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2020 – today
- 2024
[j18]Sunyang Fu
, Liwei Wang, Huan He, Andrew Wen, Nansu Zong, Anamika Kumari, Feifan Liu, Sicheng Zhou, Rui Zhang, Chenyu Li, Yanshan Wang, Jennifer St Sauver, Hongfang Liu, Sunghwan Sohn:
A taxonomy for advancing systematic error analysis in multi-site electronic health record-based clinical concept extraction. J. Am. Medical Informatics Assoc. 31(7): 1493-1502 (2024)- [j17]Shaika Chowdhury, Yongbin Chen, Pengyang Li, Sivaraman Rajaganapathy, Andrew Wen, Xiao Ma, Qiying Dai, Yue Yu, Sunyang Fu, Xiaoqian Jiang, Zhe He, Sunghwan Sohn, Xiaoke Liu, Suzette J. Bielinski, Alanna M. Chamberlain, James R. Cerhan, Nansu Zong:
Stratifying heart failure patients with graph neural network and transformer using Electronic Health Records to optimize drug response prediction. J. Am. Medical Informatics Assoc. 31(8): 1671-1681 (2024) - [j16]Sunyang Fu, Heling Jia, Maria Vassilaki, Vipina Kuttichi Keloth, Yifang Dang, Yujia Zhou, Muskan Garg, Ronald C. Petersen, Jennifer St Sauver, Sungrim Moon, Liwei Wang, Andrew Wen, Fang Li, Hua Xu, Cui Tao, Jungwei Fan, Hongfang Liu, Sunghwan Sohn:
FedFSA: Hybrid and federated framework for functional status ascertainment across institutions. J. Biomed. Informatics 152: 104623 (2024) - [i9]Qiuhao Lu, Rui Li, Andrew Wen, Jinlian Wang, Liwei Wang, Hongfang Liu:
Large Language Models Struggle in Token-Level Clinical Named Entity Recognition. CoRR abs/2407.00731 (2024) - [i8]Qiuhao Lu, Rui Li, Elham Sagheb, Andrew Wen, Jinlian Wang, Liwei Wang, Jungwei W. Fan, Hongfang Liu:
Explainable Diagnosis Prediction through Neuro-Symbolic Integration. CoRR abs/2410.01855 (2024) - 2023
- [j15]Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert T. Miller, Andrew E. Williams, Daniel R. Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-El-Rub, Dalton Schutte, Rui Zhang, Masoud Rouhizadeh, John D. Osborne, Yongqun He, Umit Topaloglu, Stephanie S. Hong, Joel H. Saltz, Thomas Schaffter, Emily R. Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu:
An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C). J. Am. Medical Informatics Assoc. 30(12): 2036-2040 (2023) - [j14]Andrew Wen, Huan He, Sunyang Fu, Sijia Liu, Kurt Miller, Liwei Wang, Kirk E. Roberts, Steven Bedrick, William R. Hersh, Hongfang Liu:
The IMPACT framework and implementation for accessible in silico clinical phenotyping in the digital era. npj Digit. Medicine 6 (2023) - [c26]Rui Li, Andrew Wen, Jing Gao, Hongfang Liu:
MLGAN: a Meta-Learning based Generative Adversarial Network adapter for rare disease differentiation tasks. BCB 2023: 11:1-11:10 - 2022
- [j13]Nansu Zong, Ning Li, Andrew Wen, Victoria Ngo, Yue Yu, Ming Huang, Shaika Chowdhury, Chao Jiang, Sunyang Fu, Richard Weinshilboum, Guoqian Jiang, Lawrence Hunter, Hongfang Liu:
BETA: a comprehensive benchmark for computational drug-target prediction. Briefings Bioinform. 23(4) (2022) - [j12]Huan He, Sunyang Fu, Liwei Wang, Sijia Liu, Andrew Wen, Hongfang Liu:
MedTator: a serverless annotation tool for corpus development. Bioinform. 38(6): 1776-1778 (2022) - [j11]Sunyang Fu, Bjoerg Thorsteinsdottir, Xin Zhang, Guilherme S. Lopes, Sandeep R. Pagali, Nathan K. LeBrasseur, Andrew Wen, Hongfang Liu, Walter A. Rocca, Janet E. Olson, Jennifer St. Sauver, Sunghwan Sohn:
A hybrid model to identify fall occurrence from electronic health records. Int. J. Medical Informatics 162: 104736 (2022) - [j10]Yue Yu, Nansu Zong, Andrew Wen, Sijia Liu, Daniel J. Stone, David Knaack, Alanna M. Chamberlain, Emily R. Pfaff, Davera Gabriel, Christopher G. Chute, Nilay Shah, Guoqian Jiang:
Developing an ETL tool for converting the PCORnet CDM into the OMOP CDM to facilitate the COVID-19 data integration. J. Biomed. Informatics 127: 104002 (2022) - [j9]Nansu Zong, Andrew Wen, Sungrim Moon, Sunyang Fu, Liwei Wang, Yiqing Zhao, Yue Yu, Ming Huang, Yanshan Wang, Gang Zheng, Michelle M. Mielke, James R. Cerhan, Hongfang Liu:
Computational drug repurposing based on electronic health records: a scoping review. npj Digit. Medicine 5 (2022) - [c25]Huan He, Sunyang Fu, Liwei Wang, Andrew Wen, Sijia Liu, Sungrim Moon, Kurt Miller, Hongfang Liu:
Towards User-centered Corpus Development: Lessons Learnt from Designing and Developing MedTator. AMIA 2022 - [c24]Liwei Wang, Sunyang Fu, Andrew Wen, Xiaoyang Ruan, Huan He, Sijia Liu, Sungrim Moon, Michelle Mai, Irbaz Bin Riaz, Nan Wang, Ping Yang, Hua Xu, Jeremy L. Warner, Hongfang Liu:
Evaluation of mCODE Coverage in EHR: a Scoping Review of Cancer Natural Language Processing. ICHI 2022: 517-518 - [c23]Huan He, Sunyang Fu, Liwei Wang, Andrew Wen, Sijia Liu, Hongfang Liu:
MedTator: A Serverless Web-based Tool for Corpus Annotation. ICHI 2022: 530-531 - 2021
- [j8]Nansu Zong, Rachael Sze Nga Wong, Yue Yu, Andrew Wen, Ming Huang, Ning Li:
Drug-target prediction utilizing heterogeneous bio-linked network embeddings. Briefings Bioinform. 22(1): 568-580 (2021) - [j7]Nansu Zong, Daniel J. Stone, Deepak K. Sharma, Andrew Wen, Chen Wang, Yue Yu, Ming Huang, Sijia Liu, Hongfang Liu, Qian Shi, Guoqian Jiang:
Modeling cancer clinical trials using HL7 FHIR to support downstream applications: A case study with colorectal cancer data. Int. J. Medical Informatics 145: 104308 (2021) - [j6]Andrew Wen, Liwei Wang, Huan He, Sijia Liu, Sunyang Fu, Sunghwan Sohn, Jacob A. Kugel, Vinod C. Kaggal, Ming Huang, Yanshan Wang, Feichen Shen, Jungwei Fan, Hongfang Liu:
An aberration detection-based approach for sentinel syndromic surveillance of COVID-19 and other novel influenza-like illnesses. J. Biomed. Informatics 113: 103660 (2021) - [c22]Ming Huang, Aditya Khurana, George M. Mastorakos, Andrew Wen, Huan He, Liwei Wang, Sijia Liu, Yanshan Wang, Julie E. Prigge, Brian Costello, Nilay D. Shah, Henry Ting, Christi A. Patten, Jungwei Fan, Hongfang Liu:
Patient Asynchronous Response to Coronavirus Disease 2019 (COVID-19): A Retrospective Analysis of Patient Portal Messages. AMIA 2021 - [c21]Huan He, Liwei Wang, Andrew Wen, Ming Huang, Yanshan Wang, Hongfang Liu:
COVID-19 Dashboard: Visual Exploration of the Regional Pandemic Trend. AMIA 2021 - [c20]Ming Huang, Andrew Wen, Huan He, Liwei Wang, Sijia Liu, Yanshan Wang, Nansu Zong, Yue Yu, Julie E. Prigge, Brian Costello, Nilay D. Shah, Henry Ting, Chyke Doubeni, Jungwei Fan, Hongfang Liu, Christi A. Patten:
Disparity analysis of patient portal messaging use for COVID-19 in urban versus rural locality. AMIA 2021 - [c19]Daniel J. Stone, Sijia Liu, Yuan Luo, Andrew Wen, Nansu Zong, Luke V. Rasmussen, Prakash Adekkanattu, Pascal S. Brandt, Jennifer A. Pacheco, Fei Wang, Cui Tao, Jyotishman Pathak, Hongfang Liu, Guoqian Jiang:
FHIRTime: Standardizing Temporal Patterns Identified from Clinical Narratives Using HL7 FHIR. AMIA 2021 - [c18]Andrew Wen, Luke V. Rasmussen, Daniel J. Stone, Sijia Liu, Prakash Adekkanattu, Pascal S. Brandt, Jennifer A. Pacheco, Yuan Luo, Fei Wang, Jyotishman Pathak, Hongfang Liu, Guoqian Jiang:
On Constraints and Considerations for Extending Support for Natural Language Processing-Based FHIR Resource Generation. AMIA 2021 - [c17]Sunyang Fu, Andrew Wen, Sandeep R. Pagali, Nansu Zong, Jennifer St Sauver, Sunghwan Sohn, Jungwei Fan, Hongfang Liu:
The Implication of Latent Information Quality to the Reproducibility of Secondary Use of Electronic Health Records. MedInfo 2021: 173-177 - [i7]David Oniani, Chen Wang, Yiqing Zhao, Andrew Wen, Hongfang Liu, Feichen Shen:
Comparisons of Graph Neural Networks on Cancer Classification Leveraging a Joint of Phenotypic and Genetic Features. CoRR abs/2101.05866 (2021) - [i6]David Oniani, Chen Wang, Yiqing Zhao, Andrew Wen, Hongfang Liu, Feichen Shen:
Leveraging a Joint of Phenotypic and Genetic Features on Cancer Patient Subgrouping. CoRR abs/2103.16316 (2021) - [i5]Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert T. Miller, Andrew E. Williams, Daniel R. Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-El-Rub, Rui Zhang, John D. Osborne, Masoud Rouhizadeh, Yongqun He, Emily R. Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu:
An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C). CoRR abs/2110.10780 (2021) - 2020
- [j5]Sunyang Fu, David Chen, Huan He, Sijia Liu, Sungrim Moon, Kevin J. Peterson, Feichen Shen, Liwei Wang, Yanshan Wang, Andrew Wen, Yiqing Zhao, Sunghwan Sohn, Hongfang Liu:
Clinical concept extraction: A methodology review. J. Biomed. Informatics 109: 103526 (2020) - [c16]Sijia Liu, Sunyang Fu, Sungrim Moon, Andrew Wen, Hongfang Liu:
Predicting Section Location of Clinical Sentences using BERT Encoder - A Pilot Study. AMIA 2020 - [c15]Mohamed Y. Elwazir, Andrew Wen, Sungrim Moon, Jungwei Fan:
A Perturbation Approach to Assessing BERT Robustness for Different Linguistic Aspects in Medical Question-Answering. AMIA 2020 - [c14]Andrew Wen, Sunyang Fu, Feichen Shen, Hongfang Liu:
Accelerating Development of Learning Healthcare Systems via Distantly Supervised Knowledge Discovery. AMIA 2020 - [c13]Feichen Shen, Andrew Wen, Hongfang Liu:
Enrich Rare Disease Phenotypic Characterizations via a Graph Convolutional Network Based Recommendation System. CBMS 2020: 37-40 - [c12]Feichen Shen, Andrew Wen, Hongfang Liu:
Subgrouping Rare Disease Patients Leveraging the Human Phenotype Ontology Embeddings. CBMS 2020: 169-172 - [c11]Andrew Wen, Feichen Shen, Sungrim Moon, Hongfang Liu, Jungwei Fan:
A Deep Profiling and Visualization Framework to Audit Clinical Assessment Variation. CBMS 2020: 546-551 - [c10]Steve Chamberlin, Steven Bedrick, Aaron M. Cohen, Yanshan Wang, Andrew Wen, Sijia Liu, Hongfang Liu, William R. Hersh:
A Query Taxonomy Describes Performance of Patient-Level Retrieval from Electronic Health Record Data. HSDM@WSDM 2020: 27-33
2010 – 2019
- 2019
- [j4]Yue Yu, Kathryn J. Ruddy, Na Hong, Shintaro Tsuji, Andrew Wen, Nilay D. Shah, Guoqian Jiang:
ADEpedia-on-OHDSI: A next generation pharmacovigilance signal detection platform using the OHDSI common data model. J. Biomed. Informatics 91 (2019) - [j3]Feichen Shen, Suyuan Peng, Yadan Fan, Andrew Wen, Sijia Liu, Yanshan Wang, Liwei Wang, Hongfang Liu:
HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology. J. Biomed. Informatics 96 (2019) - [j2]Na Hong, Andrew Wen, Daniel J. Stone, Shintaro Tsuji, Paul R. Kingsbury, Luke V. Rasmussen, Jennifer A. Pacheco, Prakash Adekkanattu, Fei Wang, Yuan Luo, Jyotishman Pathak, Hongfang Liu, Guoqian Jiang:
Developing a FHIR-based EHR phenotyping framework: A case study for identification of patients with obesity and multiple comorbidities from discharge summaries. J. Biomed. Informatics 99 (2019) - [j1]Andrew Wen, Sunyang Fu, Sungrim Moon, Mohamed El Wazir, Andrew Rosenbaum, Vinod C. Kaggal, Sijia Liu, Sunghwan Sohn, Hongfang Liu, Jungwei Fan:
Desiderata for delivering NLP to accelerate healthcare AI advancement and a Mayo Clinic NLP-as-a-service implementation. npj Digit. Medicine 2 (2019) - [c9]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 - [c8]Andrew Wen, Yanshan Wang, Vinod C. Kaggal, Sijia Liu, Hongfang Liu, Jungwei Fan:
Enhancing Clinical Information Retrieval through Context-Aware Queries and Indices. IEEE BigData 2019: 2800-2807 - [i4]Sijia Liu, Yanshan Wang, Andrew Wen, Liwei Wang, Na Hong, Feichen Shen, Steven Bedrick, William R. Hersh, Hongfang Liu:
CREATE: Cohort Retrieval Enhanced by Analysis of Text from Electronic Health Records using OMOP Common Data Model. CoRR abs/1901.07601 (2019) - [i3]Jun Jiang, Shumao Pang, Xia Zhao, Liwei Wang, Andrew Wen, Hongfang Liu, Qianjin Feng:
Cross-lingual Data Transformation and Combination for Text Classification. CoRR abs/1906.09543 (2019) - [i2]Sunyang Fu, David Chen, Sijia Liu, Sungrim Moon, Kevin J. Peterson, Feichen Shen, Yanshan Wang, Liwei Wang, Andrew Wen, Yiqing Zhao, Sunghwan Sohn, Hongfang Liu:
Development of Clinical Concept Extraction Applications: A Methodology Review. CoRR abs/1910.11377 (2019) - [i1]Andrew Wen, Mohamed Y. Elwazir, Sungrim Moon, Jungwei Fan:
Adapting and evaluating a deep learning language model for clinical why-question answering. CoRR abs/1911.05604 (2019) - 2018
- [c7]Na Hong, Andrew Wen, Majid Rastegar-Mojarad, Sunghwan Sohn, Hongfang Liu, Guoqian Jiang:
Standardizing Heterogeneous Annotation Corpora Using HL7 FHIR for Facilitating their Reuse and Integration in Clinical NLP. AMIA 2018 - [c6]Shintaro Tsuji, Andrew Wen, Guoqian Jiang:
Developing a RadLex-based Name Entity Recognition Tool for Mining Free-Text Radiology Reports. AMIA 2018 - [c5]Yanshan Wang, Andrew Wen, Sijia Liu, Hongfang Liu:
EMIRS: An Electronic Medical Information Retrieval System by Leveraging both Structured and Unstructured Electronic Health Records. AMIA 2018 - [c4]Su-Yuan Peng, Yadan Fan, Liwei Wang, Andrew Wen, Xusheng Liu, Hongfang Liu, Feichen Shen:
Leveraging Association Rule Mining to Detect Pathophysiological Mechanisms of Chronic Kidney Disease Complicated by Metabolic Syndrome. BIBM 2018: 1302-1309 - [c3]Feichen Shen, Sijia Liu, Yanshan Wang, Liwei Wang, Andrew Wen, Andrew H. Limper, Hongfang Liu:
Constructing Node Embeddings for Human Phenotype Ontology to Assist Phenotypic Similarity Measurement. ICHI Workshops 2018: 29-33 - [c2]Yanshan Wang, Andrew Wen, Sijia Liu, Hongfang Liu:
MayoNLPTeam at the TREC 2018 Precision Medicine Track: Simple Information Retrieval Approach Is the Best. TREC 2018 - 2017
- [c1]Stephen T. Wu, Andrew Wen, Yanshan Wang, Sijia Liu, Hongfang Liu:
Aligned-Layer Text Search in Clinical Notes. MedInfo 2017: 629-633
Coauthor Index
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