Temporal expressions identification in biomedical texts
1 like1,026 views
The document discusses Michele Filannino's final presentation on identifying temporal expressions in biomedical texts. It provides context on natural language processing and information extraction. It then defines temporal expressions and discusses their importance for tasks like question answering and summarization. The presentation outlines the forms temporal expressions can take, common annotation and normalization methods used, and gives an example. It also notes the lack of freely available corpora and describes Filannino's contributions of building the first freely available timex corpus and a temporal expression normalizer. The presentation concludes with discussing some examples of human annotation mistakes and Filannino's remaining to-do items.
Temporal expressions identification in biomedical texts
- 1. COMP80122: final presentation temporal expressions identification in biomedical texts Michele Filannino Manchester, 29/02/2012
- 2. presentation temporal expressions where we are ■ Computer science ● natural language processing ▶ information extraction ★ temporal expressions extraction 29/02/2012, Michele Filannino 2 / 23
- 3. presentation temporal expressions temporal 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 annotation guidelines, v. 1.0.2,” MITRE, 2001 29/02/2012, Michele Filannino 3 / 23
- 4. presentation temporal expressions why? ■ 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
- 5. presentation temporal expressions why clinical domain? ■ diagnosis explanation ■ disease progression modelling ■ analysis of effectiveness of treatment 29/02/2012, Michele Filannino 5 / 23
- 6. presentation temporal expressions scientific 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 2012 Source: Google Scholar (last update 27/02/2012) 29/02/2012, Michele Filannino 6 / 23
- 7. presentation temporal expressions temporal 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 hour 1 J. Poveda, M. Surdeanu, and J. Turmo, “An analysis of Bootstrapping for the Recognition of Temporal Expressions”, 2009 29/02/2012, Michele Filannino 7 / 23
- 8. presentation temporal expressions temporal 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 occur 1 J. Poveda, M. Surdeanu, and J. Turmo, “An analysis of Bootstrapping for the Recognition of Temporal Expressions”, 2009 29/02/2012, Michele Filannino 8 / 23
- 9. presentation temporal expressions methodology ■ 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
- 10. presentation temporal expressions example: 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
- 11. presentation temporal expressions example: 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
- 12. presentation temporal expressions example: 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
- 13. presentation temporal expressions lack of corpora 29/02/2012, Michele Filannino 13 / 23
- 14. presentation temporal expressions my 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
- 15. presentation temporal expressions human 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
- 16. presentation temporal expressions my 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 remaining 0 3 6 9 12 15 18 21 24 27 30 29/02/2012, Michele Filannino 16 / 23
- 17. Thank you.