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Welcome to the THYME project
Welcome to the Temporal Histories of Your Medical Event (THYME) project (THYME is pronounced [taim]).
The overarching long-term vision of our research is to create novel technologies for processing clinical free text. Such technologies will enable sophisticated and efficient indexing, retrieval and data mining over the ever increasing amounts of electronic clinical data. Processing free text poses a number of challenges to which the fields of Artificial intelligence, natural language processing and computer science in general have made advances. Methods for processing free text are informed by linguistic theory combined with the power of modern machine learning. A key component to the next step, natural language understanding, is discovering events and their relations on a timeline. Temporal relations are of prime importance in biomedicine as they are intrinsically linked to diseases, signs and symptoms, and treatments. Understanding the timeline of clinically relevant events is key to the next generation of translational research where the importance of generalizing over large amounts of data holds the promise of deciphering biomedical puzzles.
The best methods have been/will be released as part of the cTAKES (ctakes.apache.org) for the larger community to use and contribute to. We will test the methods against biomedical queries.
Funding
Phase 1 of the project (2010-2014) was supported by THYME R01LM010090 from the National Library Of Medicine and in part by the i2b2 project (U54LM008748 from the National Library of Medicine).
Phase 2 (2015-2018) and Phase 3 (2019-2023) are supported by THYME R01LM010090 from the National Library Of Medicine.
The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Library Of Medicine or the National Institutes of Health.
Who We Are
- Boston Childrens Hospital/Harvard Medical School
- Guergana Savova (MPI)
- Timothy Miller
- Sean Finan
- Chen Lin
- David Harris
- University of Colorado -- Boulder
- Martha Palmer (MPI)
- Jim Martin
- Kristin Wright-Bettner
- a small army of Lingustics and Computer Science graduate students
- past -- Wayne Ward, Jordan Boyd-Graber, Will Styler III, Arrick Lanfranchi (through August, 2012), Tim O'Gorman, Kevin Crooks (through December 2013), Mariah Hamang, Jinho Cho
- University of Arizona
- Steven Bethard
- graduate students
- Loyola University Chicago
- Dmitriy Dligach
- graduate students
- University of Minnesota
- Piet de Groen
- University of Alabama, Birmingham
- John Osborne
- Mayo Clinic
- past -- Piet de Groen, Brad Erickson, James Masanz (through July, 2015), Donna Ihrke (through December, 2012), Pauline Funk (through January, 2013)
- Brandeis University
- James Pustejovsky
Publications and presentations crediting THYME
2021
- Lin, Chen, Timothy Miller, Dmitriy Dligach, Steven Bethard, and Guergana Savova. "EntityBERT: Entity-centric Masking Strategy for Model Pretraining for the Clinical Domain." In Proceedings of the 20th Workshop on Biomedical Language Processing, pp. 191-201. 2021.
- Kulshrestha S, Dligach D, Joyce C, Baker MS, Gonzalez R, O’Rourke AP, Glazer JM, Stey A, Kruser JM, Churpek MM, Afshar M. Comparison and Interpretability of Machine Learning Models to Predict Severity of Injury. JAMIA Open. 2021.
- Savova, Guergana . 2021. “Natural Language Processing for Biomedicine”. Informatics and Implementation Science Learning Series (I2S2). April 2021. Brown University, RI
2020
- Ahuja, Y. et al. Leveraging electronic health records data to predict multiple sclerosis disease activity. Ann. Clin. Transl. Neurol. n/a. https://onlinelibrary.wiley.com/doi/10.1002/acn3.51324
- Kristin Wright-Bettner, Chen Lin, Timothy Miller, Steven Bethard, Dmitriy Dligach, Martha Palmer, James H Martin, Guergana Savova, Defining and Learning Refined Temporal Relations in the Clinical Narrative, Proceedings of the 11th International Workshop on Health Text Mining and Information Analysis, 104-114, 2020/11.https://www.aclweb.org/anthology/2020.louhi-1.12/
- Chen Lin, Timothy Miller, Dmitriy Dligach, Farig Sadeque, Steven Bethard, Guergana Savova, A BERT-based One-Pass Multi-Task Model for Clinical Temporal Relation Extraction, Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing, 70-75, 2020/7. https://www.aclweb.org/anthology/2020.bionlp-1.7/
- Alon Geva, Steven H Abman, Shannon F Manzi, Dunbar D Ivy, Mary P Mullen, John Griffin, Chen Lin, Guergana K Savova, Kenneth D Mandl. 2020. Adverse drug event rates in pediatric pulmonary hypertension: a comparison of real-world data sources. Journal of the American Medical Informatics Association, Vol. 27, issue 2, pp. 249-300. PMID: 31769835 PMCID: PMC7025334 DOI: 10.1093/jamia/ocz194. https://academic.oup.com/jamia/article/27/2/294/5643900
- Sujay Kulshrestha, Dmitriy Dligach, Cara Joyce, Marshall S Baker, Richard Gonzalez, Ann P O’Rourke, Joshua M Glazer, Anne Stey, Jacqueline M Kruser, Matthew M Churpek, Majid Afshar. Prediction of severe chest injury using natural language processing from the electronic health record. Injury. 2020.
- Anoop Mayampurath, Matthew Churpek, Xin Su, Sameep Shah, Elizabeth Munroe, Bhakti Patel, Dmitriy Dligach, and Majid Afshar. External Validation of an Acute Respiratory Distress Syndrome Prediction Model Using Radiology Reports. Critical Care Medicine. 2020.
- To D, Sharma B, Karnik N, Joyce C, Dligach D, Afshar M. Validation of an alcohol misuse classifier in hospitalized patients. Alcohol. 2020 May;84:49-55. doi: 10.1016/j.alcohol.2019.09.008. Epub 2019 Sep 28. PubMed PMID: 31574300; PubMed Central PMCID: PMC7101259.
- Lin, Chen. 2020 . Customize cTAKES for Automated Adverse Drug Event Surveillance in Pediatric Pulmonary Hypertension. ApacheCon 2020, cTAKES track. October 2020. Virtual due to COVID-19. https://www.apachecon.com/acah2020/tracks/ctakes.html
- Savova, Guergana. 2020 . “Natural Language Processing for Cancer Deep Phenotyping”. Observational Health Data Sciences and Informatics (OHDSI) consortium. October 2020.
- Savova, Guergana . 2020. “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. Virtual due to COVID-19
2019
- Kristin Wright-Bettner , Martha Palmer, Guergana Savova, Piet de Groen and Timothy Miller. 2019. Cross-document coreference: An approach to capturing coreference without context. In LOUHI 2019: The Tenth International Workshop on Health Text Mining and Information Analysis. Hong Kong, Nov 3, 2019.https://www.aclweb.org/anthology/D19-6201/
- Dmitriy Dligach, Majid Afshar, Timothy Miller. Towards a Universal Document-Level Clinical Text Encoder: Methods for Neural Network Pre-training with Applications to Substance Misuse. American Medical Informatics Association Symposium. Washington DC, November, 2019.
- Lin, Chen, Miller, Timothy , Dligach, Dmitriy, Bethard, Steven & Savova, Guergana. 2019. A BERT-based Universal Model for Both Within- and Cross-sentence Clinical Temporal Relation Extraction. in Clinical NLP Workshop (2019). Conference North American Association of Computational Linguistics. Minneapolis, MN. June 3-7 2019. https://www.aclweb.org/anthology/W19-1908.pdf
- Guergana Savova, Ioana Danciu, Folami Alamudun, Timothy Miller, Chen Lin, Danielle S Bitterman, Georgia Tourassi and Jeremy L Warner. 2019. Use of Natural Language Processing to Extract Clinical Cancer Phenotypes from Electronic Medical Records. Cancer Research. doi: 10.1158/0008-5472.CAN-19-0579. PMID: 31395609
- To D, Sharma B, Karnik N, Joyce C, Dligach D, Afshar M. Validation of an Alcohol Misuse Classifier in Hospitalized Patients. Alcohol. 2019 Sep 28;. doi: 10.1016/j.alcohol.2019.09.008.
- Dongfang Xu , Egoitz Laparra, Steven Bethard. Pre-trained Contextualized Character Embeddings Lead to Major Improvements in Time Normalization: a Detailed Analysis. Proceedings of the Eighth Joint Conference on Lexical and Computational Semantics (*SEM 2019). Minneapolis, MN. June 2019. https://www.aclweb.org/anthology/S19-1008.
- Piet de Groen, 2019. Challenges and Limitations of Natural Language Processing. Mayo Clinic Conference: Current Applications and Future of Artificial Intelligence in Cardiology. July 20, 2019. San Francisco, California
- Piet de Groen, 2019. Artificial Intelligence: Challenges and Limitations of Natural Language Processing in Healthcare. December 12, 2019 – Medical Grand Rounds: University of Minnesota, Minneapolis, MN
2018
- Lin, Chen; Miller, Timothy; Dligach, Dmitriy; Amiry, Hadi; Bethard, Steven; Savova, Guergana. 2018. Self-training improves Recurrent Neural Networks performance for Temporal Relation Extraction. LOUHI 2018: The Ninth International Workshop on Health Text Mining and Information Analysis. October 31, 2018, Brussels, Belgium
2017
- 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.
- 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
- Natalia Viani, Timothy Miller, Dmitriy Dligach, Steven Bethard, Carlo Napolitano, Silvia Priori, Riccardo Bellazzi, Lucia Sacchi and Guergana Savova. 2017. Recurrent Neural Network Architectures for Event Extraction from Italian Medical Reports. AIME 2017 16th Conference on Artificial Intelligence in Medicine. Vienna, Austria June 21-24, 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
- Timothy A. Miller, Dmitriy Dligach, Chen Lin, Steven Bethard, Guergana Savova. Cross-domain Coreference Feature Exploration. Annual Symposium of the American Medical Informatics Association, Chicago, IL, 2016.
- Steven Bethard, Guergana Savova, Martha Palmer, and James Pustejovsky. SemEval-2017 Task 12: Clinical TempEval. Proceedings of the 11th International Workshop on Semantic Evaluation (SemEval-2017), Vancouver, Canada, August 3-4, 2017.
- Clinical TempEval 2017: http://alt.qcri.org/semeval2017/task12/
2016
- 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
- Miller, Timothy; Dligach, Dmitriy; Chen, Lin; Bethard, Steven; Savova, Guergana. 2016. Cross-domain Coreference Feature Exploration. AMIA Annual Symposium. Chicago, IL. November, 2016
- Steven Bethard and Jonathan Parker (May 2016). “A Semantically Compositional Annotation Scheme for Time Normalization”. In: Proceedings of the Tenth International Conference on Language Resources and Evaluation (LREC 2016).
- Steven Bethard, Guergana Savova, Wei-Te Chen, Leon Derczynski, James Pustejovsky, and Marc Verhagen. 2016. “SemEval-2016 Task 12: Clinical TempEval”. In: Proceedings of the 10th International Workshop on Semantic Evaluation (SemEval 2016). San Diego, CA
- 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
- Clinical TempEval 2016: http://alt.qcri.org/semeval2016/task12/
2015
- 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
- Bethard, Steven; Derczynski, Leon; Savova, Guergana; Pustejovsky, James; Verhagen, Marc. 2015. SemEval-2015 Task 6: Clinical TempEval. Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015). http://www.aclweb.org/anthology/S15-2136. http://aclweb.org/anthology/S/S15/S15-2136.pdf
- Miller, Timothy; Bethard, Steven; Dligach, Dmitriy; Lin, Chen; Savova, Guergana. 2015. Extracting Time Expressions from Clinical Text. Proceedings of BioNLP 15. http://www.aclweb.org/anthology/W15-3809
- Clinical TempEval 2015: http://alt.qcri.org/semeval2015/task6/
- Clinical TempEval 2015 papers:
- Sumithra Velupillai; Danielle L Mowery; Samir Abdelrahman; Lee Christensen; Wendy Chapman. BluLab: Temporal Information Extraction for the 2015 Clinical TempEval Challenge. http://aclweb.org/anthology/S/S15/S15-2137.pdf
- Hegler Tissot; Genevieve Gorrell; Angus Roberts; Leon Derczynski; Marcos Didonet Del Fabro. UFPRSheffield: Contrasting Rule-based and Support Vector Machine Approaches to Time Expression Identification in Clinical TempEval. http://aclweb.org/anthology/S/S15/S15-2141.pdf
2014
- Lin, Chen; Karlson, Elizabeth; Dligach, Dmitriy; Ramirez, Monica; Miller, Timothy; Mo, Huan; Braggs, Natalie; Cagan, Andrew; Denny, Joshua; Savova, Guergana. 2014. Automatic identification of Methotrexade-induced liver toxicity in Rheumatoid Arthritis patients from the electronic medical records. Journal of the Medical Informatics Association. http://jamia.bmj.com/content/early/2014/10/24/amiajnl-2014-002642.abstract
- Pascal B. Pfiffner, JiWon Oh, Timothy A. Miller, Kenneth D. Mandl. 2014. ClinicalTrials.gov as a Data Source for Semi-Automated Point-Of-Care Trial Eligibility Screening. PlosOne. DOI: 10.1371/journal.pone.0111055. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0111055#abstract0
- Pradhan, Sameer; Elhadad, Noemie; South, Brett; Martinez, David; Christensen, Lee; Vogel, Amy; Suominen, Hanna; Chapman, Wendy; Savova, Guergana.2014. Evaluating the state of the art in disorder recognition and normalization of the clinical narrative. Journal of the Medical Informatics Association. http://jamia.bmj.com/content/early/2014/08/21/amiajnl-2013-002544.full.pdf+html
- Sameer Pradhan, Noemie Elhadad, Wendy Chapman, Suresh Manandhar, Guergana Savova. 2014. SemEval 2014: Task 7. In Proceedings of the International Workshop on Semantic Evaluations, Dublin, Ireland. August. http://alt.qcri.org/semeval2014/cdrom/
- Finan, Sean; De Groen, Piet; Savova, Guergana. 2014. Narrative event and temporal relation visualization tool. American Medical Informatics Association annual symposium. November 2014. Washington, DC.
- Bethard, Steven. 2014. The state of the art of temporal relation extraction. Presentation at the NLP workshop at the 4th i2b2 Academic User Group conference. July 9, 2014. Boston, MA.
- Miller, Timothy. 2014. Methods for temporal relation discovery in the clinical narrative. Presentation at the NLP workshop at the 4th i2b2 Academic User Group conference. July 9, 2014. Boston, MA.
- Pradhan, Sameer. 2014. Extrinsic evaluation of temporal relation discovery system. Presentation at the NLP workshop at the 4th i2b2 Academic User Group conference. July 9, 2014. Boston, MA.
- Finan, Sean. 2014. Visualization tool for temporal relations from the clinical narrative. Presentation at the NLP workshop at the 4th i2b2 Academic User Group conference. July 9, 2014. Boston, MA.
- Chen, Pei. 2014. Modules for temporal relation discovery from the clinical narrative in Apache cTAKES. Presentation at the NLP workshop at the 4th i2b2 Academic User Group conference. July 9, 2014. Boston, MA.
- Sameer Pradhan, Xiaoqiang Luo, Marta Recasens, Eduard Hovy, Vincent Ng and Michael Strube. 2014. Scoring Coreference Partitions of Predicted Mentions: A Reference Implementation. Short paper. Association for Computational Linguistics Conference. Baltimore, Maryland. http://anthology.aclweb.org//
- Xiaoqiang Luo, Sameer Pradhan, Marta Recasens and Eduard Hovy. 2014. An Extension of BLANC to System Mentions. Short paper. Association for Computational Linguistics Conference. Baltimore, Maryland. http://anthology.aclweb.org//
- Chen Lin, Timothy Miller, Alvin Kho, Steven Bethard, Dmitriy Dligach, Sameer Pradhan and Guergana Savova. 2014. Descending-Path Convolution Kernel for Syntactic Structures. Short paper. Association for Computational Linguistics Conference. Baltimore, Maryland. http://anthology.aclweb.org//
- Savova, Guergana. 2014. Temporal relation discovery from the clinical narrative. Invited talk at the National Library of Medicine Informatics Series. June 4, 2014. Bethesda, MD.
- Finan, Sean; de Groen, Piet; Savova, Guergana. 2014. Narrative Event and Temporal Relation Visualization Tool. Workshop: Exploring Temporal Patterns in Electronic Health Record Data. 31 Annual Human-Computer Interaction Lab Symposium. May 29 2014. University of Maryland. http://www.cs.umd.edu/hcil/eventflow/workshop2014/
- Bethard, Steven; Ogren, Philip; Becker, Lee. 2014. ClearTK 2.0: Design Patterns for Machine Learning in UIMA. In: Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC'14). http://anthology.aclweb.org//
- Styler, William; Bethard, Steven; Finan, Sean; Palmer, Martha; Pradhan, Sameer; de Groen, Piet; Erickson, Brad; Miller, Timothy; Chen, Lin; Savova, Guergana K.; Pustejovsky, James. 2014. Temporal annotations in the clinical domain. Transactions of the Association for Computational Linguistics. http://www.transacl.org/wp-content/uploads/2014/04/47.pdf
- Savova, Guergana; Pradhan, Sameer; Palmer, Martha; Styler, Will; Chapman, Wendy; Elhadad, Noemie. (in press). Annotating the clinical text – MiPACQ, ShARe, SHARPn and THYME corpora. In Handbook of Linguistic Annotations. Ed. James Pustejovsky and Nancy Ide. Springer.
- Miller, Tim. 2014. Discovering narrative containers in clinical text. i2b2 All Hands meeting, Jan 17, 2014. Boston, MA (presentation)
2013
- Albright, Daniel; Lanfranchi, Arrick; Fredriksen, Anwen; Styler, William; Warner, Collin; Hwang, Jena; Choi, Jinho; Dligach, Dmitriy; Nielsen, Rodney; Martin, James; Ward, Wayne; Palmer, Martha; Savova, Guergana. 2013. Towards syntactic and semantic annotations of the clinical narrative. Journal of the American Medical Informatics Association. 2013;0:1–9. doi:10.1136/amiajnl-2012-001317; http://jamia.bmj.com/cgi/rapidpdf/amiajnl-2012-001317?ijkey=z3pXhpyBzC7S1wC&keytype=ref. PMID: 23355458
- Miller, Timothy; Dligach, Dmitriy; Bethard, Steven; Pradhan, Sameer; Lin, Chen; Savova, Guergana. 2013. Discovering time expressions in clinical text. Late breaking abstract. American Medical Informatics Association Conference. November, 2014. Washington, DC.
- Chen, Wei-Te and Styler, Will. 2013. Anafora: A Web-based General Purpose Annotation Tool. Proceeding of the North American Association for Computational Linguistics Conference. Atlanta, GA, June 9-13. http://www.aclweb.org/anthology/N13-3004. Anafora is available open source from https://github.com/weitechen/anafora
- Miller, Timothy; Bethard, Steven; Dligach, Dmitriy; Pradhan, Sameer; Lin, Chen; and Savova, Guergana. 2013. Discovering narrative containers in clinical text. BioNLP workshop at the Association for Computational Linguistics. http://aclweb.org/anthology/W/W13/W13-1903.pdf
- Bethard, Steven. 2013. A Synchronous Context Free Grammar for Time Normalization. In: Proceedings of the 2013 Conference on Empirical Methods in Natural Language Processing. http://www.aclweb.org/anthology/D13-1078
- Bethard, Steven. 2013. ClearTK-TimeML: A minimalist approach to TempEval 2013. In: Second Joint Conference on Lexical and Computational Semantics (*SEM), Volume 2: Proceedings of the Seventh International Workshop on Semantic Evaluation (SemEval 2013). Atlanta, Georgia, USA: Association for Computational Linguistics, pp. 10-14. http://www.aclweb.org/anthology/S13-2002
- Sameer Pradhan, Alessandro Moschitti, Nianwen Xue, Hwee Tou Ng, Anders Bjorkelund, Olga Uryupina, Yuchen Zhang and Zhi Zhong. 2013. Towards Robust Linguistic Analysis Using OntoNotes. Proceedings of the Conference on Natural Language Learning. Sofia, Bulgaria. August, 2013.
- Dligach, Dmitriy; Bethard, Steven; Becker, Lee; Miller, Timothy; Savova, Guergana. 2013. Discovering body site and severity modifiers in clinical texts. Journal of the American Medical Informatics Association. http://jamia.bmj.com/content/early/2013/10/03/amiajnl-2013-001766.full
- Dmitriy Dligach, Timothy A. Miller, Guergana K. Savova. 2013. Active Learning for Phenotyping Tasks. In Proceedings of the 2013 NLP for Medicine and Biology workshop held in conjunction with RANLP-2013. September 2013. Hissar, Bulgaria. http://aclweb.org/anthology//W/W13/W13-5101.pdf
- Finan, Sean. 2013. Challenges of visually representing rich temporal information of the clinical narrative. Workshop: Exploring Temporal Patterns in Electronic Health Record Data. 30th Annual Human-Computer Interaction Lab Symposium. May 22-23 2013. University of Maryland. http://www.cs.umd.edu/hcil/eventflow/workshop2013/
- American Medical Informatics Association (AMIA) national webinar. “Towards semantic annotations of the clinical narrative”. National webinar. April 2013 (invited presentation)
- Natural Language Processing Working Group Pre-Symposium – doctoral consortium and a data workshop. “Shared Annotated Resources for the Clinical Domain”. American Medical Informatics Association. Washington, DC, USA. November 2013.
- Savova, Guergana; Chapman, Wendy; Elhadad, Noemie; Palmer, Martha. 2013. Shared resources, shared code and shared activities in clinical natural language processing. AMIA Annual Symposium, Panel. Washington, DC.
- AMIA Fall symposium workshop on Natural Language Processing and data. Dr. Savova presented THYME work as part of the data workshop.
2012
- Savova, Guergana. 2012. Shared Annotated Resources for the Clinical Domain. Natural Language Processing (NLP) Annotation workshop collocated with the 2nd annual IEEE International Conference on Healthcare Informatics, Imaging and Systems Biology. San Diego, CA, USA. September 2012.
- Drs. Pustejovsky, Palmer and Savova are members of the Program Committee of the 2012 i2b2 shared task whose topic is temporal relations in the clinical domain. The THYME annotation guidelines are the basis of the annotation guidelines for that shared task.
- Participation in the State of the Art of Clinical NLP workshop organized by the NLM in April, 2012. Dr. Savova chaired a session, Prof. Pustejovsky was an invited speaker presenting on Temporal relations/TimeML.
- Participation and presentation in the AMIA Fall symposium workshop on Natural Language Processing and data. Dr. Savova presented THYME work as part of the data workshop.
2011
- Savova, Guergana; Chapman, Wendy; Elhadad, Noemie; Palmer, Martha. 2011. Shared annotated resources for the clinical domain. AMIA Annual Symposium, Panel. Washington, DC.
- CLEF/ShARe 2014 (in collaboration with the ShARe project): http://clefehealth2014.dcu.ie/task-2
- SemEval 2014 Analysis of Clinical Text Task 7 (in collaboration with the ShARe project): http://alt.qcri.org/semeval2014/task7/
- SemEval 2015 Analysis of Clinical Text Task 14 (in collaboration with the ShARe project): http://alt.qcri.org/semeval2015/task14/
- SemEval 2015 Clinical TempEval Task 6: http://alt.qcri.org/semeval2015/task6/
- SemEval 2016 Clinical TempEval Task 12: http://alt.qcri.org/semeval2016/task12/
- SemEval 2017 Clinical TempEval Task 12: http://alt.qcri.org/semeval2017/task12/
Getting access to the THYME corpus and gold standard annotations
The THYME corpus with the gold standard annotations is available to others involved in NLP research under a data use agreement (DUA) with Mayo Clinic. The corpus is distributed through the hNLP Center (center.healthnlp.org). Please, visit the hNLP Center website for more details.
When using the THYME corpus, please
- Include the Mayo Clinic in your acknowledgements
- Cite the article: William F. Styler IV, Steven Bethard, Sean Finan, Martha Palmer, Sameer Pradhan, Piet C. de Groen, Brad Erickson, Timothy Miller, Chen Lin, Guergana Savova, James Pustejovsky. Temporal Annotation in the Clinical Domain. Transactions of the Association for Computational Linguistics. Vol 2 (2014). https://tacl2013.cs.columbia.edu/ojs/index.php/tacl/article/view/305
THYME Gold Standard Annotations
Annotation layers are treebank and propbank annotations as well as temporal annotations for events, temporal expressions and temporal relations.
Annotation guidelines
- The THYME Temporal Relations Guidelines (PDF) - The current version of the THYME Temporal Relations Guidelines and release notes. Updated February 28th, 2014.
- i2b2 Simplified THYME Guidelines (PDF) The guidelines provided to the organizers of the 2012 Temporal relations i2b2 challenge for consideration during planning. They reflect an earlier stage of our guidelines.
- Syntactic Tree (Treebank): http://clear.colorado.edu/compsem/documents/treebank_guidelines.pdf
- Semantic Role (Propbank): http://clear.colorado.edu/compsem/documents/propbank_guidelines.pdf
- UMLS entity and relations annotations/templates: http://clear.colorado.edu/compsem/documents/umls_guidelines.pdf
- Clinical coreference guidelines (based on ODIE, OntoNotes, MUC-7): http://clear.colorado.edu/compsem/documents/Coreference%20Guidelines.pdf
Tool for viewing the gold standard annotations - Anafora
We developed a web-based annotation tool. It is open source and available at https://github.com/weitechen/anafora. Use it to view the THYME annotations. Citation for the tool is:
Chen, Wei-Te and Styler, Will. 2013. Anafora: A Web-based General Purpose Annotation Tool. Proceeding of the North American Association for Computational Linguistics Conference. Atlanta, GA, June 9-13. http://www.aclweb.org/anthology/N13-3004.
Viewing the gold standard annotations (Anafora)
(available to the team only)
To view the Temporal-Entity data, use the URL:
https://verbs.colorado.edu/anafora/annotate/Temporal/ColonCancer/TASK_NAME/Temporal.Entity/gold/
TASK_NAME is the filestem, for example, ID074_path_219b
to view Temporal-Relation data:
https://verbs.colorado.edu/anafora/annotate/Temporal/ColonCancer/TASK_NAME/Temporal.Relation/gold/
you could find the available Entity/Relation gold data on verbs by using:
find /data/anafora/anaforaProjectFile/Temporal/ -name "*Temporal-Entity.gold.completed.xml" find /data/anafora/anaforaProjectFile/Temporal/ -name "*Temporal-Relation.gold.completed.xml"
Train/Development/Test splits
- Use this split for experiments with the THYME data (% 8)!
- (A note about Protege/Knowtator and Anafora annotation tools: annotations)
Colon Cancer Data
- Train sets (Residue 0,1,2,3): [1, 2, 3, 8, 9, 10, 11, 16, 17, 18, 19, 24, 25, 26, 27, 32, 33, 34, 35, 40, 41, 42, 43, 48, 49, 50, 51, 56, 57, 58, 59, 64, 65, 66, 67, 72, 73, 74, 75, 80, 81, 82, 83, 88, 89, 90, 91, 96, 97, 98, 99, 104, 105, 106, 107, 112, 113, 114, 115, 120, 121, 122, 123, 128, 129, 130, 131, 136, 137, 138, 139, 144, 145, 146, 147, 152, 153, 154, 155, 160, 161, 162, 163, 168, 169, 170, 171, 176, 177, 178, 179, 184, 185, 186, 187, 192, 193, 194, 195, 200, 201, 202, 203, 208, 209, 210, 211, 216, 217]
- Development sets (Residue 4,5): [4, 5, 12, 13, 20, 21, 28, 29, 36, 37, 44, 45, 52, 53, 60, 61, 68, 69, 76, 77, 84, 85, 92, 93, 100, 101, 108, 109, 116, 117, 124, 125, 132, 133, 140, 141, 148, 149, 156, 157, 164, 165, 172, 173, 180, 181, 188, 189, 196, 197, 204, 205, 212, 213]
- Test sets (Residue 6,7): [6, 7, 14, 15, 22, 23, 30, 31, 38, 39, 46, 47, 54, 55, 62, 63, 70, 71, 78, 79, 86, 87, 94, 95, 102, 103, 110, 111, 118, 119, 126, 127, 134, 135, 142, 143, 150, 151, 158, 159, 166, 167, 174, 175, 182, 183, 190, 191, 198, 199, 206, 207, 214, 215]
Brain Cancer Data
- Train sets: [1, 2, 3, 8, 9, 10, 11, 16, 17, 18, 19, 24, 25, 26, 27, 32, 33, 34, 35, 40, 41, 42, 43, 48, 49, 50, 51, 56, 57, 58, 59, 64, 65, 66, 67, 72, 73, 74, 75, 80, 81, 82, 83, 88, 89, 90, 91, 96, 97, 98, 99, 104, 105, 106, 107, 112, 113, 114, 115, 120, 121, 122, 123, 128, 129, 130, 131, 136, 137, 138, 139, 144, 145, 146, 147, 152, 153, 154, 155, 160, 161, 162, 163, 168, 169, 170, 171, 176, 177, 178, 179, 184, 185, 186, 187, 192, 193, 194, 195, 200, 201]
- Development sets: [4, 5, 12, 13, 20, 21, 28, 29, 36, 37, 44, 45, 52, 53, 60, 61, 68, 69, 76, 77, 84, 85, 92, 93, 100, 101, 108, 109, 116, 117, 124, 125, 132, 133, 140, 141, 148, 149, 156, 157, 164, 165, 172, 173, 180, 181, 188, 189, 196, 197]
- Test sets: [6, 7, 14, 15, 22, 23, 30, 31, 38, 39, 46, 47, 54, 55, 62, 63, 70, 71, 78, 79, 86, 87, 94, 95, 102, 103, 110, 111, 118, 119, 126, 127, 134, 135, 142, 143, 150, 151, 158, 159, 166, 167, 174, 175, 182, 183, 190, 191, 198, 199]
THYME Software
The THYME system is available as part of Apache cTAKES at http://ctakes.apache.org/
Demo of the system: ctakes.apache.org -> get started -> demos -> ctakes-temporal (http://alt.qcri.org/semeval2016/task12/)
We have developed a visualization tool (THYME viz tool) available in Apache cTAKES sandbox. A prototype and details of the THYME vizualization tool was presented by Sean Finan at several annual workshops:
- Finan, Sean. 2013. Challenges of visually representing rich temporal information of the clinical narrative. Workshop: Exploring Temporal Patterns in Electronic Health Record Data. 30th Annual Human-Computer Interaction Lab Symposium. May 22-23 2013. University of Maryland. http://www.cs.umd.edu/hcil/eventflow/workshop2013/
- Finan, Sean. De Groen, Piet. Savova, Guergana. 2014. Narrative Event and Temporal Relation Visualization Tool. Workshop: Exploring Temporal Patterns in Electronic Health Record Data. 31st Annual Human-Computer Interaction Lab Symposium. May 29 2014. University of Maryland. http://www.cs.umd.edu/hcil/eventflow/workshop2014/
- Finan, Sean. De Groen, Piet. Savova, Guergana. 2014. Narrative Event and Temporal Relation Visualization Tool. Natural Language Processing Workshop. Informatics for Integrating Biology & the Bedside (I2B2). 4th Annual Academic User Group Meeting. July 9 2014. Harvard Medical School.
https://www.i2b2.org/events/slides/NarrativeVisualizer.pdf
Relevant Background Papers
Reading Group
Internal Presentations
Venues for manuscript submissions
Venues for manuscript submissions/publications
Project materials
Tasks, leads, teams and deadlines
Annotations - Describes the corpus, the layers of annotations and annotation progress
Annotation Tools - Describes the progress and information pertaining to the Anafora annotation tool
Communication
- Bi-weekly team meetings, Fri 11am-noon ET
- Weekly methods meetings: Weds 12noon-1:30PM Eastern time
IDEAS notebook
Meeting Notes
- Oct 16, 2024 Methods meeting
- Oct 9, 2024 Methods meeting
- Oct 2, 2024 Methods meeting
- Methods call on Sept 25, 2024 is CANCELLED
- Sept 18, 2024 Methods meeting
- Sept 11, 2024 Methods meeting
- Meetings on Aug 28, 2024 and Sept 4, 2024 CANCELLED
- Aug 21, 2024 Methods meeting
- Aug 14, 2024 Methods meeting
- Aug 7, 2024 Methods meeting
- Jul 31, 2024 Methods meeting
- Jul 24, 2024 Methods meeting
- Jul 17, 2024 Methods meeting
- Jul 10, 2024 Methods meeting
- Jun 26, 2024 Methods meeting
- Jun 19, 2024 CANCELLED -- Juneteenth Holiday!
- Jun 12, 2024 Methods meeting
- Jun 5, 2024 Methods meeting
- May 29, 2024 Methods meeting
- May 22, 2024 Methods meeting
- May 14, 2024 Methods meeting
- May 8, 2024 Methods meeting
- May 1, 2024 Methods meeting
- Apr 24, 2024 Methods meeting
- Apr 17, 2024 Methods meeting
- Apr 10, 2024 Methods meeting
- Apr 3, 2024 Methods meeting
- Mar 27, 2024 Methods meeting
- Mar 13, 2024 Methods meeting
- Mar 6, 2024 Methods meeting
- Feb 28, 2024 Methods meeting
- Feb 21, 2024 Methods meeting
- Feb 14, 2024 Methods meeting
- Feb 7, 2024 Methods meeting
- Jan 31, 2024 Methods meeting
- Jan 24, 2024 Methods meeting
- Jan 17, 2024 Methods meeting
- Jan 10, 2024 Methods meeting
- Canceled for Dec 27 and Jan 3, resuming Jan 10
- 2023 Meeting notes
- 2022 Meeting notes
- 2021 Meeting notes
- 2020 Meeting notes
- 2019 Meeting notes
- 2018 Meeting notes
- 2017 Meeting notes
- 2016 Meeting notes
- 2015 Meeting notes
- 2014 Meeting notes
- 2013 Meeting notes
- 2012 Meeting notes
Getting started
Contact
If you need assistance and/or if you have questions about the project, feel free to send e-mail to guergana dot savova at childrens dot harvard dot edu, martha dot palmer at colorado dot edu, or bethard at email dot arizona dot edu.