natural language processing for automated inference

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


Tagger


SentenceExtractor

SemanticMapper


Adapted from PennBioTagger

Tokenizer


Tagger


SentenceExtractor

SemanticMapper


Tokenizer


Tagger


SentenceExtractor

SemanticMapper


Customized tags

“transduction”“activation"

Tokenizer


Tagger


SentenceExtractor

SemanticMapper


Sleator & TemperleyLinkParser

+

Relationship Extractor

Tokenizer


Tagger


SentenceExtractor

SemanticMapper


Abstracts Relex outputfrom syntactical

origins

Tokenizer


Tagger


SentenceExtractor

SemanticMapper


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 inhib1, inhib2 inhib1, inhib2

Similarity SubstitutionSimilarity Substitution

EvalEval subj (prev1, inhib1) subj (prev1, inhib1)

InhInh inhib1, inhib2 inhib1, inhib2

|-|-


DeductionDeduction


InhInh inhib,causal_event inhib,causal_event

|-|-

InhInh inhib2, causal_event inhib2, causal_event


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)

|-|-



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 (inhib2, DLC) subj (inhib2, DLC)

Eval subj (prev1, DLC)Eval subj (prev1, DLC)

|-|-

Eval subj (prev1, DLC) Eval subj (prev1, DLC)

natural language processing for automated inference

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