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Last Name

Feifan Liu PhD

TitleAssistant Professor
InstitutionUniversity of Massachusetts Medical School
DepartmentPopulation and Quantitative Health Sciences
AddressUniversity of Massachusetts Medical School
368 Plantation Street, AS9-1075
Worcester MA 01605
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    Other Positions
    InstitutionUMMS - School of Medicine
    DepartmentPopulation and Quantitative Health Sciences

    InstitutionUMMS - School of Medicine

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentClinical Population Health Research

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentMasters in Clinical Investigation

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    Collapse education and training
    Shandong University, Jinan, , ChinaBSElectrical Engineering
    Shandong University, Jinan, , ChinaMSScience
    Chinese Academy of Sciences, Beijing, , ChinaPHDComputer Science
    University of Texas at Dallas, Dallas, USAPostdoc Fellow08/2009Machine Learning in Language Understanding

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    Dr. Liu completed doctoral training in pattern recognition and artificial intelligence, with strong expertise on natural language processing, machine learning (deep learning), and biomedical informatics. His research focuses on exploiting advanced computational models to analyze heterogeneous and complex healthcare data for knowledge extraction, predictive modeling and preventative data analytics, in the areas of suicide prevention, HIV prevention, cancer informatics and stroke management.   

    Over more than 10 years in this field, Dr. Liu has published more than 60 peer reviewed manuscripts (29 first-author) on premium journals and top computer science conferences. He have served co-investigator (lead data scientist) on 5 NIH-funded R01 projects, and participated NSF study sections in the area of machine learning and natural language processing. Through developing advanced machine learning methods, Dr. Liu has won the first place in two international challenge tasks: Medical Visual Question Answering (2018) and Gene Mutation/Disease Relation Extraction (2019).

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Deer RR, Rock MA, Vasilevsky N, Carmody L, Rando H, Anzalone AJ, Basson MD, Bennett TD, Bergquist T, Boudreau EA, Bramante CT, Byrd JB, Callahan TJ, Chan LE, Chu H, Chute CG, Coleman BD, Davis HE, Gagnier J, Greene CS, Hillegass WB, Kavuluru R, Kimble WD, Koraishy FM, Köhler S, Liang C, Liu F, Liu H, Madhira V, Madlock-Brown CR, Matentzoglu N, Mazzotti DR, McMurry JA, McNair DS, Moffitt RA, Monteith TS, Parker AM, Perry MA, Pfaff E, Reese JT, Saltz J, Schuff RA, Solomonides AE, Solway J, Spratt H, Stein GS, Sule AA, Topaloglu U, Vavougios GD, Wang L, Haendel MA, Robinson PN. Characterizing Long COVID: Deep Phenotype of a Complex Condition. EBioMedicine. 2021 Dec; 74:103722. PMID: 34839263.
      View in: PubMed
    2. Sharafeldin N, Bates B, Song Q, Madhira V, Shao YR, Liu F, Bergquist T, Su J, Topaloglu U. Reply to K. Takada et al. J Clin Oncol. 2021 Oct 08; JCO2102150. PMID: 34623872.
      View in: PubMed
    3. Liu F, Zhou P, Baccei SJ, Masciocchi MJ, Amornsiripanitch N, Kiefe CI, Rosen MP. Qualifying Certainty in Radiology Reports through Deep Learning-Based Natural Language Processing. AJNR Am J Neuroradiol. 2021 Aug 19. PMID: 34413062.
      View in: PubMed
    4. Boudreaux ED, Rundensteiner E, Liu F, Wang B, Larkin C, Agu E, Ghosh S, Semeter J, Simon G, Davis-Martin RE. Applying Machine Learning Approaches to Suicide Prediction Using Healthcare Data: Overview and Future Directions. Front Psychiatry. 2021; 12:707916. PMID: 34413800.
      View in: PubMed
    5. Sharafeldin N, Bates B, Song Q, Madhira V, Yan Y, Dong S, Lee E, Kuhrt N, Shao YR, Liu F, Bergquist T, Guinney J, Su J, Topaloglu U. Outcomes of COVID-19 in Patients With Cancer: Report From the National COVID Cohort Collaborative (N3C). J Clin Oncol. 2021 07 10; 39(20):2232-2246. PMID: 34085538.
      View in: PubMed
    6. Wang B, Liu F, Deveaux L, Ash A, Gosh S, Li X, Rundensteiner E, Cottrell L, Adderley R, Stanton B. Adolescent HIV-related behavioural prediction using machine learning: a foundation for precision HIV prevention. AIDS. 2021 May 01; 35(Suppl 1):S75-S84. PMID: 33867490.
      View in: PubMed
    7. Rando HM, Bennett TD, Byrd JB, Bramante C, Callahan TJ, Chute CG, Davis HE, Deer R, Gagnier J, Koraishy FM, Liu F, McMurry JA, Moffitt RA, Pfaff ER, Reese JT, Relevo R, Robinson PN, Saltz JH, Solomonides A, Sule A, Topaloglu U, Haendel MA. Challenges in defining Long COVID: Striking differences across literature, Electronic Health Records, and patient-reported information. medRxiv. 2021 Mar 26. PMID: 33791733.
      View in: PubMed
    8. Rawat BPS, Jagannatha A, Liu F, Yu H. Inferring ADR causality by predicting the Naranjo Score from Clinical Notes. AMIA Annu Symp Proc. 2020; 2020:1041-1049. PMID: 33936480.
      View in: PubMed
    9. Liu F, Zheng X, Yu H, Tjia J. Neural Multi-Task Learning for Adverse Drug Reaction Extraction. AMIA Annu Symp Proc. 2020; 2020:756-762. PMID: 33936450.
      View in: PubMed
    10. Liu F, Wang B, Larkin C, Kiefe C, Boudreaux E. Identify suicidal encounters in emergency department (ED) setting using machine learning and natural language processing. APHA Annual Meeting and Expo. 2020.
    11. Peng C, He M, Cutrona SL, Kiefe CI, Liu F, Wang Z. Theme Trends and Knowledge Structure on Mobile Health Apps: Bibliometric Analysis. JMIR Mhealth Uhealth. 2020 Jul 27; 8(7):e18212. PMID: 32716312.
      View in: PubMed
    12. Liu F., Zheng X., Wang B., Kiefe C. DeepGeneMD: A Joint Deep Learning Model for Extracting Gene Mutation-Disease Knowledge from PubMed Literature. BioNLP-OST at Empirical Methods in Natural Language Processing (EMNLP). 2019.
    13. Liu F., Peng Y., Rosen M.P. An Effective Deep Transfer Learning and Information Fusion Framework for Medical Visual Question Answering. Experimental IR Meets Multilinguality, Multimodality, and Interaction. 2019; 11696.
    14. Liu F, Pradhan R, Druhl E, Freund E, Liu W, Sauer BC, Cunningham F, Gordon AJ, Peters CB, Yu H. Learning to detect and understand drug discontinuation events from clinical narratives. J Am Med Inform Assoc. 2019 Apr 29. PMID: 31034028.
      View in: PubMed
    15. Li R, Hu B, Liu F, Liu W, Cunningham F, McManus DD, Yu H. Detection of Bleeding Events in Electronic Health Record Notes Using Convolutional Neural Network Models Enhanced With Recurrent Neural Network Autoencoders: Deep Learning Approach. JMIR Med Inform. 2019 Feb 08; 7(1):e10788. PMID: 30735140.
      View in: PubMed
    16. Liu F, Jagannatha A, Yu H. Towards Drug Safety Surveillance and Pharmacovigilance: Current Progress in Detecting Medication and Adverse Drug Events from Electronic Health Records. Drug Saf. 2019 Jan 16. PMID: 30649734.
      View in: PubMed
    17. Jagannatha A, Liu F, Liu W, Yu H. Overview of the First Natural Language Processing Challenge for Extracting Medication, Indication, and Adverse Drug Events from Electronic Health Record Notes (MADE 1.0). Drug Saf. 2019 Jan 16. PMID: 30649735.
      View in: PubMed
    18. Munkhdalai T, Liu F, Yu H. Clinical Relation Extraction Toward Drug Safety Surveillance Using Electronic Health Record Narratives: Classical Learning Versus Deep Learning. JMIR Public Health Surveill. 2018 Apr 25; 4(2):e29. PMID: 29695376.
      View in: PubMed
    19. Liu F, Chen J, Jagannatha A, Yu H. Learning for Biomedical Information Extraction: Methodological Review of Recent Advances. arXiv:1606.07993. 2016.
    20. Liu F, Yu H. Learning to rank figures within a biomedical article. PLoS One. 2014; 9(3):e61567. PMID: 24625719; PMCID: PMC3953065.
    21. Liu F, Moosavinasab S, Agarwal S, Bennett A, Yu H. Automatically Identifying Health- and Clinical-Related Content in Wikipedia. Proceedings of the 14th World Conference on Medical and Health Informatics (MEDINFO). 2013.
    22. Liu F, Moosavinasab S, Houston TK, Yu H. MedTxting: learning based and knowledge rich SMS-style medical text contraction. AMIA Annu Symp Proc. 2012; 2012:558-67. PMID: 23304328.
      View in: PubMed
    23. Agarwal S, Liu F, Yu H. Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions. BMC Bioinformatics. 2011 Oct 03; 12 Suppl 8:S10. PMID: 22151701.
      View in: PubMed
    24. Liu F, Antieau LD, Yu H. Toward automated consumer question answering: automatically separating consumer questions from professional questions in the healthcare domain. J Biomed Inform. 2011 Dec; 44(6):1032-8. PMID: 21856442.
      View in: PubMed
    25. Liu F, Tur G, Hakkani-Tür D, Yu H. Towards spoken clinical-question answering: evaluating and adapting automatic speech-recognition systems for spoken clinical questions. J Am Med Inform Assoc. 2011 Sep-Oct; 18(5):625-30. PMID: 21705457.
      View in: PubMed
    26. Liu F, Liu F, Liu Y. A Supervised Framework for Keyword Extraction from Meeting Transcripts. IEEE Transactions on Audio, Speech and Language Processing. 2011; 19(3):538-548.
    27. Cao Y, Liu F, Simpson P, Antieau L, Bennett A, Cimino JJ, Ely J, Yu H. AskHERMES: An online question answering system for complex clinical questions. J Biomed Inform. 2011 Apr; 44(2):277-88. PMID: 21256977.
      View in: PubMed
    28. Liu F, Liu F, Liu Y. Learning from Chinese-English Parallel Data for Chinese Tense Prediction. Proceedings of International Joint Conference on Natural Language Processing (IJCNLP 2011). 2011.
    29. Yu H, Liu F, Ramesh BP. Automatic figure ranking and user interfacing for intelligent figure search. PLoS One. 2010 Oct 07; 5(10):e12983. PMID: 20949102.
      View in: PubMed
    30. Li Z, Liu F, Antieau L, Cao Y, Yu H. Lancet: a high precision medication event extraction system for clinical text. J Am Med Inform Assoc. 2010 Sep-Oct; 17(5):563-7. PMID: 20819865.
      View in: PubMed
    31. Cao Y, Li Z, Liu F, Agarwal S, Zhang Q, Yu H. An IR-aided machine learning framework for the BioCreative II.5 Challenge. IEEE/ACM Trans Comput Biol Bioinform. 2010 Jul-Sep; 7(3):454-61. PMID: 20671317.
      View in: PubMed
    32. Liu F, Liu Y. Exploring Correlation between ROUGE and Human Evaluation on Meeting Summaries. IEEE Transactions on Audio, Speech and Language Processing. 2010; 18(1):187-196.
    33. Liu F, Liu Y. Identification of Soundbite and Its Speaker Name Using Transcripts of Broadcast News Speech. ACM Transactions on Asian Language Information Processing. 2010; 9(1).
    34. Liu F, Wang D, Li B, Liu Y. . Improving Blog Polarity Classification via Topic Analysis and Adaptive Methods. Proceedings of NAACL-HLT. 2010.
    35. Liu F, Pennell D, Liu F, Liu Y. . Unsupervised Approaches to Automatic Keyword Extraction Using Meeting Transcripts. Proceedings of NAACL-HLT. 2009.
    36. Liu F, Liu Y. . Correlation between ROUGE and Human Evaluation of Extractive Meeting Summaries. Proceedings of ACL. 2008.
    37. Liu F, Liu Y. . Look Who is Talking: Soundbite Speaker Name Recognition in Broadcast News Speech. Proceedings of NAACL/HLT. 2007.
    38. Liu F, Liu Y. Unsupervised Language Model Adaptation Incorporating Name Entity Information. Proceedings of ACL. 2007.
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