DeepPhe

Related Publications, Presentations, Panels

  1. Lin C, Miller T, Dligach D, Bethard S, Savova G. EntityBERT: Entity-centric Masking Strategy for Model Pretraining for the Clinical Domain. BioNLP workshop at the 2021 North American Association for Computational Linguistics (NAACL) conference; 2021 June.
  2. Wright-Bettner K, Lin C, Miller T, Bethard S, Dligach D, Palmer M, Martin JH, Savova G. Defining and Learning Refined Temporal Relations in the Clinical Narrative. virtual conference due to COVID-19 pandemic: 11th International Workshop on Health Text Mining and Information Analysis (LOUHI) at EMNLP 2020; 2020 November. Available from: https://www.aclweb.org/anthology/2020.louhi-1.12.pdf.
  3. Bitterman DS, Miller TA, Mak RH, Savova GK. Clinical Natural Language Processing for Radiation Oncology: A Review and Practical Primer. Int J Radiat Oncol Biol Phys. 2021 Feb 3;. doi: 10.1016/j.ijrobp.2021.01.044. [Epub ahead of print] Review. PubMed PMID: 33545300.
  4. Jeon H, You SC, Kang SY, Seo SI, Warner JL, Belenkaya R, Park RW. Characterizing the Anticancer Treatment Trajectory and Pattern in Patients Receiving Chemotherapy for Cancer Using Harmonized Observational Databases: Retrospective Study. Journal of Medical Internet Research. 2021 Apr 6;9(4):e25035. PMID: 33720842; PMCID: PMC8058693.
  5. Yuan Z, Finan S, Warner J, Savova G, Hochheiser H. Interactive Exploration of Longitudinal Cancer Patient Histories Extracted From Clinical Text. JCO Clin Cancer Inform. 2020 May;4:412-420. doi: 10.1200/CCI.19.00115. PubMed PMID: 32383981; PubMed Central PMCID: PMC7265796.
  6. Ye Y (U Pitt), Boyce RD (U Pitt), Davis MK (U Pitt), Elliston K (tranSMART Foundation & Axiomedix, Inc.), Davatzikos C (U Penn), Fedorov A (Harvard), Fillion-Robin JC (Kitware Inc.), Foster I (U Chicago), Gilbertson J (U Pitt), Heiskanen M (NCI ITCR), Klemm J (NCI ITCR), Lasso A (Queen’s University), Miller JV (GE Research), Morgan M (RPCI), Pieper S (Isomics Inc.), Raumann B (U Chicago), Sarachan B (GE Research), Savova G (Harvard), Silverstein JC (U Pitt), Taylor D (U Pitt), Zelnis J (U Pitt), Zhang GQ (UT Health) and Becich MJ (U Pitt). 2019. Open Source Software Sustainability Models: Initial White Paper from the Informatics Technology for Cancer Research Sustainability and Industry Partnership Work Group. Arxiv. https://arxiv.org/ftp/arxiv/papers/1912/1912.12371.pdf
  7. Savova GK, Danciu I, Alamudun F, Miller T, Lin C, Bitterman DS, Tourassi G, Warner JL. Use of Natural Language Processing to Extract Clinical Cancer Phenotypes from Electronic Medical Records. Cancer Res. 2019 Nov 1;79(21):5463-5470. doi: 10.1158/0008-5472.CAN-19-0579. Epub 2019 Aug 8. Review. PubMed PMID: 31395609; PubMed Central PMCID: PMC7227798.
  8. Warner JL, Dymshyts D, Reich CG, Gurley MJ, Hochheiser H, Moldwin ZH, Belenkaya R, Williams AE, Yang PC. HemOnc: A new standard vocabulary for chemotherapy regimen representation in the OMOP common data model. J Biomed Inform. 2019 Aug;96:103239. doi: 10.1016/j.jbi.2019.103239. Epub 2019 Jun 22. PubMed PMID: 31238109; PubMed Central PMCID: PMC6697579.
  9. Malty AM, Jain SK, Yang PC, Harvey K, Warner JL. Computerized Approach to Creating a Systematic Ontology of Hematology/Oncology Regimens. JCO Clin Cancer Inform. 2018;2. doi: 10.1200/CCI.17.00142. Epub 2018 May 11. PubMed PMID: 30238070; PubMed Central PMCID: PMC6141041.
  10. Miller, Timothy; Dligach, Dmitriy; Bethard, Steven; Lin, Chen; Savova, Guergana. 2017. Towards Portable Entity-Centric Clinical Coreference Resolution. Journal of Biomedical Informatics. Vol. 69, May 2017, pp. 251-258. https://doi.org/10.1016/j.jbi.2017.04.015; http://www.sciencedirect.com/science/article/pii/S1532046417300850
  11. Castro SM, Tseytlin E, Medvedeva O, Mitchell K, Visweswaran S, Bekhuis T, Jacobson RS. 2017. Automated annotation and classification of BI-RADS assessment from radiology reports. J Biomed Inform. 2017 May;69:177-187. doi: 10.1016/j.jbi.2017.04.011. PMID: 28428140; PMCID: PMC5706448 [Available on 2018-05-01] DOI:10.1016/j.jbi.2017.04.011
  12. Lin, Chen; Miller, Timothy; Dligach, Dmitriy; Bethard, Steven; Savova, Guergana. 2017. Representations of Time Expressions for Temporal Relation Extraction with Convolutional Neural Networks. BioNLP workshop at the Association for Computational Linguistics conference. Vancouver, Canada, Friday August 4, 2017
  13. Miller, T; Bethard, S; Amiri, H; Savova, G. 2017. Unsupervised Domain Adaptation for Clinical Negation Detection. BioNLP workshop at the Association for Computational Linguistics conference. Vancouver, Canada, Friday August 4, 2017
  14. Savova, G., Tseytlin, E., Finan, S., Castine, M., Miller, T., Medvedeva, O., Haris, D., Hochheiser, H., Lin, C., Chavan, G., Jacobson R. 2017. DeepPhe - A Natural Language Processing System for Extracting Cancer Phenotypes from Clinical Records. Annual Symposium of the American Medical Informatics Association (AMIA). Nov 2017. Washington DC
  15. Savova, G., Tseytlin, E., Finan, S., Castine, M., Miller, T., Medvedeva, O., Haris, D., Hochheiser, H., Lin, C., Chavan, G., Jacobson R. 2017. DeepPhe: A Natural Language Processing System for Extracting Cancer Phenotypes from Clinical Records Cancer Research 77(21), November 2017 DOI: 10.1158/0008-5472.CAN-17-0615.
  16. Savova, G; Miller, T. 2018. DeepPhe and Extraction of Oncology Patient Phenotypes from Unstructured Text Using NLP and Other AI Tools. Presentation to Dana Farber Cancer Institute. January 24 2018. Boston, MA.
  17. Chen, Lin; Miller, Timothy; Dligach, Dmitriy; Bethard, Steven; Savova, Guergana. 2016. Improving Temporal Relation Extraction with Training Instance Augmentation. BioNLP workshop at the Association for Computational Linguistics conference. Berlin, Germany, Aug 2016
  18. Hochheiser, Harry; Castine, Melissa; Harris, David; Savova, Guergana; Jacobson, Rebecca. 2016. An Information Model for Cancer Phenotypes. BMC Medical Informatics and Decision Making. https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-016-0358-4
  19. Ethan Hartzell, Chen Lin. 2016. Enhancing Clinical Temporal Relation Discovery with Syntactic Embeddings from GloVe. International Conference on Intelligent Biology and Medicine (ICIBM 2016). December 2016, Houston, Texas, USA
  20. Dligach, Dmitriy; Miller, Timothy; Lin, Chen; Bethard, Steven; Savova, Guergana. 2017. Neural temporal relation extraction. European Chapter of the Association for Computational Linguistics (EACL 2017). April 3-7, 2017. Valencia, Spain.
  21. Hochheiser H; Jacobson R; Washington N; Denny J; Savova G. 2015. Natural language processing for phenotype extraction: challenges and representation. AMIA Annual Symposium. Nov 2015, San Francisco, CA.
  22. Dmitriy Dligach, Timothy Miller, Guergana K. Savova. 2015. Semi-supervised Learning for Phenotyping Tasks. AMIA Annual Symposium. Nov 2015, San Francisco, CA.
  23. Chen, Lin; Dligach, Dmitriy; Miller, Timothy; Bethard, Steven; Savova, Guergana. 2015. Layered temporal modeling for the clinical domain. Journal of the American Medical Informatics Association. http://jamia.oxfordjournals.org/content/early/2015/10/31/jamia.ocv113
  24. Savova G, Hochheiser H. Cancer Deep Phenotyping from Electronic Medical Records. In Workshop at 2021 North American Association of Central Cancer Registries. 2021 June. Virtual due to COVID-19.
  25. Savova G, Hochheiser H. Cancer Deep Phenotyping from Electronic Medical Records. Seminar series at Department of Biomedical Informatics, Vanderbilt University. 2021 April; Nashville, TN.
  26. Savova G. Natural Language Processing for Biomedicine. Informatics and Implementation Science Learning Series (I2S2).. 2021 April; Brown University, RI, USA.
  27. Meystre S, Silverstein J, Savova G, Petkov V, Savova G, Malin B. De-identification of Clinical Text: Stakeholder’s Perspectives and Acceptance of Automatic De-identification. Panel at the American Medical Informatics Association Annual Symposium. 2020 November; virtual due to COVID-19.
  28. Savova G. Natural Language Processing for Cancer Deep Phenotyping. Observational Health Data Sciences and Informatics (OHDSI) consortium. 2020 October; virtual due to COVID-19 pandemic.
  29. Savova G. Clinical Natural Language Processing, Some Tasks and Applications in Medicine. 11th International Workshop on Heath Text Mining and Information Analysis (LOUHI), Conference on Empirical Methods for Natural Language Processing (EMNLP). 2020 October; Virtual due to COVID-19.
  30. Savova G. Current status, performance, and future development of clinical text de-identification systems: MIST system. National Cancer Institute, National Institutes of Health. 2020 February; Washington, DC.
  31. Savova G. Acceptance of machine text de-identification of EMR data by all stakeholders: What do we need to consider?. National Cancer Institute, National Institutes of Health. 2020 February; Washington, DC.
  32. Savova G, Hochheiser H. Cancer Deep Phenotype Extraction from Electronic Medical Records. Data Science Seminar Series. National Cancer Institute, National Institutes of Health. 2019 October; Washington, DC.
  33. Warner J, Durbin E, Petkov V, Savova G. Tools and Software to Automate and Normalize the Cancer Data Abstraction Workflow. Vancouver, Canada: Workshop at 2019 Conference of the North American Association of Central Cancer Registries and the International Association of Cancer Registries; 2019 June.
  34. Savova G. Cancer Deep Phenotype Extraction from Electronic Medical Records. Molecular Med Tri-con. 2019 March; San Francisco, CA, USA.
  35. Yuan Z, Finan S, Warner J, Savova G, Hochheiser H. Toward Longitudinal Visual Analytics for Cancer Patient Trajectories Extracted from Clinical Text. 2018 Workshop on Visual Analytics and Healthcare, Demonstration Presentation. AMIA 2018. 2018 November; San Francisco, CA, USA.
  36. Warner J, Elhadad N, Bastrache L, Gotz D, Savova G. Panel - Didactic: Computable Longitudinal Patient Trajectories. Annual Symposium of the American Medical Informatics Association. 2018 November; San Francisco, CA, USA.
  37. Savova G. Software and Research Challenges for Clinical NLP. Dana Farber Cancer Institute. 2018 October; Boston, MA, USA.
  38. Savova G. Software and Research Challenges for Clinical NLP. UPMC. 2018 September; Pittsburgh, PA, United States.
  39. Savova G. Cancer Deep Phenotype Extraction form Electronic Medical Records (DeepPhe). Astra Zeneca (invited talk). 2018 July; Waltham, MA, USA.
  40. Savova G, Tseytlin E, Finan S, Castine M, Miller T, Medvedeva O, Harris D, Hochheiser H, Lin C, Chavan G, Warner J, Jacobson R. DeepPhe – a natural language processing system for extracting cancer phenotypes from clinical records. Annual conference of the North American Association of Central Cancer Registries (NAACCR). 2018 June; Pittsburgh, PENNSYLVANIA, United States.
  41. Yang C, Malty A, Jain S, Harvey K, Finan S, Warner J. A Comprehensive Ontology of Hematology/Oncology Regimens. Annual conference of the North American Association of Central Cancer Registries (NAACCR). 2018 June; Pittsburgh, PENNSYLVANIA, United States.
  42. Warner J, Harris D, Rubenstein S, Finan S, Lin C, Miller T, Amiri H, Hochheiser H, Savova G. Capturing high-resolution temporal cancer phenotypes using DeepPhe. Annual conference of the North American Association of Central Cancer Registries (NAACCR). 2018 June; Pittsburgh, PENNSYLVANIA, United States.
  43. Savova G, Miller T. DeepPhe and Extraction of Oncology Patient Phenotypes from Unstructured Text Using NLP and Other AI Tools. Dana Farber Cancer Institute. 2018 January; Boston, MA, USA.
  44. Warner J. Supporting cancer registries through automated extraction of pathology and chemotherapy regimen information. CDC/NCI/FDA/VA Clinical Natural Language Processing Workshop (invited). 2017 December; Atlanta, GA, USA.
  45. Savova G. Select Applications of Natural Language Processing in Biomedicine. Natural Language Processing Symposium, Boston University (invited). 2017 November; Boston, MA, United States.
  46. Jacobson R. Invited presentation at Case Western University Comprehensive Cancer Center Seminar Series. Case Western University Comprehensive Cancer Center Seminar Series. 2017 March; Cleveland, OH, USA.
  47. Jacobson R. Invited presentation at Ohio State University James Cancer Center Grand Rounds. Ohio State University James Cancer Center Grand Rounds. 2017 January; Columbus, OH, USA.
  48. Jacobson R, Savova G. Invited presentation at SEER meeting. SEER meeting. 2016 December; Gaithersburg, MD, USA.
  49. Jacobson R. Invited presentation at University of Pittsburgh Cancer Institute Scientific Retreat. University of Pittsburgh Cancer Institute Scientific Retreat. 2016 June; Pittsburgh, PENNSYLVANIA, United States.
  50. Jacobson R. Invited presentation at Pathology Informatics. Pathology Informatics. 2016 May; Pittsburgh, PENNSYLVANIA, United States.
  51. Jacobson R. Invited presentation at University of Michigan Department of Learning Health Sciences. University of Michigan Department of Learning Health Sciences. 2016 April; Ann Arbor, MI, USA.
  52. Finan S. Invited presentation at CI4CC. Cancer Informatics for Cancer Centers. 2016 March; Napa, CA, USA.
  53. Jacobson R. Invited presentation at University of Pittsburgh Cancer Informatics (UPCI) External Advisory Board. University of Pittsburgh Cancer Informatics (UPCI). 2016 March; Pittsburgh, PENNSYLVANIA, United States.
  54. Jacobson R. Invited presentation at SEER PI meeting. SEER PI meeting. 2016 March; New Mexico, NM, USA.

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