Extracting Time Expressions from Clinical Text

Temporal information extraction is important to understanding text in clinical documents. Temporal expression extraction provides explicit grounding of events in a narrative. In this work we provide a direct comparison of various ways of extracting temporal expressions, using similar features as much as possible to explore the advantages of the methods themselves. We evaluate these systems on both the THYME (Temporal History of Your Medical Events) and i2b2 Challenge corpora. Our main findings are that simple sequence taggers outperform conditional random fields on the new data, and higher-level syntactic features do not seem to improve performance.

[1]  Chih-Jen Lin,et al.  LIBSVM: A library for support vector machines , 2011, TIST.

[2]  Jun'ichi Tsujii,et al.  An end-to-end system to identify temporal relation in discharge summaries: 2012 i2b2 challenge , 2013, J. Am. Medical Informatics Assoc..

[3]  Thomas G. Dietterich What is machine learning? , 2020, Archives of Disease in Childhood.

[4]  Steven Bethard,et al.  ClearTK 2.0: Design Patterns for Machine Learning in UIMA , 2014, LREC.

[5]  Corinna Cortes,et al.  Support-Vector Networks , 1995, Machine Learning.

[6]  Andrew McCallum,et al.  Conditional Random Fields: Probabilistic Models for Segmenting and Labeling Sequence Data , 2001, ICML.

[7]  Goran Nenadic,et al.  Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives , 2013, J. Am. Medical Informatics Assoc..

[8]  James Pustejovsky,et al.  SemEval-2013 Task 1: TempEval-3: Evaluating Time Expressions, Events, and Temporal Relations , 2013, *SEMEVAL.

[9]  Maria Leonor Pacheco,et al.  of the Association for Computational Linguistics: , 2001 .

[10]  Eric Fosler-Lussier,et al.  Temporal Classification of Medical Events , 2012, BioNLP@HLT-NAACL.

[11]  Cui Tao,et al.  Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification , 2013, J. Am. Medical Informatics Assoc..

[12]  Steven Bethard,et al.  ClearTK-TimeML: A minimalist approach to TempEval 2013 , 2013, *SEMEVAL.

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

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

[15]  Michael Gertz,et al.  HeidelTime: High Quality Rule-Based Extraction and Normalization of Temporal Expressions , 2010, *SEMEVAL.

[16]  James Pustejovsky,et al.  SemEval-2007 Task 15: TempEval Temporal Relation Identification , 2007, Fourth International Workshop on Semantic Evaluations (SemEval-2007).

[17]  Tommaso Caselli,et al.  SemEval-2010 Task 13: TempEval-2 , 2010, *SEMEVAL.

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

[19]  Wendy W. Chapman,et al.  Anaphoric relations in the clinical narrative: corpus creation , 2011, J. Am. Medical Informatics Assoc..

[20]  Michael Gertz,et al.  HeidelTime: Tuning English and Developing Spanish Resources for TempEval-3 , 2013, *SEMEVAL.