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Olivia Contradictions
Olivia Contradictions
Olivia Contradictions
Olivia Contradictions
Olivia Contradictions
Olivia Contradictions
Olivia Contradictions
Olivia Contradictions
Olivia Contradictions
Olivia Contradictions
Olivia Contradictions
Olivia Contradictions
Olivia Contradictions
Olivia Contradictions
Olivia Contradictions
Olivia Contradictions
Olivia Contradictions
Olivia Contradictions
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Olivia Contradictions

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  • 1. Detecting Contradictions A Chapter in a Thesis by Olivia Sanchez    
  • 2. 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 –    
  • 3. 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.    
  • 4. 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. ●    
  • 5. 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.    
  • 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 ● There's a CONTRAST word; – There's a FINDING word; – There's a PPI. –    
  • 8. 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 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  ● 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  ● 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% –    
  • 12. Evaluation Causes of errors  ● Wrong parsing – PPI recognition – Missing PPI due to anaphoric problems –    
  • 13. 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. ●    
  • 14. 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. ●    
  • 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  ● value State of a PPI – Tables of ● Cue word – Manner word – Polarity, degree, direction,... –    
  • 17. Tables and Examples    
  • 18. Evaluation Kappa ● Tested with ● 5 biologists – 4 non­biologists – the system – Performed almost like biologists and better than  ● non­biologists    

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