Temporal expressions identification in biomedical texts

COMP80122: ﬁnal presentationtemporal expressions identiﬁcation in biomedical texts Michele Filannino Manchester, 29/02/2012

presentation temporal expressionswhere we are■ Computer science ● natural language processing ▶ information extraction ★ temporal expressions extraction 29/02/2012, Michele Filannino 2 / 23

presentation temporal expressionstemporal expression deﬁnition ■ natural language phrase that denotes a temporal entity: an interval, or an instant (Ferro et Al.)1 ● She has been at work for more than a month ● He wrapped up a three-hour meeting with the Iraqi president in Baghdad today.1 L. Ferro, I. Mani, B. Sundheim, and G. Wilson, “Tides temporal annotationguidelines, v. 1.0.2,” MITRE, 2001 29/02/2012, Michele Filannino 3 / 23

presentation temporal expressionswhy?■ user’s perspective ● temporal aspects of events and entities provide a natural mechanism for organising information.■ machine’s perspective ● improvements in ▶ question answering, summarisation, browsing 29/02/2012, Michele Filannino 4 / 23

presentation temporal expressionswhy clinical domain? ■ diagnosis explanation ■ disease progression modelling ■ analysis of eﬀectiveness of treatment 29/02/2012, Michele Filannino 5 / 23

presentation temporal expressionsscientiﬁc interest “temporal expressions” AND “clinical” 70 63 56 49 42 35 61 28 49 46 46 21 43 38 14 25 18 16 7 15 10 12 10 0 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012Source: Google Scholar (last update 27/02/2012) 29/02/2012, Michele Filannino 6 / 23

presentation temporal expressionstemporal forms 1 ■ time or date references ● 11pm, February 14th, 2005 ■ time references that anchor on another time ● one hour after midnight, two weeks before Christmas ■ durations ● few months, two days, ﬁve years ■ recurring times ● every third month, twice in the hour1 J. Poveda, M. Surdeanu, and J. Turmo, “An analysis of Bootstrapping for theRecognition of Temporal Expressions”, 2009 29/02/2012, Michele Filannino 7 / 23

presentation temporal expressionstemporal forms 1 ■ context-dependent times ● today, last year ■ vague references ● somewhere in the middle of June, the near future ■ times indicated by an event ● the day S. Berlusconi resigned ▶ an event is considered a cover term for situations that happen or occur1 J. Poveda, M. Surdeanu, and J. Turmo, “An analysis of Bootstrapping for theRecognition of Temporal Expressions”, 2009 29/02/2012, Michele Filannino 8 / 23

presentation temporal expressionsmethodology■ annotation ● recognition ▶ automatically detect and delimitate expressions ▶ mostly machine-learning techniques ● normalisation ▶ assign attributes values for all the recognised expressions ▶ using a shared and formal format ▶ mostly rule-based techniques■ reasoning or searching 29/02/2012, Michele Filannino 9 / 23

presentation temporal expressionsexample: raw text That means Unisys must pay about $100 million in interest every quarter, on top of $27 million in dividends on preferred stock.Source: TRIOS TimeBank v.0.1 29/02/2012, Michele Filannino 10 / 23

presentation temporal expressionsexample: recognition That means Unisys must <ev>pay</ev> about $100 million in interest <te>every quarter</te>, on top of $27 million in dividends on preferred stock.Source: TRIOS TimeBank v.0.1 29/02/2012, Michele Filannino 11 / 23

presentation temporal expressionsexample: normalisation That means Unisys must <EVENT eid="e110" ...>pay</EVENT> about $100 million in interest <TIMEX3 tid="t256" type="SET" value="P1Q" temporalFunction="false" functionInDocument="NONE" quant="every">every quarter</ TIMEX3>, on top of $27 million in dividends on preferred stock. <TLINK lid="l32" relType="BEFORE" relatedToEvent="e110" eventID="e107"/> <TLINK lid="l26" relType="OVERLAP" eventID="e110" relatedToTime="t256"/>Source: TRIOS TimeBank v.0.1 29/02/2012, Michele Filannino 12 / 23

presentation temporal expressionslack of corpora 29/02/2012, Michele Filannino 13 / 23

presentation temporal expressionsmy contributions■ built the ﬁrst timex corpus using all the possible freely available timexes ● {timex, type, normalised_value, utterance_reference} ● 2822 diﬀerent timexes■ built a normaliser ● as TRIOS’ extension (University of Rochester) ● 71.66% accuracy from 62.57% 29/02/2012, Michele Filannino 14 / 23

presentation temporal expressionshuman mistakes utterance expression type annotation - three years before DATE FUTURE_REF 26/09/2011 this morning DATE 1998-02-06TMO - two decades DURATION P20Y - the summer of 1862 DATE FUTURE_REF - centuries DURATION PXE - the last half of ‘80s DATE 198 29/02/2012, Michele Filannino 15 / 23

presentation temporal expressionsmy to-do list ✓ study the literature ✓ build a corpus of timexes ✓ build a normaliser ■ release my timexes corpus freely ■ literature review 22 days elapsed 8 days remaining0 3 6 9 12 15 18 21 24 27 30 29/02/2012, Michele Filannino 16 / 23

Thank you.

Temporal expressions identification in biomedical texts

by Michele Filannino

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