olivia contradictions
TRANSCRIPT
Detecting Contradictions
A Chapter in a Thesisby
Olivia Sanchez
The Aim
● To find two statements p and not p– Either in the same document or in two different
documents.– The statements concern proteinprotein interactions
(PPIs).– “Protein A interacts with protein B.” Author X– “Protein A doesn't interact with protein B.” Author Y
Explicit vs. Implicit Contradictions
● Explicit contradictions– The paper clearly states the contradiction
● “Although the activation of X by Y would contradict previous observations...”
● Implicit contradictions– In two different articles or in different sentences of
the same article.
Implicit Contradiction
● Example:– Doc1: C2ceramide has no effect on PI 3kinase in
NIH3T3 fibroblasts or 3T3L1 adipocytes.
– Doc2: C2ceramide potently inhibits PI 3kinase activation.
● Just potential contradiction.● The rest is done by curators.
Explicit Contradictions
● They are used to tune and test a system to detect the implicit ones.
● They happen near words expressing contradiction and findings.
● They most often occur in Discussion and rarely in the Abstract. Other sections lie in between.
Finding Explicit Contradictions● CONTRAST WORDS
– contradict, contradiction, contradictory, conflict, negate, negation, disagree, disagreement, refute, refutation, differ, dissent, discrepancy, inconsistency, inconsistent, contrast, controversy
● FINDING WORDS
– observation, report, notion, evidence, finding, research, hypothesis, knowledge, interpretation, conclusion, model, data, fact, study, inform, document, work, proposal, result, view, assertion, assay
Explicit – Clue Words
● There is an explicit contradiction when– There's a CONTRAST word;– There's a FINDING word;– There's a PPI.
Method to Find Explicit C
● Rather vague definitions of dependency parse and some other concept.– There may be an explicit CPPI in a sentence if
there is a direct path of a maximum length of 3 Γbetween a finding word and a contradiction word, and a path of a maximum length of 10 between Φthe contradiction word and the cue word denoting a PPI (affirmative or negative cases).
Example of XC
● “Although the activation of AMPK by insulin would contradict previous observations (28,29), AMPK activation is known to accelerate glucose uptake and utilization in the heart.”
Example of XC
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Evaluation
● Sentences from 500 JBC articles with contradiction and finding words
● Analyse manually and automatically ● Results
– True positives 22 Recall 36.07%– False positives 2 Precision 91.67%– False negatives 39 Fscore 51.76%
Evaluation
● Causes of errors – Wrong parsing– PPI recognition– Missing PPI due to anaphoric problems
Method to Find Implicit C
● Map the sentences to their meanings– These should map to the same meaning
● ATP inhibition of adenosine monophosphateactivated protein kinase.
● Inhibition of ATP by AMPK.● ATP inhibits AMPK.
Method to Find Implicit C
● Map the sentences to their “meaning”s– These should map to the same “meaning”
● ATP inhibition of adenosine monophosphateactivated protein kinase.
● Inhibition of ATP by AMPK.● ATP inhibits AMPK.
Syntax – Semantic Map (Example)
Semantic class Inactivatecue word inhibitP1 ATPP2 AMPKAuxiliar molecule –Polarity PositiveDirection of cue word NegativeCertainty –Manner (of the cue word) NeutralOrganism –Location –
The Method
● Map the semantic representation (“meaning”) to a numeric value
– State of a PPI● Tables of
– Cue word
– Manner word
– Polarity, degree, direction,...
Tables and Examples
Evaluation
● Kappa● Tested with
– 5 biologists– 4 nonbiologists– the system
● Performed almost like biologists and better than nonbiologists