Andrew Wen - RankMe

65 papers B 3Misc 13Journal 37Unranked 12

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Clinical Document Metadata Extraction: A Scoping Review. CoRR Kurt Miller, Qiuhao Lu, William R. Hersh, Kirk Roberts, Steven Bedrick, Andrew Wen, Hongfang Liu
2026	J	`jnl`	Context matching is not reasoning when performing generalized clinical evaluation of generative language models. npj Digit. Medicine Andrew Wen, Qiuhao Lu, Yu-Neng Chuang, Guanchu Wang, Jiayi Yuan, Jiamu Zhang, Liwei Wang, Sunyang Fu, Kurt Miller, Heling Jia, Stephen Bedrick, William R. Hersh, Kirk E. Roberts, Xia (Ben) Hu, Hongfang Liu
2026	—	`conf`	FaithLM: Towards Faithful Explanations for Large Language Models. EACL (Volume 1: Long Papers) Yu-Neng Chuang, Guanchu Wang, Chia-Yuan Chang, Ruixiang Tang, Shaochen Zhong, Fan Yang, Andrew Wen, Mengnan Du, Xuanting Cai, Vladimir Braverman, Xia Hu
2025	J	`jnl`	A scoping review of OMOP CDM adoption for cancer research using real world data. npj Digit. Medicine Liwei Wang, Andrew Wen, Sunyang Fu, Xiaoyang Ruan, Ming Huang, Rui Li, Qiuhao Lu, Heather Lyu, Andrew E. Williams, Hongfang Liu
2025	J	`jnl`	An Agentic Model Context Protocol Framework for Medical Concept Standardization. CoRR Jaerong Ahn, Andrew Wen, Nan Wang, Heling Jia, Zhiyi Yue, Sunyang Fu, Hongfang Liu
2025	J	`jnl`	Discovering signature disease trajectories in pancreatic cancer and soft-tissue sarcoma from longitudinal patient records. J. Biomed. Informatics Liwei Wang, Rui Li, Andrew Wen, Qiuhao Lu, Jinlian Wang, Xiaoyang Ruan, Adriana Gamboa, Neha Malik, Christina L. Roland, Matthew H. G. Katz, Heather Lyu, Hongfang Liu
2025	J	`jnl`	Dynamic few-shot prompting for clinical note section classification using lightweight, open-source large language models. J. Am. Medical Informatics Assoc. Kurt Miller, Steven Bedrick, Qiuhao Lu, Andrew Wen, William R. Hersh, Kirk Roberts, Hongfang Liu
2025	J	`jnl`	Multi-Label Classification with Generative AI Models in Healthcare: A Case Study of Suicidality and Risk Factors. CoRR Ming Huang, Zehan Li, Yan Hu, Wanjing Wang, Andrew Wen, Scott Lane, Salih Selek, Lokesh Shahani, Rodrigo Machado-Vieira, Jair Soares, Hua Xu, Hongfang Liu
2025	—	`conf`	ReasonerRank: Redefining Language Model Evaluation with Ground-Truth-Free Ranking Frameworks. ACL (Findings) Jiamu Zhang, Jiayi Yuan, Andrew Wen, Hoang Anh Duy Le, Yu-Neng Chuang, Soo-Hyun Choi, Rui Chen, Xia Hu
2025	J	`jnl`	Stop Overthinking: A Survey on Efficient Reasoning for Large Language Models. CoRR Yang Sui, Yu-Neng Chuang, Guanchu Wang, Jiamu Zhang, Tianyi Zhang, Jiayi Yuan, Hongyi Liu, Andrew Wen, Shaochen Zhong, Hanjie Chen, Xia Ben Hu
2025	J	`jnl`	Stop Overthinking: A Survey on Efficient Reasoning for Large Language Models. Trans. Mach. Learn. Res. Yang Sui, Yu-Neng Chuang, Guanchu Wang, Jiamu Zhang, Tianyi Zhang, Jiayi Yuan, Hongyi Liu, Andrew Wen, Shaochen Zhong, Na Zou, Hanjie Chen, Xia Hu
2025	J	`jnl`	The Science of Evaluating Foundation Models. CoRR Jiayi Yuan, Jiamu Zhang, Andrew Wen, Xia Hu
2024	J	`jnl`	A taxonomy for advancing systematic error analysis in multi-site electronic health record-based clinical concept extraction. J. Am. Medical Informatics Assoc. 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
2024	J	`jnl`	Explainable Diagnosis Prediction through Neuro-Symbolic Integration. CoRR Qiuhao Lu, Rui Li, Elham Sagheb, Andrew Wen, Jinlian Wang, Liwei Wang, Jungwei W. Fan, Hongfang Liu
2024	J	`jnl`	FedFSA: Hybrid and federated framework for functional status ascertainment across institutions. J. Biomed. Informatics 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
2024	J	`jnl`	Large Language Models Struggle in Token-Level Clinical Named Entity Recognition. CoRR Qiuhao Lu, Rui Li, Andrew Wen, Jinlian Wang, Liwei Wang, Hongfang Liu
2024	J	`jnl`	Stratifying heart failure patients with graph neural network and transformer using Electronic Health Records to optimize drug response prediction. J. Am. Medical Informatics Assoc. 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
2023	J	`jnl`	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. 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
2023	—	`conf`	MLGAN: a Meta-Learning based Generative Adversarial Network adapter for rare disease differentiation tasks. BCB Rui Li, Andrew Wen, Jing Gao, Hongfang Liu
2023	J	`jnl`	The IMPACT framework and implementation for accessible in silico clinical phenotyping in the digital era. npj Digit. Medicine Andrew Wen, Huan He, Sunyang Fu, Sijia Liu, Kurt Miller, Liwei Wang, Kirk E. Roberts, Steven Bedrick, William R. Hersh, Hongfang Liu
2022	J	`jnl`	A hybrid model to identify fall occurrence from electronic health records. Int. J. Medical Informatics 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
2022	J	`jnl`	BETA: a comprehensive benchmark for computational drug-target prediction. Briefings Bioinform. 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
2022	J	`jnl`	Computational drug repurposing based on electronic health records: a scoping review. npj Digit. Medicine 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
2022	J	`jnl`	Developing an ETL tool for converting the PCORnet CDM into the OMOP CDM to facilitate the COVID-19 data integration. J. Biomed. Informatics 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
2022	—	`conf`	Evaluation of mCODE Coverage in EHR: a Scoping Review of Cancer Natural Language Processing. ICHI 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
2022	—	`conf`	MedTator: A Serverless Web-based Tool for Corpus Annotation. ICHI Huan He, Sunyang Fu, Liwei Wang, Andrew Wen, Sijia Liu, Hongfang Liu
2022	J	`jnl`	MedTator: a serverless annotation tool for corpus development. Bioinform. Huan He, Sunyang Fu, Liwei Wang, Sijia Liu, Andrew Wen, Hongfang Liu
2022	Misc	`conf`	Towards User-centered Corpus Development: Lessons Learnt from Designing and Developing MedTator. AMIA Huan He, Sunyang Fu, Liwei Wang, Andrew Wen, Sijia Liu, Sungrim Moon, Kurt Miller, Hongfang Liu
2021	J	`jnl`	An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C). CoRR 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
2021	J	`jnl`	An aberration detection-based approach for sentinel syndromic surveillance of COVID-19 and other novel influenza-like illnesses. J. Biomed. Informatics 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
2021	Misc	`conf`	COVID-19 Dashboard: Visual Exploration of the Regional Pandemic Trend. AMIA Huan He, Liwei Wang, Andrew Wen, Ming Huang, Yanshan Wang, Hongfang Liu
2021	J	`jnl`	Comparisons of Graph Neural Networks on Cancer Classification Leveraging a Joint of Phenotypic and Genetic Features. CoRR David Oniani, Chen Wang, Yiqing Zhao, Andrew Wen, Hongfang Liu, Feichen Shen
2021	Misc	`conf`	Disparity analysis of patient portal messaging use for COVID-19 in urban versus rural locality. AMIA 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
2021	J	`jnl`	Drug-target prediction utilizing heterogeneous bio-linked network embeddings. Briefings Bioinform. Nansu Zong, Rachael Sze Nga Wong, Yue Yu, Andrew Wen, Ming Huang, Ning Li
2021	Misc	`conf`	FHIRTime: Standardizing Temporal Patterns Identified from Clinical Narratives Using HL7 FHIR. AMIA 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
2021	J	`jnl`	Leveraging a Joint of Phenotypic and Genetic Features on Cancer Patient Subgrouping. CoRR David Oniani, Chen Wang, Yiqing Zhao, Andrew Wen, Hongfang Liu, Feichen Shen
2021	J	`jnl`	Modeling cancer clinical trials using HL7 FHIR to support downstream applications: A case study with colorectal cancer data. Int. J. Medical Informatics Nansu Zong, Daniel J. Stone, Deepak K. Sharma, Andrew Wen, Chen Wang, Yue Yu, Ming Huang, Sijia Liu, Hongfang Liu, Qian Shi, Guoqian Jiang
2021	Misc	`conf`	On Constraints and Considerations for Extending Support for Natural Language Processing-Based FHIR Resource Generation. AMIA 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
2021	Misc	`conf`	Patient Asynchronous Response to Coronavirus Disease 2019 (COVID-19): A Retrospective Analysis of Patient Portal Messages. AMIA 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
2021	—	`conf`	The Implication of Latent Information Quality to the Reproducibility of Secondary Use of Electronic Health Records. MedInfo Sunyang Fu, Andrew Wen, Sandeep R. Pagali, Nansu Zong, Jennifer St Sauver, Sunghwan Sohn, Jungwei Fan, Hongfang Liu
2020	B	`conf`	A Deep Profiling and Visualization Framework to Audit Clinical Assessment Variation. CBMS Andrew Wen, Feichen Shen, Sungrim Moon, Hongfang Liu, Jungwei Fan
2020	Misc	`conf`	A Perturbation Approach to Assessing BERT Robustness for Different Linguistic Aspects in Medical Question-Answering. AMIA Mohamed Y. Elwazir, Andrew Wen, Sungrim Moon, Jungwei Fan
2020	—	`conf`	A Query Taxonomy Describes Performance of Patient-Level Retrieval from Electronic Health Record Data. HSDM@WSDM Steve Chamberlin, Steven Bedrick, Aaron M. Cohen, Yanshan Wang, Andrew Wen, Sijia Liu, Hongfang Liu, William R. Hersh
2020	Misc	`conf`	Accelerating Development of Learning Healthcare Systems via Distantly Supervised Knowledge Discovery. AMIA Andrew Wen, Sunyang Fu, Feichen Shen, Hongfang Liu
2020	J	`jnl`	Clinical concept extraction: A methodology review. J. Biomed. Informatics 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
2020	B	`conf`	Enrich Rare Disease Phenotypic Characterizations via a Graph Convolutional Network Based Recommendation System. CBMS Feichen Shen, Andrew Wen, Hongfang Liu
2020	Misc	`conf`	Predicting Section Location of Clinical Sentences using BERT Encoder - A Pilot Study. AMIA Sijia Liu, Sunyang Fu, Sungrim Moon, Andrew Wen, Hongfang Liu
2020	B	`conf`	Subgrouping Rare Disease Patients Leveraging the Human Phenotype Ontology Embeddings. CBMS Feichen Shen, Andrew Wen, Hongfang Liu
2019	J	`jnl`	ADEpedia-on-OHDSI: A next generation pharmacovigilance signal detection platform using the OHDSI common data model. J. Biomed. Informatics Yue Yu, Kathryn J. Ruddy, Na Hong, Shintaro Tsuji, Andrew Wen, Nilay D. Shah, Guoqian Jiang
2019	J	`jnl`	Adapting and evaluating a deep learning language model for clinical why-question answering. CoRR Andrew Wen, Mohamed Y. Elwazir, Sungrim Moon, Jungwei Fan
2019	J	`jnl`	CREATE: Cohort Retrieval Enhanced by Analysis of Text from Electronic Health Records using OMOP Common Data Model. CoRR Sijia Liu, Yanshan Wang, Andrew Wen, Liwei Wang, Na Hong, Feichen Shen, Steven Bedrick, William R. Hersh, Hongfang Liu
2019	Misc	`conf`	Clinical Use of an Information Retrieval Framework for Cohort Discovery from Electronic Health Records. AMIA Yanshan Wang, Andrew Wen, Sijia Liu, Jennifer L. St. Sauver, Adil E. Bharucha, Chunhua Weng, Hongfang Liu
2019	J	`jnl`	Cross-lingual Data Transformation and Combination for Text Classification. CoRR Jun Jiang, Shumao Pang, Xia Zhao, Liwei Wang, Andrew Wen, Hongfang Liu, Qianjin Feng
2019	J	`jnl`	Desiderata for delivering NLP to accelerate healthcare AI advancement and a Mayo Clinic NLP-as-a-service implementation. npj Digit. Medicine Andrew Wen, Sunyang Fu, Sungrim Moon, Mohamed El Wazir, Andrew Rosenbaum, Vinod C. Kaggal, Sijia Liu, Sunghwan Sohn, Hongfang Liu, Jungwei Fan
2019	J	`jnl`	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 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
2019	J	`jnl`	Development of Clinical Concept Extraction Applications: A Methodology Review. CoRR 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
2019	—	`conf`	Enhancing Clinical Information Retrieval through Context-Aware Queries and Indices. IEEE BigData Andrew Wen, Yanshan Wang, Vinod C. Kaggal, Sijia Liu, Hongfang Liu, Jungwei Fan
2019	J	`jnl`	HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology. J. Biomed. Informatics Feichen Shen, Suyuan Peng, Yadan Fan, Andrew Wen, Sijia Liu, Yanshan Wang, Liwei Wang, Hongfang Liu
2018	—	`conf`	Constructing Node Embeddings for Human Phenotype Ontology to Assist Phenotypic Similarity Measurement. ICHI Workshops Feichen Shen, Sijia Liu, Yanshan Wang, Liwei Wang, Andrew Wen, Andrew H. Limper, Hongfang Liu
2018	Misc	`conf`	Developing a RadLex-based Name Entity Recognition Tool for Mining Free-Text Radiology Reports. AMIA Shintaro Tsuji, Andrew Wen, Guoqian Jiang
2018	Misc	`conf`	EMIRS: An Electronic Medical Information Retrieval System by Leveraging both Structured and Unstructured Electronic Health Records. AMIA Yanshan Wang, Andrew Wen, Sijia Liu, Hongfang Liu
2018	—	`conf`	Leveraging Association Rule Mining to Detect Pathophysiological Mechanisms of Chronic Kidney Disease Complicated by Metabolic Syndrome. BIBM Su-Yuan Peng, Yadan Fan, Liwei Wang, Andrew Wen, Xusheng Liu, Hongfang Liu, Feichen Shen
2018	—	`conf`	MayoNLPTeam at the TREC 2018 Precision Medicine Track: Simple Information Retrieval Approach Is the Best. TREC Yanshan Wang, Andrew Wen, Sijia Liu, Hongfang Liu
2018	Misc	`conf`	Standardizing Heterogeneous Annotation Corpora Using HL7 FHIR for Facilitating their Reuse and Integration in Clinical NLP. AMIA Na Hong, Andrew Wen, Majid Rastegar-Mojarad, Sunghwan Sohn, Hongfang Liu, Guoqian Jiang
2017	—	`conf`	Aligned-Layer Text Search in Clinical Notes. MedInfo Stephen T. Wu, Andrew Wen, Yanshan Wang, Sijia Liu, Hongfang Liu