natural language processing for automated inference
Post on 30-Dec-2015
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Natural Language Natural Language Processing for Automated Processing for Automated
InferenceInference
Tokenizer
Gene, Protein, and Malignancy
Tagger
NominalizationTagger
SentenceExtractor
SemanticMapper
ProbabilisticInference
The pipelineThe pipeline
Tokenizer
Gene, Protein, and Malignancy
Tagger
NominalizationTagger
SentenceExtractor
SemanticMapper
ProbabilisticInference
Adapted from PennBioTagger
Tokenizer
Gene, Protein, and Malignancy
Tagger
NominalizationTagger
SentenceExtractor
SemanticMapper
ProbabilisticInference
Tokenizer
Gene, Protein, and Malignancy
Tagger
NominalizationTagger
SentenceExtractor
SemanticMapper
ProbabilisticInference
Customized tags
“transduction”“activation"
Tokenizer
Gene, Protein, and Malignancy
Tagger
NominalizationTagger
SentenceExtractor
SemanticMapper
ProbabilisticInference
Sleator & TemperleyLinkParser
+
Relationship Extractor
Tokenizer
Gene, Protein, and Malignancy
Tagger
NominalizationTagger
SentenceExtractor
SemanticMapper
ProbabilisticInference
Abstracts Relex outputfrom syntactical
origins
Tokenizer
Gene, Protein, and Malignancy
Tagger
NominalizationTagger
SentenceExtractor
SemanticMapper
ProbabilisticInference
PLN
NovamenteAI Engine
What it doesWhat it does
Any of the sentencesAny of the sentences
Kim kissed Pat. Kim kissed Pat. Pat was kissed by Kim. Pat was kissed by Kim.
Is mapped into the set of relationshipsIs mapped into the set of relationships
subj(kiss_0, Kim)subj(kiss_0, Kim)obj(kiss_0, Pat)obj(kiss_0, Pat)
inheritance(kiss_0, kiss)inheritance(kiss_0, kiss)
How the semantic mapping How the semantic mapping rules look likerules look like
The ruleThe rule
by($x, $y) & inheritance($x, transitive_event) by($x, $y) & inheritance($x, transitive_event) subj($x, $y) subj($x, $y)
Maps the relex-produced relationshipMaps the relex-produced relationship
by(prevention, inhibition) by(prevention, inhibition)
Into the abstract conceptual relationshipInto the abstract conceptual relationship
subj(prevention, inhibition)subj(prevention, inhibition)
Which is suitable for inference by PLN. Which is suitable for inference by PLN.
Example (Bioliterate)Example (Bioliterate)
Premise 1Premise 1Importantly, bone loss was almost Importantly, bone loss was almost completely prevented by p38 MAPK completely prevented by p38 MAPK inhibition. (PID 16447221) inhibition. (PID 16447221)
Premise 2Premise 2
Thus, our results identify DLC as a novel Thus, our results identify DLC as a novel inhibitor of the p38 pathway and provide a inhibitor of the p38 pathway and provide a molecular mechanism by which cAMP molecular mechanism by which cAMP suppresses p38 activation and promotes suppresses p38 activation and promotes apoptosis. (PID 16449637) apoptosis. (PID 16449637)
(Uncertain)(Uncertain)
ConclusionsConclusionsDLC prevents bone loss.DLC prevents bone loss.
cAMP prevents bone loss. cAMP prevents bone loss.
Importantly, bone loss was almost completely prevented Importantly, bone loss was almost completely prevented by p38 MAPK inhibition.by p38 MAPK inhibition.
_subj-n(bone, loss) _subj-n(bone, loss)
_obj(prevention, loss) _obj(prevention, loss)
_subj-r(almost, completely) _subj-r(almost, completely)
_subj-r(completely, _subj-r(completely, prevention) prevention)
by(prevention, inhibition) by(prevention, inhibition)
_subj-n(p38 MAPK, _subj-n(p38 MAPK, inhibition)inhibition)
subj (prevention, inhibition)subj (prevention, inhibition)
obj (prevention, loss)obj (prevention, loss)
obj (inhibition, p38_MAPK)obj (inhibition, p38_MAPK)
obj (loss, bone) obj (loss, bone)
Thus, our results identify DLC as a novel inhibitor of the Thus, our results identify DLC as a novel inhibitor of the p38 pathway and provide a molecular mechanism by p38 pathway and provide a molecular mechanism by which cAMP suppresses p38 activation and promotes which cAMP suppresses p38 activation and promotes apoptosis.apoptosis.
_subj(identify, results) _subj(identify, results)
as(identify, inhibitor) as(identify, inhibitor)
_obj(identify, DLC) _obj(identify, DLC)
_subj-a(novel, inhibitor) _subj-a(novel, inhibitor)
of(inhibitor, pathway) of(inhibitor, pathway)
_subj-n(p38, pathway)_subj-n(p38, pathway)
subj (inhibition, DLC)subj (inhibition, DLC)
obj (inhibition, pathway)obj (inhibition, pathway)
inh(pathway, p38) inh(pathway, p38)
Background knowledge Background knowledge utilizedutilized
ImplicationImplication
ANDANDinh $x causal_eventinh $x causal_eventinh $y causal_eventinh $y causal_eventsubj($y, $x)subj($y, $x)subj($x, $z)subj($x, $z)
subj($y,$z)subj($y,$z)
Probabilistic InferenceProbabilistic Inference
AbductionAbduction
InhInh inhib1, inhib inhib1, inhib
InhInh inhib2, inhib inhib2, inhib
|- |-
InhInh inhib1, inhib2 inhib1, inhib2
Similarity SubstitutionSimilarity Substitution
EvalEval subj (prev1, inhib1) subj (prev1, inhib1)
InhInh inhib1, inhib2 inhib1, inhib2
|-|-
EvalEval subj (prev1, inhib2) subj (prev1, inhib2)
DeductionDeduction
InhInh inhib2, inhib inhib2, inhib
InhInh inhib,causal_event inhib,causal_event
|-|-
InhInh inhib2, causal_event inhib2, causal_event
Probabilistic InferenceProbabilistic Inference
AndAndInh Inh inhib2, causal_eventinhib2, causal_eventInhInh prev1, causal_event prev1, causal_eventEvalEval subj (prev1, inhib2) subj (prev1, inhib2) EvalEval subj (inhib2, DLC) subj (inhib2, DLC)|-|-AND AND Inh Inh inhib2, causal_eventinhib2, causal_event InhInh prev1, causal_event prev1, causal_event EvalEval subj (prev1, inhib2) subj (prev1, inhib2) EvalEval subj (inhib2, DLC) subj (inhib2, DLC)
UnificationUnificationForAllForAll ($x, $y, $z) ($x, $y, $z)
ImpImp ANDAND
InhInh $x, causal_event $x, causal_eventInhInh $y, causal_event $y, causal_event
EvalEval subj ($y, $x) subj ($y, $x) EvalEval subj ($x, $z) subj ($x, $z)
EvalEval subj ($y, $z) subj ($y, $z)
ANDAND Inh Inh inhib2, causal_eventinhib2, causal_event InhInh prev1, causal_event prev1, causal_event EvalEval subj (prev1, inhib2) subj (prev1, inhib2) EvalEval subj (inhib2, DLC) subj (inhib2, DLC)
|-|-
EvalEval subj (prev1, inhib2) subj (prev1, inhib2)
Probabilistic InferenceProbabilistic Inference
Implication Breakdown (Modus Implication Breakdown (Modus Ponens)Ponens)
ImpImp
ANDAND
Inh Inh inhib2, causal_eventinhib2, causal_event
InhInh prev1, causal_event prev1, causal_event
EvalEval subj (prev1, inhib2) subj (prev1, inhib2)
EvalEval subj (inhib2, DLC) subj (inhib2, DLC)
Eval subj (prev1, DLC)Eval subj (prev1, DLC)
|-|-
Eval subj (prev1, DLC) Eval subj (prev1, DLC)
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