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2020 – today
- 2021
[j21]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): 2546 (2021)- [j20]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) - [c40]Yanbo Guo, Chen Wang, Raymond M. Moore, Hongfang Liu, Feichen Shen:
POKR: Building a Computable Heterogeneous Knowledge Resource for Precision Oncology. MedInfo 2021: 243-247 - [i10]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) - [i9]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) - 2020
- [j19]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): 1259-1267 (2020) - [j18]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): 1529-1537 (2020) - [j17]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): 1808-1812 (2020) - [j16]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) - [j15]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): 57-72 (2020) - [c39]Huan He, Feichen Shen, Michael Lin, Hongfang Liu:
Identifying Rare Disease Studies by Natural Language Processing. AMIA 2020 - [c38]Andrew Wen, Sunyang Fu, Feichen Shen, Hongfang Liu:
Accelerating Development of Learning Healthcare Systems via Distantly Supervised Knowledge Discovery. AMIA 2020 - [c37]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 - [c36]Feichen Shen, Andrew Wen, Hongfang Liu:
Enrich Rare Disease Phenotypic Characterizations via a Graph Convolutional Network Based Recommendation System. CBMS 2020: 37-40 - [c35]Feichen Shen, Andrew Wen, Hongfang Liu:
Subgrouping Rare Disease Patients Leveraging the Human Phenotype Ontology Embeddings. CBMS 2020: 169-172 - [c34]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
2010 – 2019
- 2019
- [j14]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) - [j13]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) - [j12]Feichen Shen, Vipin Chaudhary, Yan Liu, Che Ngufor, Hongfang Liu:
Special Issue on Healthcare Knowledge Discovery and Management. J. Heal. Informatics Res. 3(2): 157-158 (2019) - [j11]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): 267-282 (2019) - [j10]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): 329-344 (2019) - [j9]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): 1:1-1:13 (2019) - [j8]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): 32:1-32:11 (2019) - [j7]Liwei Wang, Yanshan Wang, Feichen Shen, Majid Rastegar-Mojarad, Hongfang Liu:
Discovering associations between problem list and practice setting. BMC Medical Informatics Decis. Mak. 19-S(3): 13-22 (2019) - [c33]Feichen Shen, Yiqing Zhao, Hongfang Liu:
Leveraging a Data-Driven Strategy to Enrich Rare Disease Knowledge. AMIA 2019 - [c32]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: 1-4 - [i8]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) - [i7]Feichen Shen:
Towards Semantic Big Graph Analytics for Cross-Domain Knowledge Discovery. CoRR abs/1902.07688 (2019) - [i6]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) - 2018
- [j6]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: bay102 (2018) - [j5]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: 34-49 (2018) - [j4]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: 12-20 (2018) - [c31]Feichen Shen, Hongfang Liu:
Incorporating Knowledge-Driven Insights into a Collaborative Filtering Model to Facilitate the Differential Diagnosis of Rare Diseases. AMIA 2018 - [c30]Feichen Shen, Hongfang Liu:
Combining Knowledge and Data Driven Insights to Facilitate the Differential Diagnosis of Rare Diseases. AMIA 2018 - [c29]Majid Rastegar-Mojarad, Sijia Liu, Yanshan Wang, Naveed Afzal, Liwei Wang, Feichen Shen, Sunyang Fu, Hongfang Liu:
BioCreative/OHNLP Challenge 2018. BCB 2018: 575 - [c28]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 - [c27]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: 1310-1317 - [c26]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 - [c25]Liwei Wang, Yanshan Wang, Feichen Shen, Majid Rastegar-Mojarad, Hongfang Liu:
Predicting Practice Setting Using Topic Modeling. ICHI Workshops 2018: 62-63 - [i5]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 abs/1802.00400 (2018) - [i4]Feichen Shen, Yugyung Lee:
MedTQ: Dynamic Topic Discovery and Query Generation for Medical Ontologies. CoRR abs/1802.03855 (2018) - [i3]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 abs/1803.08850 (2018) - [i2]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 abs/1804.07814 (2018) - [i1]Yanshan Wang, Naveed Afzal, Sunyang Fu, Liwei Wang, Feichen Shen, Majid Rastegar-Mojarad, Hongfang Liu:
MedSTS: A Resource for Clinical Semantic Textual Similarity. CoRR abs/1808.09397 (2018) - 2017
- [j3]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: 78-84 (2017) - [c24]Naveed Afzal, Yanshan Wang, Feichen Shen, Liwei Wang, Hongfang Liu:
A Resource for Clinical Semantic Textual Similarity. AMIA 2017 - [c23]Kevin J. Peterson, Guoqian Jiang, Scott M. Brue, Feichen Shen, Hongfang Liu:
Mining Hierarchies and Similarity Clusters from Value Set Repositories. AMIA 2017 - [c22]Feichen Shen, Sijia Liu, Yanshan Wang, Liwei Wang, Naveed Afzal, Hongfang Liu:
Leveraging Collaborative Filtering to Accelerate Rare Disease Diagnosis. AMIA 2017 - [c21]Feichen Shen, Sijia Liu, Yanshan Wang, Liwei Wang, Naveed Afzal, Hongfang Liu:
Accelerating Rare Disease Diagnosis with Collaborative Filtering. AMIA 2017 - [c20]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 - [c19]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 - [c18]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: 36-43 - [c17]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: 1495-1500 - [c16]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 - [c15]Yanshan Wang, Liwei Wang, Majid Rastegar-Mojarad, Sijia Liu, Feichen Shen, Hongfang Liu:
Content Analysis of Free-Text Family History. CRI 2017 - [c14]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: 21-25 - [c13]Feichen Shen, Liwei Wang, Hongfang Liu:
Phenotypic Analysis of Clinical Narratives Using Human Phenotype Ontology. MedInfo 2017: 581-585 - [c12]Feichen Shen, Liwei Wang, Hongfang Liu:
Using Human Phenotype Ontology for Phenotypic Analysis of Clinical Notes. MedInfo 2017: 1285 - [c11]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: 956-960 - 2015
- [j2]Zhiqiang Chen, Jianfei Chen, Feichen Shen, Yugyung Lee:
Collaborative Mobile-Cloud Computing for Civil Infrastructure Condition Inspection. J. Comput. Civ. Eng. 29(5) (2015) - [c10]Feichen Shen, Hongfang Liu, Sunghwan Sohn, David W. Larson, Yugyung Lee:
BmQGen: Biomedical query generator for knowledge discovery. BIBM 2015: 1092-1097 - [c9]Feichen Shen, Yugyung Lee:
SAMAF: Situation aware mobile apps framework. PerCom Workshops 2015: 26-31 - [c8]Feichen Shen:
A pervasive framework for real-time activity patterns of mobile users. PerCom Workshops 2015: 248-250 - [c7]Prakash Vaka, Feichen Shen, Mayanka Chandrashekar, Yugyung Lee:
PEMAR: A pervasive middleware for activity recognition with smart phones. PerCom Workshops 2015: 409-414 - 2014
- [j1]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): 805-821 (2014) - [c6]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 - [c5]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: 531-534 - [c4]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: 43-50 - [c3]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: 172-182 - 2013
- [c2]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: 72-75 - [c1]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: 31-32
Coauthor Index
[j20] [c40] [i10] [i9] [j19] [j16] [j15] [c39] [c38] [c37] [c36] [c35] [c34] [j14] [j13] [j12] [j11] [j9] [j8] [j7] [c33] [c32] [i8] [i6] [j6] [j5] [j4] [c31] [c30] [c29] [c28] [c27] [c26] [c25] [i5] [i3] [i2] [i1] [j3] [c24] [c23] [c22] [c21] [c20] [c19] [c18] [c17] [c16] [c15] [c14] [c13] [c12] [c11] [c10] [c6] [c5] [c4] [c2] [c1]
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