Publications

  1. Seligson ND, Warner JL, Dalton WS, Martin D, Miller RS, Patt D, Kehl KL, Palchuk MB, Alterovitz G, Wiley LK, Huang M, Shen F, Wang Y, Nguyen KA, Wong AF, Meric-Bernstam F, Bernstam EV, Chen JL. Recommendations for patient similarity classes: results of the AMIA 2019 workshop on defining patient similarity. J Am Med Inform Assoc. 2020 Sep 4 Epub 2020 Sept 04
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  2. Fu S, Chen D, He H, Liu S, Moon S, Peterson KJ, Shen F, Wang L, Wang Y, Wen A, Zhao Y, Sohn S, Liu H. Clinical concept extraction: A methodology review. J Biomed Inform. 2020 Aug 6; 109:103526 Epub 2020 Aug 06
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  3. Oniani D, Jiang G, Liu H, Shen F. Constructing co-occurrence network embeddings to assist association extraction for COVID-19 and other coronavirus infectious diseases. J Am Med Inform Assoc. 2020 Aug 1; 27 (8):1259-1267
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  4. Zhao Y, Yu H, Fu S, Shen F, Davila JI, Liu H, Wang C. Data-driven Sublanguage Analysis for Cancer Genomics Knowledge Modeling: Applications in Mining Oncological Genetics Information from Patients' Genetic Reports. AMIA Jt Summits Transl Sci Proc. 2020; 2020:720-729 Epub 2020 May 30
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  5. Peng S, Shen F, Wen A, Wang L, Fan Y, Liu X, Liu H. Detecting Lifestyle Risk Factors for Chronic Kidney Disease With Comorbidities: Association Rule Mining Analysis of Web-Based Survey Data. J Med Internet Res. 2019 Dec 10; 21 (12):e14204
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  6. Liu C, Ta CN, Rogers JR, Li Z, Lee J, Butler AM, Shang N, Kury FSP, Wang L, Shen F, Liu H, Ena L, Friedman C, Weng C. Ensembles of natural language processing systems for portable phenotyping solutions. J Biomed Inform. 2019 Dec; 100:103318 Epub 2019 Oct 23
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  7. Hong N, Wen A, Shen F, Sohn S, Wang C, Liu H, Jiang G. Developing a scalable FHIR-based clinical data normalization pipeline for standardizing and integrating unstructured and structured electronic health record data. JAMIA Open. 2019 Dec; 2 (4):570-579 Epub 2019 Oct 18
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  8. Hong N, Wang K, Wu S, Shen F, Yao L, Jiang G. An Interactive Visualization Tool for HL7 FHIR Specification Browsing and Profiling. J Healthc Inform Res. 2019 Sep; 3 (3):329-344 Epub 2019 Jan 10
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  9. Shen F, Larson DW, Naessens JM, Habermann EB, Liu H, Sohn S. Detection of Surgical Site Infection Utilizing Automated Feature Generation in Clinical Notes. J Healthc Inform Res. 2019 Sep; 3 (3):267-282 Epub 2018 Nov 06
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  10. Shen F, Peng S, Fan Y, Wen A, Liu S, Wang Y, Wang L, Liu H. HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology. J Biomed Inform. 2019 Aug; 96:103246 Epub 2019 June 27
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  11. Tafti AP, Wang Y, Shen F, Sagheb E, Kingsbury P, Liu H. Integrating word embedding neural networks with PubMed abstracts to extract keyword proximity of chronic diseases 2019 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI). 2019.
  12. Wang L, Wang Y, Shen F, Rastegar-Mojarad M, Liu H. Discovering associations between problem list and practice setting. BMC Med Inform Decis Mak. 2019 Apr 4; 19 (Suppl 3):69 Epub 2019 Apr 04
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  13. Shen F, Zhao Y, Wang L, Mojarad MR, Wang Y, Liu S, Liu H. Rare disease knowledge enrichment through a data-driven approach. BMC Med Inform Decis Mak. 2019 Feb 14; 19 (1):32
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  14. Wang Y, Sohn S, Liu S, Shen F, Wang L, Atkinson EJ, Amin S, Liu H. A clinical text classification paradigm using weak supervision and deep representation. BMC Med Inform Decis Mak. 2019 Jan 7; 19 (1):1 Epub 2019 Jan 07
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  15. Fan Y, Wen A, Shen F, Sohn S, Liu H, Wang L. Evaluating the Impact of Dictionary Updates on Automatic Annotations Based on Clinical NLP Systems. AMIA Jt Summits Transl Sci Proc. 2019; 2019:714-721 Epub 2019 May 06
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  16. Peng S, Fan Y, Wang L, Wen A, Liu X, Liu H, Shen F. Leveraging Association Rule Mining to Detect Pathophysiological Mechanisms of Chronic Kidney Disease Complicated by Metabolic Syndrome IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2018; 1302-1309.
  17. Shen F, Larson D, Naessens J, Habermann E, Liu H, Sohn S. Detection of Surgical Site Infection Utilizing Automated Feature Generation in Clinical Notes Journal of Healthcare Informatics Reserach. 2018.
  18. Wang Y, Liu S, Afzal N, Rastegar-Mojarad M, Wang L, Shen F, Kingsbury P, Liu H. A comparison of word embeddings for the biomedical natural language processing. J Biomed Inform. 2018 Nov; 87:12-20 Epub 2018 Sept 12
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  19. Shen F, Liu S, Wang Y, Wen A, Wang L, Liu H. Utilization of Electronic Medical Records and Biomedical Literature to Support the Diagnosis of Rare Diseases Using Data Fusion and Collaborative Filtering Approaches. JMIR Med Inform. 2018 Oct 10; 6 (4):e11301
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  20. Son JH, Xie G, Yuan C, Ena L, Li Z, Goldstein A, Huang L, Wang L, Shen F, Liu H, Mehl K, Groopman EE, Marasa M, Kiryluk K, Gharavi AG, Chung WK, Hripcsak G, Friedman C, Weng C, Wang K. Deep Phenotyping on Electronic Health Records Facilitates Genetic Diagnosis by Clinical Exomes. Am J Hum Genet. 2018 Jul 5; 103 (1):58-73 Epub 2018 June 28
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  21. Shen F, Liu S, Wang Y, Wang L, Wen A, Limper A, Liu H. Constructing Node Embeddings for Human Phenotype Ontology to Assist Phenotypic Similarity Measurement IEEE International Conference on Healthcare Informatics Workshop (ICHI-W). 2018; 29-33.
  22. Shen F, Lee Y. BioBroker: Knowledge Discovery Framework for Heterogeneous Biomedical Ontologies and Data Journal of Intelligent Learning Systems and Applications. 2018.
  23. Hong N, Wen A, Shen F, Sohn S, Liu S, Liu H, Jiang G. Integrating Structured and Unstructured EHR Data Using an FHIR-based Type System: A Case Study with Medication Data. AMIA Jt Summits Transl Sci Proc. 2018; 2017:74-83 Epub 2018 May 18
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  24. Liu S, Shen F, Komandur Elayavilli R, Wang Y, Rastegar-Mojarad M, Chaudhary V, Liu H. Extracting chemical-protein relations using attention-based neural networks. Database (Oxford). 2018 Jan 1; 2018 Epub 2018 Jan 01
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  25. Wang L, Rastegar-Mojarad M, Ji Z, Liu S, Liu K, Moon S, Shen F, Wang Y, Yao L, Davis Iii JM, Liu H. Detecting Pharmacovigilance Signals Combining Electronic Medical Records With Spontaneous Reports: A Case Study of Conventional Disease-Modifying Antirheumatic Drugs for Rheumatoid Arthritis. Front Pharmacol. 2018; 9:875 Epub 2018 Aug 07
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  26. Wang Y, Wang L, Rastegar-Mojarad M, Moon S, Shen F, Afzal N, Liu S, Zeng Y, Mehrabi S, Sohn S, Liu H. Clinical information extraction applications: A literature review. J Biomed Inform. 2018 Jan; 77:34-49 Epub 2017 Nov 21
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  27. Zhang Y, Shen F, Mojarad MR, Li D, Liu S, Tao C, Yu Y, Liu H. Systematic identification of latent disease-gene associations from PubMed articles. PLoS One. 2018; 13 (1):e0191568 Epub 2018 Jan 26
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  28. Wang Y, Afzal N, Fu S, Wang L, Shen F, Rastegar-Mojarad M, Liu H. MedSTS: a resource for clinical semantic textual similarity Language Resources and Evaluation. 2018; 1-6.
  29. Wang L, Wang Y, Shen F, Rastegar-Mojarad M, Liu H. Predicting practice setting using topic modeling Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018. 2018; 62-3. Epub 1900 Jan 01.
  30. Shen F, Liu H. Incorporating Knowledge-Driven Insights into a Collaborative Filtering Model to Facilitate the Differential Diagnosis of Rare Diseases. AMIA Annu Symp Proc. 2018; 2018:1505-1514 Epub 2018 Dec 05
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  31. Rastegar-Mojarad M, Sohn S, Wang L, Shen F, Bleeker TC, Cliby WA, Liu H. Need of informatics in designing interoperable clinical registries. Int J Med Inform. 2017 Dec; 108:78-84 Epub 2017 Oct 10
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  32. Shen F, Liu S, Wang Y, Wang L, Afzal N, Liu H. Accelerating Rare Disease Diagnosis with Collaborative Filtering. American Medical Informatics Association (AMIA) Annual Symposium 2017.. 2017.
  33. Moon S, Liu S, Kingsbury P, Chen D, Wang Y, Shen F, Chaudhry R, Liu H. Medical concept intersection between outside medical records and consultant notes: A case study in transferred cardiovascular patients 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2017; 1495-1500.
  34. Zeng Y, Liu X, Wang Y, Shen F, Liu S, Rastegar-Mojarad M, Wang L, Liu H. Recommending Education Materials for Diabetic Questions Using Information Retrieval Approaches. J Med Internet Res. 2017 Oct 16; 19 (10):e342
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  35. Liu S, Wang Y, Hong N, Shen F, Wu S, Hersh W, Liu H. On Mapping Textual Queries to a Common Data Model 2017 IEEE International Conference on Healthcare Informatics. 2017.
  36. Peterson KJ, Jiang G, Brue SM, Shen F, Liu H. Mining Hierarchies and Similarity Clusters from Value Set Repositories. AMIA Annu Symp Proc. 2017; 2017:1372-1381 Epub 2018 Apr 16
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  37. Shen F, Liu S, Wang Y, Wang L, Afzal N, Liu H. Leveraging Collaborative Filtering to Accelerate Rare Disease Diagnosis. AMIA Annu Symp Proc. 2017; 2017:1554-1563 Epub 2018 Apr 16
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  38. Shen F, Wang L, Liu H. Phenotypic Analysis of Clinical Narratives Using Human Phenotype Ontology. Stud Health Technol Inform. 2017; 245:581-585
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  39. Shen F, Wang L, Liu H. Using Human Phenotype Ontology for Phenotypic Analysis of Clinical Notes. Stud Health Technol Inform. 2017; 245:1285
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  40. Wang Y, Wang L, Rastegar-Mojarad M, Liu S, Shen F, Liu H. Systematic Analysis of Free-Text Family History in Electronic Health Record. AMIA Jt Summits Transl Sci Proc. 2017; 2017:104-113 Epub 2017 July 26
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  41. Shen F, Sohn S, Rastegar-Mojarad M, Liu S, Pankratz JJ, Hatton MA, Sowada N, Shrestha OK, Shurson SL, Liu H. Populating Physician Biographical Pages Based on EMR Data. AMIA Jt Summits Transl Sci Proc. 2017; 2017:522-530 Epub 2017 July 26
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  42. Wang Y, Liu S, Shen F, Liu H, Rastegar-Mojarad M, Liu F. Dependency and AMR embeddings for drug-drug interaction extraction from biomedical literature ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. 2017; 36-43. Epub 1900 Jan 01.
  43. Li D, Wang Z, Wang L, Sohn S, Shen F, Murad MH, Liu H. A Text-Mining Framework for Supporting Systematic Reviews. Am J Inf Manag. 2016 Nov; 1 (1):1-9 Epub 2016 Aug 31
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  44. Shen F, Liu H, Sohn S, Larson DW, Lee Y. Predicate Oriented Pattern Analysis for Biomedical Knowledge Discovery. Intell Inf Manag. 2016 May; 8 (3):66-85
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  45. Shen F, Lee Y. Knowledge Discovery from Biomedical Ontologies in Cross Domains. PLoS One. 2016; 11 (8):e0160005 Epub 2016 Aug 22
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  46. Li D, Afzal N, Rastegar M, Komandur R, Liu S, Wang Y, Shen F, Liu H. Resolution of Chemical Disease Relations with Diverse Features and Rules Proceedings of the Fifth BioCreative Challenge Evaluation Workshop. 2015; 280-285.
  47. Shen F. A pervasive framework for real-time activity patterns of mobile users 2015 IEEE International Conference on Pervasive Computing and Communication Workshops (PerCom Workshops). 2015; 248-250.
  48. Shen F, Lee Y. SAMAF: Situation aware mobile apps framework 2015 IEEE International Conference on Pervasive Computing and Communication Workshops (PerCom Workshops). 2015; 26-31.
  49. Vaka P, Shen F, Chandrashekar M, Lee Y. PEMAR: A pervasive middleware for activity recognition with smart phones 2015 IEEE International Conference on Pervasive Computing and Communication Workshops (PerCom Workshops). 2015; 409-414.
  50. Shen F, Liu H, Sohn S, Larson DW, Lee Y. BmQGen: Biomedical query generator for knowledge discovery Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. 2015; 1092-7.
  51. Zhu Q, Tao C, Shen F, Chute CG. Exploring the pharmacogenomics knowledge base (PharmGKB) for repositioning breast cancer drugs by leveraging Web ontology language (OWL) and cheminformatics approaches. Pac Symp Biocomput. 2014; 172-82
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  52. Shen F, Li D, Liu H, Lee Y, Pathak J, Chute CG, Tao C. Using semantic web technologies for quality measure phenotyping algorithm representation and automatic execution on EHR data. 2014 IEEE-EMBS International Conference on Biomedical and Health Informatics, BHI 2014. 2014(3):531-4.
  53. Li D, Wang Z, Shen F, Murad MH, Liu H. Towards a multi-level framework for supporting systematic review - A pilot study. Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014. 2014; 43-50.
  54. Chen Z, Chen J, Shen F, Lee Y. Collaborative Mobile-Cloud Computing for Civil Infrastructure Condition. Journal of Computing in Civil Engineering. 2014; 29(5).
  55. Dasgupta S, Aroor A, Shen F, Lee Y. SMARTSPACE: Multiagent Based Distributed Platform for Semantic Service Discovery. IEEE Transactions on Systems, Man, and Cybernetics: Systems. 2013; 44(7):805-821.
  56. Tao C, Li D, Shen F, Lian Z, Pathak J, Liu H, Chute CG. Phenotyping on EHR data using OWL and semantic web technologies. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2013; 8040 LNCS:31-2.
  57. Zhang Y, Li D, Tao C, Shen F, Liu H. An integrative computational approach to identify disease-specific networks from PubMed literature information. Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013. 2013; 72-5.