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.