1. Detecting Contradictions
A Chapter in a Thesis
by
Olivia Sanchez

2. The Aim
To find two statements p and not p
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Either in the same document or in two different
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documents.
The statements concern protein­protein interactions
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(PPIs).
“Protein A interacts with protein B.” ­Author X
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“Protein A doesn't interact with protein B.” ­Author Y
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3. Explicit vs. Implicit Contradictions
Explicit contradictions
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The paper clearly states the contradiction
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“Although the activation of X by Y would contradict
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previous observations...”
Implicit contradictions
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In two different articles or in different sentences of
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the same article.

4. Implicit Contradiction
Example:
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Doc1: C2­ceramide has no effect on PI 3­kinase in
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NIH­3T3 fibroblasts or 3T3­L1 adipocytes.
Doc2: C2­ceramide potently inhibits PI 3­kinase
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activation.
Just potential contradiction.
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The rest is done by curators.
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5. Explicit Contradictions
They are used to tune and test a system to
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detect the implicit ones.
They happen near words expressing
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contradiction and findings.
They most often occur in Discussion and rarely
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in the Abstract. Other sections lie in between.

6. Finding Explicit Contradictions
CONTRAST WORDS FINDING WORDS
● ●
contradict, contradiction, observation, report, notion,
– –
contradictory, conflict, evidence, finding, research,
negate, negation, disagree, hypothesis, knowledge,
disagreement, refute, interpretation, conclusion,
refutation, differ, dissent, model, data, fact, study,
discrepancy, inconsistency, inform, document, work,
inconsistent, contrast, proposal, result, view,
controversy assertion, assay

7. Explicit – Clue Words
There is an explicit contradiction when
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There's a CONTRAST word;
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There's a FINDING word;
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There's a PPI.
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8. Method to Find Explicit C
Rather vague definitions of dependency parse
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and some other concept.
There may be an explicit C­PPI in a sentence if
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there is a direct path Γ of a maximum length of 3
between a finding word and a contradiction word,
and a path Φ of a maximum length of 10 between
the contradiction word and the cue word denoting
a PPI (affirmative or negative cases).

9. Example of XC
“Although the activation of AMPK by insulin
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would contradict previous observations (28,29),
AMPK activation is known to accelerate glucose
uptake and utilization in the heart.”

10. Example of XC
file:///home/farzaneh/Desktop/Screenshot-1.png

11. Evaluation
Sentences from 500 JBC articles with
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contradiction and finding words
Analyse manually and automatically
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Results
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True positives 22 Recall 36.07%
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False positives 2 Precision 91.67%
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False negatives 39 F­score 51.76%
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12. Evaluation
Causes of errors
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Wrong parsing
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PPI recognition
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Missing PPI due to anaphoric problems
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13. Method to Find Implicit C
Map the sentences to their meanings
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These should map to the same meaning
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ATP inhibition of adenosine monophosphate­activated
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protein kinase.
Inhibition of ATP by AMPK.
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ATP inhibits AMPK.
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14. Method to Find Implicit C
Map the sentences to their “meaning”s
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These should map to the same “meaning”
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ATP inhibition of adenosine monophosphate­activated
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protein kinase.
Inhibition of ATP by AMPK.
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ATP inhibits AMPK.
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15. Syntax – Semantic Map (Example)
Semantic class Inactivate
cue word inhibit
P1 ATP
P2 AMPK
Auxiliar molecule –
Polarity Positive
Direction of cue word Negative
Certainty –
Manner (of the cue word) Neutral
Organism –
Location –

16. The Method
Map the semantic representation (“meaning”) to a numeric
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value
State of a PPI
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Tables of
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Cue word
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Manner word
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Polarity, degree, direction,...
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17. Tables and Examples

18. Evaluation
Kappa
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Tested with
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5 biologists
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4 non­biologists
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the system
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Performed almost like biologists and better than
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non­biologists