77]Yingcheng Sun, Alex M. Butler, Fengyang Lin, Hao Liu, Latoya A. Stewart, Jae Hyun Kim, Betina Ross S. Idnay, Qingyin Ge, Xinyi Wei, Cong Liu, Chi Yuan, Chunhua Weng:
The COVID-19 Trial Finder. J. Am. Medical Informatics Assoc. 28(3): 616-621 (2021) - [j76]Tian Kang, Adler J. Perotte, Youlan Tang, Casey N. Ta, Chunhua Weng:
UMLS-based data augmentation for natural language processing of clinical research literature. J. Am. Medical Informatics Assoc. 28(4): 812-823 (2021) - [j75]Tian Kang, Ali Turfah, Jaehyun Kim, Adler J. Perotte, Chunhua Weng:
A neuro-symbolic method for understanding free-text medical evidence. J. Am. Medical Informatics Assoc. 28(8): 1703-1711 (2021) - [j74]Chi Yuan, Patrick B. Ryan, Casey N. Ta, Jae Hyun Kim, Ziran Li, Chunhua Weng:
From clinical trials to clinical practice: How long are drugs tested and then used by patients? J. Am. Medical Informatics Assoc. 28(11): 2456-2460 (2021) - [j73]Lauren Franks, Hao Liu, Mitchell S. V. Elkind, Muredach P. Reilly, Chunhua Weng, Shing M. Lee:
Misalignment between COVID-19 hotspots and clinical trial sites. J. Am. Medical Informatics Assoc. 28(11): 2461-2466 (2021) - [j72]Betina Ross S. Idnay, Caitlin N. Dreisbach, Chunhua Weng, Rebecca Schnall:
A systematic review on natural language processing systems for eligibility prescreening in clinical research. J. Am. Medical Informatics Assoc. 29(1): 197-206 (2021) - [j71]Jia Guo, Chi Yuan, Ning Shang, Tian Zheng, Natalie A. Bello, Krzysztof Kiryluk, Chunhua Weng, Shuang Wang:
Similarity-based health risk prediction using Domain Fusion and electronic health records data. J. Biomed. Informatics 116: 103711 (2021) - [j70]Hao Liu, Chi Yuan, Alex M. Butler, Yingcheng Sun, Chunhua Weng:
A knowledge base of clinical trial eligibility criteria. J. Biomed. Informatics 117: 103771 (2021) - [j69]Yingcheng Sun, Alex M. Butler, Latoya A. Stewart, Hao Liu, Chi Yuan, Christopher T. Southard, Jae Hyun Kim, Chunhua Weng:
Building an OMOP common data model-compliant annotated corpus for COVID-19 clinical trials. J. Biomed. Informatics 118: 103790 (2021) - [j68]James R. Rogers, George Hripcsak, Ying Kuen Cheung, Chunhua Weng:
Clinical comparison between trial participants and potentially eligible patients using electronic health record data: A generalizability assessment method. J. Biomed. Informatics 119: 103822 (2021) - [j67]Amelia J. Averitt, Patrick B. Ryan, Chunhua Weng, Adler J. Perotte:
A conceptual framework for external validity. J. Biomed. Informatics 121: 103870 (2021) - [j66]Ning Shang, Atlas Khan, Fernanda Polubriaginof, Francesca Zanoni, Karla Mehl, David Fasel, Paul E. Drawz, Robert J. Carroll, Joshua C. Denny, Matthew A. Hathcock, Adelaide M. Arruda-Olson, Peggy L. Peissig, Richard A. Dart, Murray H. Brilliant, Eric B. Larson, David S. Carrell, Sarah A. Pendergrass, Shefali Setia Verma, Marylyn D. Ritchie, Barbara Benoit, Vivian S. Gainer, Elizabeth W. Karlson, Adam S. Gordon, Gail P. Jarvik, Ian B. Stanaway, David R. Crosslin, Sumit Mohan, Iuliana Ionita-Laza, Nicholas P. Tatonetti, Ali G. Gharavi, George Hripcsak, Chunhua Weng, Krzysztof Kiryluk:
Medical records-based chronic kidney disease phenotype for clinical care and "big data" observational and genetic studies. npj Digit. Medicine 4 (2021) - [j65]Danqing Xu, Chen Wang, Atlas Khan, Ning Shang, Zihuai He, Adam S. Gordon, Iftikhar J. Kullo, Shawn N. Murphy, Yizhao Ni, Wei-Qi Wei, Ali Gharavi, Krzysztof Kiryluk, Chunhua Weng, Iuliana Ionita-Laza:
Quantitative disease risk scores from EHR with applications to clinical risk stratification and genetic studies. npj Digit. Medicine 4 (2021) - [c102]Jennifer A. Pacheco, Luke V. Rasmussen, Ken Wiley, Thomas N. Person, David J. Cronkite, Sunghwan Sohn, Shawn N. Murphy, Justin H. Gundelach, Vivian S. Gainer, Victor M. Castro, Cong Liu, Todd Lingren, Frank D. Mentch, Agnes S. Sundaresan, Garrett Eickelberg, Valerie Willis, Al'ona Furmanchuk, Roshan Patel, David S. Carrell, Marc S. Williams, Elizabeth W. Karlson, Jodell E. Linder, Yuan Luo, Chunhua Weng, Wei-Qi Wei:
Evaluation of the Portability of Natural Language Processing-based Computable Phenotypes in the eMERGE Network. AMIA 2021 - [c101]Adrienne Pichon, Betina Ross S. Idnay, Rebecca Schnall, Karen Marder, Chunhua Weng:
Cognitive Function Characterization Using Electronic Health Records Notes. AMIA 2021 - [c100]Matthew E. Spotnitz, Jason Patterson, Vojtech Huser, Chunhua Weng, Karthik Natarajan:
Harmonization of Measurement Codes for Concept-Oriented Lab Data Retrieval. AMIA 2021 - [c99]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 - [c98]Matthew E. Spotnitz, Jason Patterson, Vojtech Huser, Chunhua Weng, Karthik Natarajan:
Harmonization of Measurement Codes for Concept-Oriented Lab Data Retrieval. MedInfo 2021: 12-16 - [c97]Ali Turfah, Hao Liu, Latoya A. Stewart, Tian Kang, Chunhua Weng:
Extending PICO with Observation Normalization for Evidence Computing. MedInfo 2021: 268-272 - [c96]Cong Liu, Hao Liu, Casey N. Ta, James Roger, Alex Butler, Junghwan Lee, Jaehyun Kim, Ning Shang, Chunhua Weng:
Evaluation of Criteria2Query: Towards Augmented Intelligence for Cohort Identification. MedInfo 2021: 297-300 - [c95]Yingcheng Sun, Jiaqi Tang, Alex Butler, Cong Liu, Yilu Fang, Chunhua Weng:
Interactive Similarity-Based Search of Clinical Trials. MedInfo 2021: 309-313 - [c94]Zhehuan Chen, Hao Liu, Stan Liao, Marguerite Bernard, Tian Kang, Latoya A. Stewart, Chunhua Weng:
Representation and Normalization of Complex Interventions for Evidence Computing. MedInfo 2021: 592-596 - [c93]Fengyang Lin, Hao Liu, Paul Moon, Chunhua Weng:
A Sample Size Extractor for RCT Reports. MedInfo 2021: 617-621 - [c92]Junghwan Lee, Cong Liu, Casey N. Ta, Chunhua Weng:
Towards Better Diagnosis Prediction Using Bidirectional Recurrent Neural Networks. MedInfo 2021: 1054-1055 - [c91]Zhehuan Chen, Hao Liu, Alex M. Butler, Anna Ostropolets, Chunhua Weng:
Potential Role of Clinical Trial Eligibility Criteria in Electronic Phenotyping. MIE 2021: 148-152 - [c90]Yilu Fang, Jae Hyun Kim, Betina Ross S. Idnay, Rebeca Aragon Garcia, Carmen E. Castillo, Yingcheng Sun, Hao Liu, Cong Liu, Chi Yuan, Chunhua Weng:
Participatory Design of a Clinical Trial Eligibility Criteria Simplification Method. MIE 2021: 984-988 - [i1]Yu Deng, Jennifer A. Pacheco, Anh H. Chung, Chengsheng Mao, Joshua C. Smith, Juan Zhao, Wei-Qi Wei, April Barnado, Chunhua Weng, Cong Liu, Adam Cordon, Jingzhi Yu, Yacob Tedla, Abel N. Kho, Rosalind Ramsey-Goldman, Theresa Walunas, Yuan Luo:
Natural language processing to identify lupus nephritis phenotype in electronic health records. CoRR abs/2112.10821 (2021) - 2020
- [j64]Marissa Burgermaster, Jung Hoon Son, Patricia G. Davidson, Arlene M. Smaldone, Gilad Kuperman, Daniel J. Feller, Katherine Gardner Burt, Matthew E. Levine, David J. Albers, Chunhua Weng, Lena Mamykina:
A new approach to integrating patient-generated data with expert knowledge for personalized goal setting: A pilot study. Int. J. Medical Informatics 139: 104158 (2020) - [j63]James R. Rogers, Hollis Mills, Lisa V. Grossman, Andrew Goldstein, Chunhua Weng:
Understanding the nature and scope of clinical research commentaries in PubMed. J. Am. Medical Informatics Assoc. 27(3): 449-456 (2020) - [j62]Chi Yuan, Yongli Wang, Ning Shang, Ziran Li, Ruxin Zhao, Chunhua Weng:
A graph-based method for reconstructing entities from coordination ellipsis in medical text. J. Am. Medical Informatics Assoc. 27(9): 1364-1373 (2020) - [j61]Anna Ostropolets, Christian G. Reich, Patrick B. Ryan, Ning Shang, George Hripcsak, Chunhua Weng:
Adapting electronic health records-derived phenotypes to claims data: Lessons learned in using limited clinical data for phenotyping. J. Biomed. Informatics 102: 103363 (2020) - [j60]Chunhua Weng, Nigam H. Shah, George Hripcsak:
Deep phenotyping: Embracing complexity and temporality - Towards scalability, portability, and interoperability. J. Biomed. Informatics 105: 103433 (2020) - [j59]Jacqueline Peng, Mengge Zhao, James M. Havrilla, Cong Liu, Chunhua Weng, Whitney Guthrie, Robert Schultz, Kai Wang, Yunyun Zhou:
Natural language processing (NLP) tools in extracting biomedical concepts from research articles: a case study on autism spectrum disorder. BMC Medical Informatics Decis. Mak. 20-S(11): 322 (2020) - [j58]Amelia J. Averitt, Chunhua Weng, Patrick B. Ryan, Adler J. Perotte:
Translating evidence into practice: eligibility criteria fail to eliminate clinically significant differences between real-world and study populations. npj Digit. Medicine 3 (2020) - [c89]Alex M. Butler, Junghwan Lee, Yat S. So, Linda Busacca, Karen Marder, Henry N. Ginsberg, Dianne Frederick, Ismael Castaneda, Elizabeth Guerrido, Chunhua Weng:
Impact of IMPACT: Longitudinal Analysis of an Integrated Participant Scheduling System in a Clinical Research Setting. AMIA 2020 - [c88]Hongfang Liu, Xiaoqian Jiang, Serguei V. S. Pakhomov, Chunhua Weng, Hua Xu:
The Open Health Natural Language Processing Collaboratory. AMIA 2020 - [c87]Hao Liu, Chi Yuan, Alex M. Butler, Yingcheng Sun, Chunhua Weng:
Potential Role of Clinical Trial Eligibility Criteria in Electronic Phenotyping. AMIA 2020 - [c86]Anna Ostropolets, Christian G. Reich, Patrick B. Ryan, Chunhua Weng, Anthony Molinaro, Frank J. DeFalco, Jitendra Jonnagaddala, Siaw-Teng Liaw, Hokyun Jeon, Rae Woong Park, Matthew E. Spotnitz, Karthik Natarajan, Kristin Kostka, George Argyriou, Robert T. Miller, Andrew E. Williams, Evan Minty, José D. Posada, George Hripcsak:
Characterizing database granularity using SNOMED-CT hierarchy. AMIA 2020 - [c85]James R. Rogers, Junghwan Lee, Ziheng Zhou, Patrick B. Ryan, George Hripcsak, Chunhua Weng:
Contemporary Use of Real World Data for Clinical Trial Conduct. AMIA 2020 - [c84]Ziran Li, Huanyao Chen, Chi Yuan, Chunhua Weng:
How Have Experimental Cancer Interventions Evolved over Time? MIE 2020: 252-256
2010 – 2019
- 2019
- [j57]Melissa Beauchemin, Meghan T. Murray, Lillian Sung, Dawn L. Hershman, Chunhua Weng, Rebecca Schnall:
Clinical decision support for therapeutic decision-making in cancer: A systematic review. Int. J. Medical Informatics 130 (2019) - [j56]Chi Yuan, Patrick B. Ryan, Casey N. Ta, Yixuan Guo, Ziran Li, Jill Hardin, Rupa Makadia, Peng Jin, Ning Shang, Tian Kang, Chunhua Weng:
Criteria2Query: a natural language interface to clinical databases for cohort definition. J. Am. Medical Informatics Assoc. 26(4): 294-305 (2019) - [j55]Cong Liu, Chi Yuan, Alex M. Butler, Richard D. Carvajal, Ziran Ryan Li, Casey N. Ta, Chunhua Weng:
DQueST: dynamic questionnaire for search of clinical trials. J. Am. Medical Informatics Assoc. 26(11): 1333-1343 (2019) - [j54]Shengqiang Chi, Xinhang Li, Yu Tian, Jun Li, Xiang-Xing Kong, Ke-Feng Ding, Chunhua Weng, Jing-Song Li:
Semi-supervised learning to improve generalizability of risk prediction models. J. Biomed. Informatics 92 (2019) - [j53]George Hripcsak, Ning Shang, Peggy L. Peissig, Luke V. Rasmussen, Cong Liu, Barbara Benoit, Robert J. Carroll, David S. Carrell, Joshua C. Denny, Ozan Dikilitas, Vivian S. Gainer, Kayla Marie Howell, Jeffrey G. Klann, Iftikhar J. Kullo, Todd Lingren, Frank D. Mentch, Shawn N. Murphy, Karthik Natarajan, Chunhua Weng:
Facilitating phenotype transfer using a common data model. J. Biomed. Informatics 96 (2019) - [j52]Olga Lyudovyk, Yufeng Shen, Nicholas P. Tatonetti, Susan J. Hsiao, Mahesh M. Mansukhani, Chunhua Weng:
Pathway analysis of genomic pathology tests for prognostic cancer subtyping. J. Biomed. Informatics 98 (2019) - [j51]Ning Shang, Cong Liu, Luke V. Rasmussen, Casey N. Ta, Robert J. Carroll, Barbara Benoit, Todd Lingren, Ozan Dikilitas, Frank D. Mentch, David S. Carrell, Wei-Qi Wei, Yuan Luo, Vivian S. Gainer, Iftikhar J. Kullo, Jennifer A. Pacheco, Hakon Hakonarson, Theresa L. Walunas, Joshua C. Denny, Chunhua Weng:
Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network. J. Biomed. Informatics 99 (2019) - [j50]Cong Liu, Casey N. Ta, James R. Rogers, Ziran Li, Junghwan Lee, Alex M. Butler, Ning Shang, Fabricio Sampaio Peres Kury, Liwei Wang, Feichen Shen, Hongfang Liu, Lyudmila Ena, Carol Friedman, Chunhua Weng:
Ensembles of natural language processing systems for portable phenotyping solutions. J. Biomed. Informatics 100 (2019) - [j49]Chunhua Weng, Carol Friedman, Casey A. Rommel, John F. Hurdle:
A two-site survey of medical center personnel's willingness to share clinical data for research: implications for reproducible health NLP research. BMC Medical Informatics Decis. Mak. 19-S(3): 5-12 (2019) - [j48]David A. Hanauer, Qiaozhu Mei, V. G. Vinod Vydiswaran, Karandeep Singh, Zach Landis-Lewis, Chunhua Weng:
Complexities, variations, and errors of numbering within clinical notes: the potential impact on information extraction and cohort-identification. BMC Medical Informatics Decis. Mak. 19-S(3): 59-69 (2019) - [j47]Cong Liu, Fabricio Sampaio Peres Kury, Ziran Li, Casey N. Ta, Kai Wang, Chunhua Weng:
Doc2Hpo: a web application for efficient and accurate HPO concept curation. Nucleic Acids Res. 47(Webserver-Issue): W566-W570 (2019) - [c83]Melissa Beauchemin, Rebecca Schnall, Chunhua Weng:
Completeness and Concordance in Electronic Health Record (EHR) Documentation of Chemotherapy-Induced Nausea and Vomiting (CINV) in Pediatric Cancer. AMIA 2019 - [c82]Fabricio Sampaio Peres Kury, Li-heng Fu, Chi Yuan, Ida Sim, Simona Carini, Chunhua Weng:
Hidden Gaps in Using Common Data Models to Achieve Interoperability Between Electronic Phenotypes and Clinical Data. AMIA 2019 - [c81]Yanshan Wang, Andrew Wen, Sijia Liu, Jennifer L. St. Sauver, Adil E. Bharucha, Chunhua Weng, Hongfang Liu:
Clinical Use of an Information Retrieval Framework for Cohort Discovery from Electronic Health Records. AMIA 2019 - [c80]Julia Wynn, Wei Wei, Xinhang Li, Yat So, Suzanne R. Bakken, Chunhua Weng, Wendy K. Chung:
User engagement with web-based genomics education videos and implications for designing scalable patient education materials. AMIA 2019 - [c79]Duo Helen Wei, Casey N. Ta, Harold Alan Pincus, Chunhua Weng:
Combining Clinical Data and Domain Knowledge for Analyzing Mental Disorder Concept Relatedness and Usage. ICHI 2019: 1-6 - [c78]Tian Kang, Shirui Zou, Chunhua Weng:
Pretraining to Recognize PICO Elements from Randomized Controlled Trial Literature. MedInfo 2019: 188-192 - [c77]Casey N. Ta, Chunhua Weng:
Detecting Systemic Data Quality Issues in Electronic Health Records. MedInfo 2019: 383-387 - [c76]Duo Helen Wei, Tian Kang, Harold Alan Pincus, Chunhua Weng:
Construction of Disease Similarity Networks Using Concept Embedding and Ontology. MedInfo 2019: 442-446 - [c75]Olga Lyudovyk, Chunhua Weng:
SNOMEDtxt: Natural Language Generation from SNOMED Ontology. MedInfo 2019: 1263-1267 - [c74]Chunhua Weng, Tianyong Hao, Carol Friedman, John F. Hurdle:
Crowdsourcing Public Opinion for Sharing Medical Records for the Advancement of Science. MedInfo 2019: 1393-1397 - [c73]Chunhua Weng, Amy K. Mir, David A. Hanauer, James J. Cimino:
Dialogue Analysis for Clinical Data Query Mediation. MedInfo 2019: 1398-1402 - [c72]Xinyuan Zhang, Yogasudha Veturi, Shefali Setia Verma, William Bone, Anurag Verma, Anastasia Lucas, Scott J. Hebbring, Joshua C. Denny, Ian B. Stanaway, Gail P. Jarvik, David R. Crosslin, Eric B. Larson, Laura Rasmussen-Torvik, Sarah A. Pendergrass, Jordan W. Smoller, Hakon Hakonarson, Patrick Sleiman, Chunhua Weng, David Fasel, Wei-Qi Wei, Iftikhar J. Kullo, Daniel J. Schaid, Wendy K. Chung, Marylyn D. Ritchie:
Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43, 870 individuals from the eMERGE network. PSB 2019: 272-283 - 2018
- [j46]Anando Sen, Andrew Goldstein, Shreya Chakrabarti, Ning Shang, Tian Kang, Anil Yaman, Patrick B. Ryan, Chunhua Weng:
The representativeness of eligible patients in type 2 diabetes trials: a case study using GIST 2.0. J. Am. Medical Informatics Assoc. 25(3): 239-247 (2018) - [j45]Ning Shang, Chunhua Weng, George Hripcsak:
A conceptual framework for evaluating data suitability for observational studies. J. Am. Medical Informatics Assoc. 25(3): 248-258 (2018) - [j44]Samuel J. Aronson, Lawrence J. Babb, Darren C. Ames, Richard A. Gibbs, Eric Venner, John J. Connelly, Keith Marsolo, Chunhua Weng, Marc S. Williams, Andrea L. Hartzler, Wayne H. Liang, James D. Ralston, Emily Beth Devine, Shawn N. Murphy, Christopher G. Chute, Pedro J. Caraballo, Iftikhar J. Kullo, Robert R. Freimuth, Luke V. Rasmussen, Firas H. Wehbe, Josh F. Peterson, Jamie R. Robinson, Ken Wiley, Casey Overby Taylor, eMERGE Network EHRI Working Group:
Empowering genomic medicine by establishing critical sequencing result data flows: the eMERGE example. J. Am. Medical Informatics Assoc. 25(10): 1375-1381 (2018) - [j43]Chunhua Weng, Andrew Goldstein, Chi Yuan, Zhiping Zhou:
The ranking of scientists. J. Biomed. Informatics 79: 145-146 (2018) - [j42]Chunhua Weng, Nigam Shah, George Hripcsak:
Call for papers: Deep phenotyping for Precision Medicine. J. Biomed. Informatics 87: 66-67 (2018) - [j41]Lisa V. Grossman, Elliot G. Mitchell, George Hripcsak, Chunhua Weng, David K. Vawdrey:
A method for harmonization of clinical abbreviation and acronym sense inventories. J. Biomed. Informatics 88: 62-69 (2018) - [c71]Po-Hsiang Chiu, Ning Shang, Chunhua Weng:
Sequencing EHR for Disease Subtyping. AMIA 2018 - [c70]James J. Cimino, Ziran Li, Chunhua Weng:
An Exploration of the Terminology of Clinical Cognition and Reasoning. AMIA 2018 - [c69]Sigfried Gold, Andrea Batch, Robert C. McClure, Guoqian Jiang, Hadi Kharrazi, Rishi Saripalle, Vojtech Huser, Chunhua Weng, Nancy K. Roderer, Ana Szarfman, Niklas Elmqvist, David Gotz:
Clinical Concept Value Sets and Interoperability in Health Data Analytics. AMIA 2018 - [c68]Cong Liu, Chi Yuan, Eric Pua, Paul Harris, Chunhua Weng:
Dynamic Questionnaire Generation for Efficient Patient Search of Trials. AMIA 2018 - [c67]Xiao Dong, Yaoyun Zhang, Hua Xu, Chunhua Weng:
Guideline-driven data quality assessment- A case study of warfarin management. AMIA 2018 - [c66]David A. Hanauer, Qiaozhu Mei, V. G. Vinod Vydiswaran, Karandeep Singh, Zach Landis-Lewis, Chunhua Weng:
Numerical Age Variations within Clinical Notes: The Potential Impact on De-Identification and Information Extraction. ICHI Workshops 2018: 66-67 - [c65]Chunhua Weng, Carol Friedman, Casey A. Rommel, John F. Hurdle:
A Two-Site Survey of Medical Center Personnel's Willingness to Share Clinical Data for Research: Implications for Reproducible Health NLP Research. ICHI Workshops 2018: 78-79 - [r8]Chintan Patel, Chunhua Weng:
Clinical Data and Information Models. Encyclopedia of Database Systems (2nd ed.) 2018 - [r7]Chintan Patel, Chunhua Weng:
Clinical Data Quality and Validation. Encyclopedia of Database Systems (2nd ed.) 2018 - [r6]Chintan Patel, Chunhua Weng:
Quality and Trust of Information Content and Credentialing. Encyclopedia of Database Systems (2nd ed.) 2018 - [r5]Chintan Patel, Chunhua Weng:
Reference Knowledge. Encyclopedia of Database Systems (2nd ed.) 2018 - 2017
- [j40]Deepak K. Sharma, Harold R. Solbrig, Cui Tao, Chunhua Weng, Christopher G. Chute, Guoqian Jiang:
Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies. J. Biomed. Semant. 8(1): 19:1-19:11 (2017) - [j39]Jake Luo, Weiheng Chen, Min Wu, Chunhua Weng:
Systematic data ingratiation of clinical trial recruitment locations for geographic-based query and visualization. Int. J. Medical Informatics 108: 85-91 (2017) - [j38]Tian Kang, Shaodian Zhang, Youlan Tang, Gregory William Hruby, Alexander Rusanov, Noémie Elhadad, Chunhua Weng:
EliIE: An open-source information extraction system for clinical trial eligibility criteria. J. Am. Medical Informatics Assoc. 24(6): 1062-1071 (2017) - [j37]Andrew Goldstein, Eric Venker, Chunhua Weng:
Evidence appraisal: a scoping review, conceptual framework, and research agenda. J. Am. Medical Informatics Assoc. 24(6): 1192-1203 (2017) - [j36]Shreya Chakrabarti, Anando Sen, Vojtech Huser, Gregory William Hruby, Alexander Rusanov, David J. Albers, Chunhua Weng:
An Interoperable Similarity-based Cohort Identification Method Using the OMOP Common Data Model Version 5.0. J. Heal. Informatics Res. 1(1): 1-18 (2017) - [c64]Amelia J. Averitt, Chunhua Weng, Adler J. Perotte:
Clinical Trial Eligibility Criteria Fail to Meet Burden of Generalizability. AMIA 2017 - [c63]Jung Hoon Son, Chunhua Weng:
Discordances between Patient-Reported Family History and Family Histories in EHR. AMIA 2017 - [c62]Chi Yuan, Patrick B. Ryan, Yixuan Guo, Peng Jin, Tian Kang, Chunhua Weng:
Criteria2Query: Automatically Transforming Clinical Research Eligibility Criteria Text to OMOP Common Data Model (CDM)-based Cohort Queries. AMIA 2017 - [c61]Sijia Liu, Liwei Wang, Donna M. Ihrke, Vipin Chaudhary, Cui Tao, Chunhua Weng, Hongfang Liu:
Correlating Lab Test Results in Clinical Notes with Structured Lab Data: A Case Study in HbA1c and Glucose. CRI 2017 - [c60]Jeffrey G. Klann, Vijay A. Raghavan, Chunhua Weng, Sarah Weiler, Kenneth D. Mandl, Shawn N. Murphy:
Needs-Driven Data Completeness Assessment for Clinical Research. CRI 2017 - [c59]Chunhua Weng, Monika Ahuja, Kate Fultz Hollis, Bernie LaSalle, Shira H. Fischer, Anthony E. Solomonides, Judith R. Logan:
Current Challenges in Clinical Research Informatics: A Survey of AMIA Clinical Research Informatics Working Group (CRI-WG). CRI 2017 - [c58]Yuqi Si, Chunhua Weng:
An OMOP CDM-Based Relational Database of Clinical Research Eligibility Criteria. MedInfo 2017: 950-954 - 2016
- [j35]Gregory William Hruby, Julia Hoxha, Praveen Chandar Ravichandran, Eneida A. Mendonça, David A. Hanauer, Chunhua Weng:
A data-driven concept schema for defining clinical research data needs. Int. J. Medical Informatics 91: 1-9 (2016) - [j34]Gregory William Hruby, Luke V. Rasmussen, David A. Hanauer, Vimla L. Patel, James J. Cimino, Chunhua Weng:
A multi-site cognitive task analysis for biomedical query mediation. Int. J. Medical Informatics 93: 74-84 (2016) - [j33]Julia Hoxha, Praveen Chandar Ravichandran, Zhe He, James J. Cimino, David A. Hanauer, Chunhua Weng:
DREAM: Classification scheme for dialog acts in clinical research query mediation. J. Biomed. Informatics 59: 89-101 (2016) - [j32]Zhe He, Patrick B. Ryan, Julia Hoxha, Shuang Wang, Simona Carini, Ida Sim, Chunhua Weng:
Multivariate analysis of the population representativeness of related clinical studies. J. Biomed. Informatics 60: 66-76 (2016) - [j31]Handong Mao, Chunhua Weng:
Prediction of black box warning by mining patterns of Convergent Focus Shift in clinical trial study populations using linked public data. J. Biomed. Informatics 60: 132-144 (2016) - [j30]Gregory William Hruby, Konstantina Matsoukas, James J. Cimino, Chunhua Weng:
Facilitating biomedical researchers' interrogation of electronic health record data: Ideas from outside of biomedical informatics. J. Biomed. Informatics 60: 376-384 (2016) - [j29]Julia Hoxha, Chunhua Weng:
Leveraging dialog systems research to assist biomedical researchers' interrogation of Big Clinical Data. J. Biomed. Informatics 61: 176-184 (2016) - [j28]Julia Hoxha, Guoqian Jiang, Chunhua Weng:
Automated learning of domain taxonomies from text using background knowledge. J. Biomed. Informatics 63: 295-306 (2016) - [j27]Anando Sen, Shreya Chakrabarti, Andrew Goldstein, Shuang Wang, Patrick B. Ryan, Chunhua Weng:
GIST 2.0: A scalable multi-trait metric for quantifying population representativeness of individual clinical studies. J. Biomed. Informatics 63: 325-336 (2016) - [c57]William Brown III, Chunhua Weng, David K. Vawdrey, Alex Carballo-Dieguez, Suzanne Bakken:
SMASH: A Data-driven Informatics Method to Assist Experts in Characterizing Semantic Heterogeneity among Data Elements. AMIA 2016 - [c56]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 - [c55]Ning Shang, Chunhua Weng, George Hripcsak:
A Method for Enhancing the Portability of Electronic Phenotyping Algorithms: An eMERGE Pilot Study. AMIA 2016 - [c54]Ning Shang, George Hripcsak, Patrick B. Ryan, Chunhua Weng:
The Applicability of an EHR Phenotype for Cohort Identification. CRI 2016 - [c53]Anil Yaman, Shreya Chakrabarti, Anando Sen, Chunhua Weng:
How Have Cancer Clinical Trial Eligibility Criteria Evolved Over Time? CRI 2016 - [c52]Yuanjia Wang, Peng Wu, Ying Liu, Chunhua Weng, Donglin Zeng:
Learning Optimal Individualized Treatment Rules from Electronic Health Record Data. ICHI 2016: 65-71 - [c51]Alexander Rusanov, Patric V. Prado, Chunhua Weng:
Unsupervised Time-Series Clustering Over Lab Data for Automatic Identification of Uncontrolled Diabetes. ICHI 2016: 72-80 - [c50]Handong Mao, Chunhua Weng:
Identification of Questionable Exclusion Criteria in Mental Disorder Clinical Trials Using a Medical Encyclopedia. PSB 2016: 219-230 - [e1]Fusheng Wang, Gang Luo, Chunhua Weng, Arijit Khan, Prasenjit Mitra, Cong Yu:
Biomedical Data Management and Graph Online Querying - VLDB 2015 Workshops, Big-O(Q) and DMAH, Waikoloa, HI, USA, August 31 - September 4, 2015, Revised Selected Papers. Lecture Notes in Computer Science 9579, Springer 2016, ISBN 978-3-319-41575-8 [contents] - 2015
- [j26]Riccardo Miotto, Chunhua Weng:
Case-based reasoning using electronic health records efficiently identifies eligible patients for clinical trials. J. Am. Medical Informatics Assoc. 22(e1): e141-e150 (2015) - [j25]Zhe He, Simona Carini, Ida Sim, Chunhua Weng:
Visual aggregate analysis of eligibility features of clinical trials. J. Biomed. Informatics 54: 241-255 (2015) - [j24]Claire L. Gordon, Chunhua Weng:
Combining expert knowledge and knowledge automatically acquired from electronic data sources for continued ontology evaluation and improvement. J. Biomed. Informatics 57: 42-52 (2015) - [c49]Zhe He, Praveen Chandar Ravichandran, Patrick B. Ryan, Chunhua Weng:
Simulation-based Evaluation of the Generalizability Index for Study Traits. AMIA 2015 - [c48]William Brown III, Chunhua Weng, David K. Vawdrey, Alex Carballo-Dieguez, Suzanne Bakken:
Developing an Ontology from HIV-associated Elements in Research. AMIA 2015 - [c47]Gregory William Hruby, Praveen Chandar Ravichandran, Julia Hoxha, Eneida A. Mendonça, David A. Hanauer, Chunhua Weng:
What Are Frequent Data Requests from Researchers? A Conceptual Model of Researchers' EHR Data Needs for Comparative Effectiveness Research. AMIA 2015 - [c46]Vojtech Huser, Alexa T. McCray, Neil R. Smalheiser, Asba Tasneem, Chunhua Weng:
ClinicalTrials.gov: Adding Value through Informatics. AMIA 2015 - [c45]Vojtech Huser, Anil Yaman, Chunhua Weng, James J. Cimino:
ArticlesAboutMe.org: Disseminating Clinical Trials Results to Patients. AMIA 2015 - [c44]Guoqian Jiang, Harold R. Solbrig, Eric Prud'hommeaux, Cui Tao, Chunhua Weng, Christopher G. Chute:
Quality Assurance of Cancer Study Common Data Elements Using A Post-Coordination Approach. AMIA 2015 - [c43]Tian Kang, Noémie Elhadad, Chunhua Weng:
Initial Readability Assessment of Clinical Trial Eligibility Criteria. AMIA 2015 - [c42]Mollie McKillop, Fernanda Polubriaginof, Chunhua Weng:
Exploration of Temporal ICD Coding Bias Related to Acute Diabetic Conditions. AMIA 2015 - [c41]Matthew L. Paulson, Chunhua Weng:
Desiderata for Major Eligibility Criteria in Breast Cancer Clinical Trials. AMIA 2015 - [c40]Praveen Chandar Ravichandran, Anil Yaman, Julia Hoxha, Zhe He, Chunhua Weng:
Similarity-Based Recommendation of New Concepts to a Terminology. AMIA 2015 - [c39]Jeremiah Geronimo Ronquillo, Chunhua Weng, William T. Lester:
Understanding Challenges and Opportunities in Precision Medicine and Interoperability Using Informatics Approaches. AMIA 2015 - [c38]Evelyn Rustia, Chunhua Weng, Carol Friedman:
Representation of Genetic Variants in Genomic Sequencing Reports. AMIA 2015 - [c37]Ning Shang, Chunhua Weng, George Hripcsak:
A Framework for Assessing Clinical Data Suitability for Observational Study. AMIA 2015 - [c36]Nicole Gray Weiskopf, Chunhua Weng:
A Guideline for Assessing EHR Data Quality for Secondary Use. AMIA 2015 - [c35]Zhe He, Shuang Wang, Elhaam Borhanian, Chunhua Weng:
Assessing the Collective Population Representativeness of Related Type 2 Diabetes Trials by Combining Public Data from ClinicalTrials.gov and NHANES. MedInfo 2015: 569-573 - [c34]Gregory William Hruby, Jessica S. Ancker, Chunhua Weng:
Use of Self-Service Query Tools Varies by Experience and Research Knowledge. MedInfo 2015: 1023 - 2014
- [j23]Stephen B. Johnson, Michael E. Bales, Daniel Dine, Suzanne Bakken, Paul J. Albert, Chunhua Weng:
Automatic generation of investigator bibliographies for institutional research networking systems. J. Biomed. Informatics 51: 8-14 (2014) - [j22]Tianyong Hao, Alexander Rusanov, Mary Regina Boland, Chunhua Weng:
Clustering clinical trials with similar eligibility criteria features. J. Biomed. Informatics 52: 112-120 (2014) - [j21]Mary Regina Boland, Alexander Rusanov, Yat So, Carlos Lopez-Jimenez, Linda Busacca, Richard C. Steinman, Suzanne Bakken, J. Thomas Bigger, Chunhua Weng:
From expert-derived user needs to user-perceived ease of use and usefulness: A two-phase mixed-methods evaluation framework. J. Biomed. Informatics 52: 141-150 (2014) - [j20]Michael E. Bales, Daniel C. Dine, Jacqueline A. Merrill, Stephen B. Johnson, Suzanne Bakken, Chunhua Weng:
Associating co-authorship patterns with publications in high-impact journals. J. Biomed. Informatics 52: 311-318 (2014) - [j19]Alexander Rusanov, Nicole Gray Weiskopf, Shuang Wang, Chunhua Weng:
Hidden in plain sight: bias towards sick patients when sampling patients with sufficient electronic health record data for research. BMC Medical Informatics Decis. Mak. 14: 51 (2014) - [c33]Zhe He, Simona Carini, Tianyong Hao, Ida Sim, Chunhua Weng:
A Method for Analyzing Commonalities in Clinical Trial Target Populations. AMIA 2014 - [c32]William Brown III, Chunhua Weng, David K. Vawdrey, Suzanne Bakken:
Integrating Diverse HIV-associated Datasets via Semantic Harmonization. AMIA 2014 - [c31]Daniel Fort, Adam B. Wilcox, Chunhua Weng:
Could Patient Self-reported Health Data Complement EHR for Phenotyping? AMIA 2014 - [c30]David A. Hanauer, Gregory William Hruby, Daniel Fort, Luke V. Rasmussen, Eneida A. Mendonça, Chunhua Weng:
What Is Asked in Clinical Data Request Forms? A Multi-site Thematic Analysis of Forms Towards Better Data Access Support. AMIA 2014 - [c29]Jamie S. Hirsch, Chunhua Weng:
Design and Evaluation of a Glomerular Disease Ontology. AMIA 2014 - [c28]Riccardo Miotto, Chunhua Weng:
Patients Screening for Clinical Trials Using EHR Representation Similarities. AMIA 2014 - [c27]Girish N. Nadkarni, Omri Gottesman, James G. Linneman, Herbert S. Chase, Richard L. Berg, Samira Farouk, Vaneet Lotay, Stephen B. Ellis, George Hripcsak, Peggy L. Peissig, Chunhua Weng, Rajiv Nadukuru, Erwin P. Bottinger:
Development and validation of an electronic phenotyping algorithm for chronic kidney disease. AMIA 2014 - [c26]Chin S. Park, Jacqueline Merrill, Chunhua Weng:
Network Analysis of Common Eligibility Criteria in Cancer Clinical Trials. AMIA 2014 - [c25]Patric V. Prado, Chunhua Weng:
Unsupervised Time-Series Clustering for Identifying Uncontrolled Type-2 Diabetic Patients. AMIA 2014 - [c24]Chunhua Weng, Anil Yaman, Kuo Lin, Zhe He:
Trend and Network Analysis of Common Eligibility Features for Cancer Trials in ClinicalTrials.gov. ICSH 2014: 130-141 - [c23]Chunhua Weng, Philip R. O. Payne, Mark Velez, Stephen B. Johnson, Suzanne Bakken:
Towards Symbiosis in Knowledge Representation and Natural Language Processing for Structuring Clinical Practice Guidelines. Nursing Informatics 2014: 461-469 - [c22]Guoqian Jiang, Deepak K. Sharma, Harold R. Solbrig, Cui Tao, Chunhua Weng, Christopher G. Chute:
Building a Semantic Web-based Metadata Repository for Facilitating Detailed Clinical Modeling in Cancer Genome Studies. SWAT4LS 2014 - 2013
- [j18]Nicole Gray Weiskopf, Chunhua Weng:
Methods and dimensions of electronic health record data quality assessment: enabling reuse for clinical research. J. Am. Medical Informatics Assoc. 20(1): 144-151 (2013) - [j17]Gregory William Hruby, James McKiernan, Suzanne Bakken, Chunhua Weng:
A centralized research data repository enhances retrospective outcomes research capacity: a case report. J. Am. Medical Informatics Assoc. 20(3): 563-567 (2013) - [j16]Zhihui Luo, Riccardo Miotto, Chunhua Weng:
A human-computer collaborative approach to identifying common data elements in clinical trial eligibility criteria. J. Biomed. Informatics 46(1): 33-39 (2013) - [j15]Chunhua Weng, Yu Li, Solomon Berhe, Mary Regina Boland, Junfeng Gao, Gregory William Hruby, Richard C. Steinman, Carlos Lopez-Jimenez, Linda Busacca, George Hripcsak, Suzanne Bakken, J. Thomas Bigger:
An Integrated Model for Patient Care and Clinical Trials (IMPACT) to support clinical research visit scheduling workflow for future learning health systems. J. Biomed. Informatics 46(4): 642-652 (2013) - [j14]Nicole Gray Weiskopf, George Hripcsak, Sushmita Swaminathan, Chunhua Weng:
Defining and measuring completeness of electronic health records for secondary use. J. Biomed. Informatics 46(5): 830-836 (2013) - [j13]Riccardo Miotto, Silis Y. Jiang, Chunhua Weng:
eTACTS: A method for dynamically filtering clinical trial search results. J. Biomed. Informatics 46(6): 1060-1067 (2013) - [j12]Riccardo Miotto, Chunhua Weng:
Unsupervised mining of frequent tags for clinical eligibility text indexing. J. Biomed. Informatics 46(6): 1145-1151 (2013) - [c21]Claire L. Gordon, Stephanie Pouch, Lindsay G. Cowell, Mary Regina Boland, Heather L. Platt, Albert Goldfain, Chunhua Weng:
Design and Evaluation of a Bacterial Clinical Infectious Diseases Ontology. AMIA 2013 - [c20]Riccardo Miotto, Chunhua Weng:
eTACTS: an Eligibility Tag Cloud-based Clinical Trial Search Engine. AMIA 2013 - [c19]Nicole Gray Weiskopf, Alex Rusanov, Chunhua Weng:
Sick Patients Have More Data: The Non-Random Completeness of Electronic Health Records. AMIA 2013 - [c18]Chunhua Weng, Michael N. Cantor, Adel Taweel, Theodoros N. Arvanitis, Rebecca Daniels Kush:
Towards Computational Reuse of Clinical Research Eligibility Criteria with Collaboration across Academia, Industry, and Standardization Organizations. AMIA 2013 - [c17]Chunhua Weng, Yu Li, George Hripcsak, Yuan Zhang, Jie Gao, Feng Liu, J. Thomas Bigger:
Using Electronic Health Records To Assess Generalizability of Clinical Trials. AMIA 2013 - [c16]Tianyong Hao, Alex Rusanov, Chunhua Weng:
Extracting and Normalizing Temporal Expressions in Clinical Data Requests from Researchers. ICSH 2013: 41-51 - [c15]Mary Regina Boland, Riccardo Miotto, Chunhua Weng:
A Method for Probing Disease Relatedness Using Common Clinical Eligibility Criteria. MedInfo 2013: 481-485 - [c14]Drashko Nakikj, Chunhua Weng:
Extending VIVO Ontology to Represent Research and Educational Resources in an Academic Biomedical Informatics Department. MedInfo 2013: 1206 - 2012
- [j11]Chunhua Weng, Paul Appelbaum, George Hripcsak, Ian Kronish, Linda Busacca, Karina W. Davidson, J. Thomas Bigger:
Using EHRs to integrate research with patient care: promises and challenges. J. Am. Medical Informatics Assoc. 19(5): 684-687 (2012) - [j10]Michael G. Kahn, Chunhua Weng:
Clinical research informatics: a conceptual perspective. J. Am. Medical Informatics Assoc. 19(e1) (2012) - [c13]Suzanne Bakken, J. Thomas Bigger, Bernadette Boden-Albala, Penny Feldman, Kathleen Gallagher, Peter D. Stetson, Chunhua Weng, Adam B. Wilcox:
Establishing Data Governance for Comparative Effectiveness Research: Experience of the Washington Heights Inwood Informatics Infrastructure for Comparative Effectiveness Research (WICER). AMIA 2012 - [c12]Gregory William Hruby, Adam B. Wilcox, Chunhua Weng:
Analysis of Query Negotiation between a Researcher and a Query Expert. AMIA 2012 - [c11]Nanfang Xu, Chunhua Weng:
An ontology-based Clinical Phenotyping Framework For eMERGE Network Algorithms. AMIA 2012 - 2011
- [j9]Chunhua Weng, Xiaoying Wu, Zhihui Luo, Mary Regina Boland, Dimitri Theodoratos, Stephen B. Johnson:
EliXR: an approach to eligibility criteria extraction and representation. J. Am. Medical Informatics Assoc. 18(Supplement): 116-124 (2011) - [j8]Di Zhao, Chunhua Weng:
Combining PubMed knowledge and EHR data to develop a weighted bayesian network for pancreatic cancer prediction. J. Biomed. Informatics 44(5): 859-868 (2011) - [j7]Zhihui Luo, Meliha Yetisgen-Yildiz, Chunhua Weng:
Dynamic categorization of clinical research eligibility criteria by hierarchical clustering. J. Biomed. Informatics 44(6): 927-935 (2011) - 2010
- [j6]Chunhua Weng, Samson W. Tu, Ida Sim, Rachel L. Richesson:
Formal representation of eligibility criteria: A literature review. J. Biomed. Informatics 43(3): 451-467 (2010)
2000 – 2009
- 2009
- [j5]Samir R. Thadani, Chunhua Weng, J. Thomas Bigger, John F. Ennever, David Wajngurt:
Case Report: Electronic Screening Improves Efficiency in Clinical Trial Recruitment. J. Am. Medical Informatics Assoc. 16(6): 869-873 (2009) - [j4]Xinxin Zhu, Jungwei Fan, David M. Baorto, Chunhua Weng, James J. Cimino:
A review of auditing methods applied to the content of controlled biomedical terminologies. J. Biomed. Informatics 42(3): 413-425 (2009) - [r4]Chintan Patel, Chunhua Weng:
Clinical Data and Information Models. Encyclopedia of Database Systems 2009: 348-349 - [r3]Chintan Patel, Chunhua Weng:
Clinical Data Quality and Validation. Encyclopedia of Database Systems 2009: 349-350 - [r2]Chintan Patel, Chunhua Weng:
Quality and Trust of Information Content and Credentialing. Encyclopedia of Database Systems 2009: 2229-2230 - [r1]Chintan Patel, Chunhua Weng:
Reference Knowledge. Encyclopedia of Database Systems 2009: 2360 - 2008
- [c10]Li Li, Herbert S. Chase, Chintan Patel, Carol Friedman, Chunhua Weng:
Comparing ICD9-Encoded Diagnoses and NLP-Processed Discharge Summaries for Clinical Trials Pre-Screening: A Case Study. AMIA 2008 - [c9]Chunhua Weng, Dympna Gallagher, Michael E. Bales, Suzanne Bakken, Henry N. Ginsberg:
Understanding Interdisciplinary Health Sciences Collaborations: A Campus-Wide Survey of Obesity Experts. AMIA 2008 - 2007
- [j3]Chunhua Weng, David W. McDonald, Dana Sparks, Jason McCoy, John H. Gennari:
Participatory design of a collaborative clinical trial protocol writing system. Int. J. Medical Informatics 76(S1): S245-S251 (2007) - [j2]Chunhua Weng, John H. Gennari, Douglas B. Fridsma:
User-centered semantic harmonization: A case study. J. Biomed. Informatics 40(3): 353-364 (2007) - 2006
- [c8]Chunhua Weng, Douglas B. Fridsma:
A Call for Collaborative Semantic Harmonization. AMIA 2006 - 2005
- [j1]John H. Gennari, Chunhua Weng, Jacqueline Benedetti, David W. McDonald:
Asynchronous communication among clinical researchers: A study for systems design. Int. J. Medical Informatics 74(10): 797-807 (2005) - [c7]Chunhua Weng:
Why It Is Hard to Support Group Work in Distributed Healthcare Organizations: Empirical Knowledge of the Social-Technical Gap. AMIA 2005 - 2004
- [c6]David W. McDonald, Chunhua Weng, John H. Gennari:
The multiple views of inter-organizational authoring. CSCW 2004: 564-573 - [c5]Chunhua Weng, John H. Gennari:
Asynchronous collaborative writing through annotations. CSCW 2004: 578-581 - [c4]John H. Gennari, Chunhua Weng, David W. McDonald, Jacqueline Benedetti, Stephanie Green:
An Ethnographic Study of Collaborative Clinical Trial Protocol Writing. MedInfo 2004: 1461-1465 - [c3]Chunhua Weng, John H. Gennari, David W. McDonald:
A Collaborative Clinical Trial Protocol Writing System. MedInfo 2004: 1481-1485 - 2003
- [c2]Chunhua Weng, John H. Gennari, David W. McDonald:
Scenario-based Participatory Design of A Collaborative Clinical Trial Protocol Authoring System. AMIA 2003 - 2002
- [c1]Chunhua Weng, Michael G. Kahn, John H. Gennari:
Temporal knowledge representation for scheduling tasks in clinical trial protocols. AMIA 2002
Coauthor Index
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