Feichen Shen

Publication Activity (10 Years)

Years Active: 2013-2021
Publications (10 Years): 59

Top Topics

Natural Language Processing

Semantic Web Technologies

Knowledge Discovery

Disease Diagnosis

Top Venues

J. Biomed. Informatics

Publications

Yanbo Guo, Chen Wang, Raymond M. Moore, Hongfang Liu, Feichen Shen
POKR: Building a Computable Heterogeneous Knowledge Resource for Precision Oncology. MedInfo (2021)
Sam Henry, Yanshan Wang, Feichen Shen, Özlem Uzuner
Corrigendum to: The 2019 National Natural language processing (NLP) Clinical Challenges (n2c2)/Open Health NLP (OHNLP) shared task on clinical concept normalization for clinical records. J. Am. Medical Informatics Assoc. 28 (11) (2021)
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 (2021)
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 (2021)
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 (2021)
Feichen Shen, Andrew Wen, Hongfang Liu
Subgrouping Rare Disease Patients Leveraging the Human Phenotype Ontology Embeddings. CBMS (2020)
Nathan D. Seligson, Jeremy L. Warner, William S. Dalton, David Martin, Robert S. Miller, Debra Patt, Kenneth L. Kehl, Matvey B. Palchuk, Gil Alterovitz, Laura K. Wiley, Ming Huang, Feichen Shen, Yanshan Wang, Khoa A. Nguyen, Anthony F. Wong, Funda Meric-Bernstam, Elmer V. Bernstam, James L. Chen
Recommendations for patient similarity classes: results of the AMIA 2019 workshop on defining patient similarity. J. Am. Medical Informatics Assoc. 27 (11) (2020)
David Oniani, Guoqian Jiang, Hongfang Liu, Feichen Shen
Constructing co-occurrence network embeddings to assist association extraction for COVID-19 and other coronavirus infectious diseases. J. Am. Medical Informatics Assoc. 27 (8) (2020)
Huan He, Feichen Shen, Michael Lin, Hongfang Liu
Identifying Rare Disease Studies by Natural Language Processing. AMIA (2020)
Yiqing Zhao, Hanzhong Yu, Luke A. Carlson, Feichen Shen, Sunyang Fu, Hongfang Liu, Chen Wang
Extracting Patient Genetic Information from Unstructured Clinical Notes. AMIA (2020)
Yanshan Wang, Naveed Afzal, Sunyang Fu, Liwei Wang, Feichen Shen, Majid Rastegar-Mojarad, Hongfang Liu
MedSTS: a resource for clinical semantic textual similarity. Lang. Resour. Evaluation 54 (1) (2020)
Andrew Wen, Sunyang Fu, Feichen Shen, Hongfang Liu
Accelerating Development of Learning Healthcare Systems via Distantly Supervised Knowledge Discovery. AMIA (2020)
Feichen Shen, Andrew Wen, Hongfang Liu
Enrich Rare Disease Phenotypic Characterizations via a Graph Convolutional Network Based Recommendation System. CBMS (2020)
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 (2020)
Andrew Wen, Feichen Shen, Sungrim Moon, Hongfang Liu, Jungwei Fan
A Deep Profiling and Visualization Framework to Audit Clinical Assessment Variation. CBMS (2020)
Sam Henry, Yanshan Wang, Feichen Shen, Özlem Uzuner
The 2019 National Natural language processing (NLP) Clinical Challenges (n2c2)/Open Health NLP (OHNLP) shared task on clinical concept normalization for clinical records. J. Am. Medical Informatics Assoc. 27 (10) (2020)
Feichen Shen, Yiqing Zhao, Liwei Wang, Majid Rastegar-Mojarad, Yanshan Wang, Sijia Liu, Hongfang Liu
Rare disease knowledge enrichment through a data-driven approach. BMC Medical Informatics Decis. Mak. 19 (1) (2019)
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)
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)
Feichen Shen, David W. Larson, James M. Naessens, Elizabeth B. Habermann, Hongfang Liu, Sunghwan Sohn
Detection of Surgical Site Infection Utilizing Automated Feature Generation in Clinical Notes. J. Heal. Informatics Res. 3 (3) (2019)
Yanshan Wang, Sunghwan Sohn, Sijia Liu, Feichen Shen, Liwei Wang, Elizabeth J. Atkinson, Shreyasee Amin, Hongfang Liu
A clinical text classification paradigm using weak supervision and deep representation. BMC Medical Informatics Decis. Mak. 19 (1) (2019)
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 (2019)
Ahmad P. Tafti, Yanshan Wang, Feichen Shen, Elham Sagheb, Paul R. Kingsbury, Hongfang Liu
Integrating word embedding neural networks with PubMed abstracts to extract keyword proximity of chronic diseases. BHI (2019)
Feichen Shen
Towards Semantic Big Graph Analytics for Cross-Domain Knowledge Discovery. CoRR (2019)
Feichen Shen, Yiqing Zhao, Hongfang Liu
Leveraging a Data-Driven Strategy to Enrich Rare Disease Knowledge. AMIA (2019)
Na Hong, Kui Wang, Sizhu Wu, Feichen Shen, Lixia Yao, Guoqian Jiang
An Interactive Visualization Tool for HL7 FHIR Specification Browsing and Profiling. J. Heal. Informatics Res. 3 (3) (2019)
Liwei Wang, Yanshan Wang, Feichen Shen, Majid Rastegar-Mojarad, Hongfang Liu
Discovering associations between problem list and practice setting. BMC Medical Informatics Decis. Mak. (3) (2019)
Feichen Shen, Vipin Chaudhary, Yan Liu, Che Ngufor, Hongfang Liu
Special Issue on Healthcare Knowledge Discovery and Management. J. Heal. Informatics Res. 3 (2) (2019)
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 (2019)
Yanshan Wang, Liwei Wang, Majid Rastegar-Mojarad, Sungrim Moon, Feichen Shen, Naveed Afzal, Sijia Liu, Yuqun Zeng, Saeed Mehrabi, Sunghwan Sohn, Hongfang Liu
Clinical information extraction applications: A literature review. J. Biomed. Informatics 77 (2018)
Yanshan Wang, Sunghwan Sohn, Sijia Liu, Feichen Shen, Liwei Wang, Elizabeth J. Atkinson, Shreyasee Amin, Hongfang Liu
A Deep Representation Empowered Distant Supervision Paradigm for Clinical Information Extraction. CoRR (2018)
Yanshan Wang, Sijia Liu, Naveed Afzal, Majid Rastegar-Mojarad, Liwei Wang, Feichen Shen, Paul R. Kingsbury, Hongfang Liu
A comparison of word embeddings for the biomedical natural language processing. J. Biomed. Informatics 87 (2018)
Feichen Shen, Hongfang Liu
Combining Knowledge and Data Driven Insights to Facilitate the Differential Diagnosis of Rare Diseases. AMIA (2018)
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)
Yanshan Wang, Naveed Afzal, Sunyang Fu, Liwei Wang, Feichen Shen, Majid Rastegar-Mojarad, Hongfang Liu
MedSTS: A Resource for Clinical Semantic Textual Similarity. CoRR (2018)
Liwei Wang, Yanshan Wang, Feichen Shen, Majid Rastegar-Mojarad, Hongfang Liu
Predicting Practice Setting Using Topic Modeling. ICHI Workshops (2018)
Feichen Shen, Yugyung Lee
MedTQ: Dynamic Topic Discovery and Query Generation for Medical Ontologies. CoRR (2018)
Yanshan Wang, Sijia Liu, Naveed Afzal, Majid Rastegar-Mojarad, Liwei Wang, Feichen Shen, Paul R. Kingsbury, Hongfang Liu
A Comparison of Word Embeddings for the Biomedical Natural Language Processing. CoRR (2018)
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)
Yiqing Zhao, Yanshan Wang, Henry Wang, Benjamin Yan, Feichen Shen, Kevin J. Peterson, Walter A. Rocca, Jennifer St. Sauver, Hongfang Liu
Annotating Cohort Data Elements with OHDSI Common Data Model to Promote Research Reproducibility. BIBM (2018)
Feichen Shen, David W. Larson, James M. Naessens, Elizabeth B. Habermann, Hongfang Liu, Sunghwan Sohn
Detection of Surgical Site Infection Utilizing Automated Feature Generation in Clinical Notes. CoRR (2018)
Feichen Shen, Hongfang Liu
Incorporating Knowledge-Driven Insights into a Collaborative Filtering Model to Facilitate the Differential Diagnosis of Rare Diseases. AMIA (2018)
Majid Rastegar-Mojarad, Sijia Liu, Yanshan Wang, Naveed Afzal, Liwei Wang, Feichen Shen, Sunyang Fu, Hongfang Liu
BioCreative/OHNLP Challenge 2018. BCB (2018)
Sijia Liu, Feichen Shen, Ravikumar Komandur Elayavilli, Yanshan Wang, Majid Rastegar-Mojarad, Vipin Chaudhary, Hongfang Liu
Extracting chemical-protein relations using attention-based neural networks. Database J. Biol. Databases Curation 2018 (2018)
Sijia Liu, Yanshan Wang, Na Hong, Feichen Shen, Stephen T. Wu, William R. Hersh, Hongfang Liu
On Mapping Textual Queries to a Common Data Model. ICHI (2017)
Yanshan Wang, Sijia Liu, Majid Rastegar-Mojarad, Liwei Wang, Feichen Shen, Fei Liu, Hongfang Liu
Dependency and AMR Embeddings for Drug-Drug Interaction Extraction from Biomedical Literature. BCB (2017)
Kevin J. Peterson, Guoqian Jiang, Scott M. Brue, Feichen Shen, Hongfang Liu
Mining Hierarchies and Similarity Clusters from Value Set Repositories. AMIA (2017)
Naveed Afzal, Yanshan Wang, Feichen Shen, Liwei Wang, Hongfang Liu
A Resource for Clinical Semantic Textual Similarity. AMIA (2017)
Yanshan Wang, Naveed Afzal, Liwei Wang, Feichen Shen, Hongfang Liu
Semantic Representations of Medical Terms: A Comparison Study of Word Embeddings Trained on Clinical Notes and PubMed Articles. AMIA (2017)
Sijia Liu, Feichen Shen, Vipin Chaudhary, Hongfang Liu
MayoNLP at SemEval 2017 Task 10: Word Embedding Distance Pattern for Keyphrase Classification in Scientific Publications. SemEval@ACL (2017)
Majid Rastegar-Mojarad, Sunghwan Sohn, Liwei Wang, Feichen Shen, Troy C. Bleeker, William A. Cliby, Hongfang Liu
Need of informatics in designing interoperable clinical registries. Int. J. Medical Informatics 108 (2017)
Yanshan Wang, Liwei Wang, Majid Rastegar-Mojarad, Sijia Liu, Feichen Shen, Hongfang Liu
Content Analysis of Free-Text Family History. CRI (2017)
Feichen Shen, Sijia Liu, Yanshan Wang, Liwei Wang, Naveed Afzal, Hongfang Liu
Leveraging Collaborative Filtering to Accelerate Rare Disease Diagnosis. AMIA (2017)
Sungrim Moon, Sijia Liu, Paul R. Kingsbury, David Chen, Yanshan Wang, Feichen Shen, Rajeev Chaudhry, Hongfang Liu
Medical concept intersection between outside medical records and consultant notes: A case study in transferred cardiovascular patients. BIBM (2017)
Yuqun Zeng, Yanshan Wang, Feichen Shen, Sijia Liu, Liwei Wang, Majid Rastegar-Mojarad, Xusheng Liu, Hongfang Liu
Recommending education materials for diabetic questions using information retrieval approaches. AMIA (2017)
Feichen Shen, Liwei Wang, Hongfang Liu
Phenotypic Analysis of Clinical Narratives Using Human Phenotype Ontology. MedInfo (2017)
Feichen Shen, Sijia Liu, Yanshan Wang, Liwei Wang, Naveed Afzal, Hongfang Liu
Accelerating Rare Disease Diagnosis with Collaborative Filtering. AMIA (2017)
Feichen Shen, Sunghwan Sohn, Majid Rastegar-Mojarad, Sijia Liu, Joshua J. Pankratz, Michael Hatton, Nancy Sowada, Om Shrestha, Shawna Shurson, Hongfang Liu
Populating Physician Biographical Pages Based on EMR Data. CRI (2017)
Feichen Shen, Liwei Wang, Hongfang Liu
Using Human Phenotype Ontology for Phenotypic Analysis of Clinical Notes. MedInfo (2017)
Prakash Vaka, Feichen Shen, Mayanka Chandrashekar, Yugyung Lee
PEMAR: A pervasive middleware for activity recognition with smart phones. PerCom Workshops (2015)
Feichen Shen
A pervasive framework for real-time activity patterns of mobile users. PerCom Workshops (2015)
Feichen Shen, Yugyung Lee
SAMAF: Situation aware mobile apps framework. PerCom Workshops (2015)
Feichen Shen, Hongfang Liu, Sunghwan Sohn, David W. Larson, Yugyung Lee
BmQGen: Biomedical query generator for knowledge discovery. BIBM (2015)
Zhiqiang Chen, Jianfei Chen, Feichen Shen, Yugyung Lee
Collaborative Mobile-Cloud Computing for Civil Infrastructure Condition Inspection. J. Comput. Civ. Eng. 29 (5) (2015)
Qian Zhu, Cui Tao, Feichen Shen, Christopher G. Chute
Exploring the Pharmacogenomics Knowledge Base (PharmGKB) for Repositioning Breast Cancer Drugs by Leveraging Web Ontology Language (OWL) and Cheminformatics Approaches. Pacific Symposium on Biocomputing (2014)
Sourish Dasgupta, Anoop Aroor, Feichen Shen, Yugyung Lee
SMARTSPACE: Multiagent Based Distributed Platform for Semantic Service Discovery. IEEE Trans. Syst. Man Cybern. Syst. 44 (7) (2014)
Feichen Shen, Dingcheng Li, Hongfang Liu, Yugyung Lee, Jyotishman Pathak, Christopher G. Chute, Cui Tao
Using semantic web technologies for quality measure phenotyping algorithm representation and automatic execution on EHR data. BHI (2014)
Dingcheng Li, Zhen Wang, Feichen Shen, Mohammad Hassan Murad, Hongfang Liu
Reducing the Screening Burden of Systematic Review with a Multiple-level Relevance Ranking System. AMIA (2014)
Dingcheng Li, Zhen Wang, Feichen Shen, Mohammad Hassan Murad, Hongfang Liu
Towards a multi-level framework for supporting systematic review - A pilot study. BIBM (2014)
Cui Tao, Dingcheng Li, Feichen Shen, Zonghui Lian, Jyotishman Pathak, Hongfang Liu, Christopher G. Chute
Phenotyping on EHR Data Using OWL and Semantic Web Technologies. ICSH (2013)
Yuji Zhang, Dingcheng Li, Cui Tao, Feichen Shen, Hongfang Liu
An integrative computational approach to identify disease-specific networks from PubMed literature information. BIBM (2013)