1.
Score-based Approach
for Anaphora Resolution in
Drug-Drug Interaction Documents
Isabel Segura Bedmar, Mario Crespo, César de Pablo Sánchez
CS Department, Universidad Carlos III de Madrid
24th
June 2009
Saarbrücken, Germany
NLDB 2009

2.
What is a Drug-Drug Interaction?

3.
 Medication errors
kill 7,000
patients per
annum in USA.
 16% of them are
DDI
 High incidence in
certain patient
groups
Things can get complicated...

4.
How do healthcare
professionals
avoid drug-drug interactions?

5.
Drug interaction Resources

6.
How Information Extraction helps?
Aspirin may decrease the effects of
probenecid, sulfinpyrazone,
and phenylbutazone.
DDI ( ASPIRIN , PROBENECID)
DDI ( ASPIRIN , SULFINPYRAZONE )
DDI ( ASPIRIN , PHENYLBUTAZONE)

7.
How Anaphora Resolution helps?
Triamterene, metformin and amiloride
should be co-administered with care as
they might increase dofetilide levels.

8.
Triamterene, metformin and amiloride
should be co-administered with care as
they might increase dofetilide levels.
DDI ( DOFETILIDE , TRIAMTERENE)
DDI ( DOFETILIDE , METFORMIN )
DDI ( DOFETILIDE , AMILORIDE)

9.
Levofloxacin, a fluoroquinolone, is one of the most
commonly prescribed antibiotics in clinical practice.
Several case reports have indicated that this drug may
signicantly potentiate the anticoagulation effect of
warfarin.

10.
Levofloxacin, a fluoroquinolone, is one of the most
commonly prescribed antibiotics in clinical practice.
Several case reports have indicated that this drug may
signicantly potentiate the anticoagulation effect of
warfarin.
DDI ( LEVOFLOXACIN , WARFARIN )

11.
Precision
Recall

12.
Build a corpus
to study
anaphora resolution
in DDI
A score-based
method to
resolve
anaphora
using
semantic info

13.
Building a corpus for DDI
DrugBank
HTML To Text
Wrapper
Corpus TXT
Drug Name Recognition
MetaMap UMLS:
Text analysis
String Matching
Algorithm
2006AA
UMLSKS
WHOINN
affixes
DDI Extraction
XML annotated with drugs and other
biomedical concepts
XML annotated with drugs
interactions

14.
DrugBank
HTML To Text
Wrapper
Corpus TXT

15.
DrugBank
HTML To Text
Wrapper
Corpus TXT

16.
Building a corpus for DDI
DrugBank
HTML To Text
Wrapper
Corpus TXT
Drug Name Recognition
MetaMap UMLS:
Text analysis
String Matching
Algorithm
2006AA
UMLSKS
WHOINN
affixes
DDI Extraction
XML annotated with drugs and other
biomedical concepts
XML annotated with drugs
interactions

17.
...and enriching it for AR
Drug Drug
Interaction
Annotattion
XML annotated with drugs and other
biomedical concepts
XML annotated with drugs
interactions
Anaphora
annotation
XML annotated with resolved
anaphoric expression
49 articles selected
● 40 sentences on average
● 716 words on average
18.035 phrases with 689 different drugs
331 anaphoric expresions

18.
Personal (it)
Reflexives (itself)
Relatives (which)
Distributives (both)
Demonstratives (these)
Indefinites (some)
0 20 40 60 80 100 120 140
23
1
120
8
12
8
Distribution of
Pronominal Anaphora

19.
Definite
Possessives
Distributives
Demonstratives
Indefinites
0 10 20 30 40 50 60 70
37
52
11
58
8
Distribution of
Nominal Anaphora

20.
Build a corpus
to study
anaphora resolution
in DDI
A score-based
method to
resolve
anaphora
using
semantic info

21.
Our approach

22.
Our approach
Identification of
anaphoric expressions

23.
Our approach
Identification of
anaphoric expressions
Selection of candidate
antecedents

24.
Our approach
Identification of
anaphoric expressions
Selection of candidate
antecedents
Scoring

25.
Anaphoric expressions

26.
Anaphoric expressions
Pronominal
Identify pronouns
Exclude first and
second personal
forms
Detect pleonastic it

27.
Anaphoric expressions
Pronominal
Identify pronouns
Exclude first and
second personal
forms
Detect pleonastic it
If it is not possible to discontinue the diuretic, the
starting dose of trandolapril should be reduced.

28.
Anaphoric expressions
Nominal
Select PP, NP and UNK
Restrict to:
● pharmacological substance
(phsu)
● Antibiotic (antb)
● clinical drugs (clnd)

29.
Anaphoric expressions
Nominal
Select PP, NP and
UNK
Restrict to:
● pharmacological substance
(phsu)
● Antibiotic (antb)
● clinical drugs (clnd)
Levofloxacin, a fluoroquinolone, is one of the most
commonly prescribed antibiotics in clinical practice.
Several case reports have indicated that this drug may
significantly potentiate the anticoagulation effect of
warfarin.

30.
Anaphoric expressions
Nominal
Select PP, NP and UNK
Restrict to:
● pharmacological substance
(phsu)
● Antibiotic (antb)
● clinical drugs (clnd)
Possessive + drug
properties

31.
Anaphoric expressions
Nominal
Select PP, NP and UNK
Restrict to:
● pharmacological substance
(phsu)
● Antibiotic (antb)
● clinical drugs (clnd)
Possessive + drug
properties
Although beta-adrenergic blockers or calcium
channel blockers and digoxin may be useful
in combination to control atrial brillation,their
additive effects on AV node conduction can
result in advanced or complete heart block.

32.
Anaphoric expressions
Pronominal
Identify pronouns
Exclude first and
second personal
forms
Detect pleonastic it
Nominal
Select PP, NP and UNK
Restrict to:
● pharmacological substance
(phsu)
● Antibiotic (antb)
● clinical drugs (clnd)
Possesives + drug
properties

33.
Candidate antecedents

34.
Candidate antecedents
Pronominal
Number agreement
(lexical number
and coodinative
structures)

35.
Candidate antecedents
Pronominal
Number agreement
(lexical number
and coodinative
structures)
As fluoxetine, sertraline and paroxetine inhibit
P450 2D6, they may vary in the extent of inhibition.

36.
Candidate antecedents
Nominal
Number agreement
(lexical number and
coodinative
structures)
Semantic type
agreement (phsu,
antb, cnld)

37.
Candidate antecedents
Nominal
Number agreement
(lexical number and
coodinative
structures)
Semantic type
agreement (phsu,
antb, cnld)
Loracarbef is a carbacephem antibiotic.
This antibiotic kills sensitive bacteria by
interfering with formation of the bacteria's
cell wall while it is growing.

38.
Candidate antecedents
Pronominal
Number agreement
(lexical number
and coodinative
structures)
Nominal
Number agreement
(lexical number and
coodinative
structures)
Semantic type
agreement (phsu,
antb, cnld)

39.
Score

40.
Score
Pronominal

41.
Score
Nominal

42.
Candidate antecedents
Pronominal Nominal

43.
Results

44.
Baseline
Several studies have focused
on Dapsone showing it
can interact with many drugs
Levofloxacin, a fluoroquinolone, is one of the
most commonly prescribed antibiotics in clinical
practice. Several case reports have indicated
that this drug may signicantly potentiate
the anticoagulation effect of warfarin.

45.
Personal
Reflexives
Relatives
Distributives
Demonstratives
Indefinites
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
26%
100%
82%
18%
0%
16%
52%
100%
96%
80%
14%
61%
Baseline
Score
Pronominal Anaphora
F-score

46.
Definite
Possessives
Distributives
Demonstratives
Indefinites
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
0%
47%
23%
2%
0%
47%
67%
57%
34%
34%
Baseline
Score
Nominal Anaphora
F-score

47.
Pronominal Nominal Total
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
66%
18%
44%
85%
50%
69%
Baseline
Score
Global results
F-score

48.
Conclusions
● Domain specific resources are needed
– Parsing with MMTx
– Semantic information
● Future work
– Centering and syntactic heuristics
– More semantics: WHOINN rules
– Evaluation in Medline corpora

49.
Does Anaphora Resolution really
helps to detect DDI?

50.
Drug Drug Interaction detection is a
promising application for IE and NLP

51.
Castano et al.,
2002
Liang and Lin,
2005
Kim et al,
2005
46 abstracts 120 sentences
(PP Interactions)
Medstract +
100 abstracts
Gasperin & Brisco,
2008
5 full articles
Biomedical anaphora approaches
Scoring approach Centering TheoryScoring approach Probabilistic
Bayes Model
F = 0.74 F=0.64
pronominal,
F=0.59
nominal
F=0.92
pronominal,
F= 0.78
nominal
28-56% precision,
35-54% recall