GUIR at SemEval-2017 Task 12: A Framework for Cross-Domain Clinical Temporal Information Extraction

Clinical TempEval 2017 (SemEval 2017 Task 12) addresses the task of cross-domain temporal extraction from clinical text. We present a system for this task that uses supervised learning for the extraction of temporal expression and event spans with corresponding attributes and narrative container relations. Approaches include conditional random fields and decision tree ensembles, using lexical, syntactic, semantic, distributional, and rule-based features. Our system received best or second best scores in TIMEX3 span, EVENT span, and CONTAINS relation extraction.

[1]  Peter Szolovits,et al.  MIMIC-III, a freely accessible critical care database , 2016, Scientific Data.

[2]  Anna Rumshisky,et al.  Evaluating temporal relations in clinical text: 2012 i2b2 Challenge , 2013, J. Am. Medical Informatics Assoc..

[3]  M. Hepple,et al.  Semantic Annotation of Clinical Text : The CLEF Corpus , 2008 .

[4]  J. Friedman Greedy function approximation: A gradient boosting machine. , 2001 .

[5]  Nate Blaylock,et al.  A corpus of clinical narratives annotated with temporal information , 2012, IHI '12.

[6]  Angus Roberts,et al.  The CLEF Corpus: Semantic Annotation of Clinical Text , 2007, AMIA.

[7]  James Pustejovsky,et al.  SemEval-2015 Task 6: Clinical TempEval , 2015, *SEMEVAL.

[8]  Jeffrey Dean,et al.  Distributed Representations of Words and Phrases and their Compositionality , 2013, NIPS.

[9]  Robert L. Mercer,et al.  Class-Based n-gram Models of Natural Language , 1992, CL.

[10]  Nathanael Chambers,et al.  Jointly Combining Implicit Constraints Improves Temporal Ordering , 2008, EMNLP.

[11]  Wayne H. Ward,et al.  Towards Temporal Relation Discovery from the Clinical Narrative , 2009, AMIA.

[12]  Tianqi Chen,et al.  XGBoost: A Scalable Tree Boosting System , 2016, KDD.

[13]  Chen Lin,et al.  Temporal Annotation in the Clinical Domain , 2014, TACL.

[14]  Yuji Matsumoto,et al.  Jointly Identifying Temporal Relations with Markov Logic , 2009, ACL.

[15]  Chen Lin,et al.  Discovering Temporal Narrative Containers in Clinical Text , 2013, BioNLP@ACL.

[16]  James Pustejovsky,et al.  SemEval-2017 Task 12: Clinical TempEval , 2017, *SEMEVAL.

[17]  Yaoyun Zhang,et al.  UTHealth at SemEval-2016 Task 12: an End-to-End System for Temporal Information Extraction from Clinical Notes , 2016, *SEMEVAL.

[18]  Daniel Gildea,et al.  The Proposition Bank: An Annotated Corpus of Semantic Roles , 2005, CL.

[19]  Nazli Goharian,et al.  GUIR at SemEval-2016 task 12: Temporal Information Processing for Clinical Narratives , 2016, SemEval@NAACL-HLT.

[20]  Olivier Bodenreider,et al.  The Unified Medical Language System (UMLS): integrating biomedical terminology , 2004, Nucleic Acids Res..

[21]  Shan Wang,et al.  Classifying Temporal Relations Between Events , 2007, ACL.

[22]  Danielle L. Mowery,et al.  BluLab: Temporal Information Extraction for the 2015 Clinical TempEval Challenge , 2015, *SEMEVAL.