Publications and Presentations

The following are publications and presentations crediting the Cancer Deep Phenotype Extraction (DeepPhe) project:

• 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.
• Dmitriy Dligach, Timothy Miller, Guergana K. Savova. 2015. Semi-supervised Learning for Phenotyping Tasks. AMIA Annual Symposium. Nov 2015, San Francisco, CA.
• Lin, Chen; 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
• Lin, Chen; 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
• Timothy A. Miller, Sean Finan, Dmitriy Dligach, Guergana Savova. Robust Sentence Segmentation for Clinical Text. Abstract presented at the Annual Symposium of the American Medical Informatics Association, San Francisco, CA, 2015.
• 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
• 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
• 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.
• 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
• Timothy A. Miller, Dmitriy Dligach, Chen Lin, Steven Bethard, Guergana Savova. Feature Portability in Cross-domain Clinical Coreference. Abstract presented at the Annual Symposium of the American Medical Informatics Association, Chicago, IL, 2016.
• 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
• Timothy A. Miller, Steven Bethard, Hadi Amiri, Guergana Savova. Unsupervised Domain Adaptation for Clinical Negation Detection. Proceedings of the 16th Workshop on Biomedical Natural Language Processing. 2017.
• Timothy A. Miller, Dmitriy Dligach, Steven Bethard, Chen Lin, and Guergana Savova. Towards generalizable entity-centric coreference resolution. Journal of Biomedical Informatics, 69; 251-258. 2017.
• 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
• 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
• 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.
• 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.
• 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.
• Warner, Jeremy. 2018. Improving Cancer Diagnosis and Care: Patient Access to Oncologic Imaging and Pathology Expertise and Technologies. the National Cancer Policy Forum of the National Academies of Sciences, Engineering, and Medicine. http://www.nationalacademies.org/hmd/Activities/Disease/NCPF/2018-FEB-12/Videos/Session%204%20Videos/32%20Warner.aspx