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COMP80122: final presentation




temporal expressions
   identification in biomedical texts
                           Michele Filannino




                                                  Manchester, 29/02/2012
presentation temporal expressions




where we are


■ Computer science
  ●   natural language processing
      ▶   information extraction
           ★ temporal expressions extraction




                                                    29/02/2012, Michele Filannino   2 / 23
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
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
presentation temporal expressions




why clinical domain?

 ■ diagnosis explanation
 ■ disease progression
   modelling

 ■ analysis of effectiveness of
   treatment



                                      29/02/2012, Michele Filannino   5 / 23
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
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
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
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
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
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
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
presentation temporal expressions




lack of corpora




                       29/02/2012, Michele Filannino   13 / 23
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
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
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
Thank you.

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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