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Extracting, representing and mining Semantic Metadata from text: Facilitating Knowledge Discovery in Biomedicine Cartic Ramakrishnan  Advisor:   Dr. Amit Sheth Committee Members:  Dr. Michael Raymer Dr. Guozhu Dong Dr. Thaddeus Tarpey Dr. Vasant Honavar Dr. Shaojun Wang
Overview ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
What Knowledge Discovery is NOT  ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
What is knowledge discovery? ,[object Object],[object Object],[object Object]
Element of surprise – Swanson’s discoveries Magnesium Migraine PubMed ? Stress Spreading Cortical Depression Calcium  Channel  Blockers Swanson’s  Discoveries Associations Discovered based on keyword searches  followed by manually analysis of text to establish possible relevant relationships 11 possible associations found
Knowledge Discovery in AI- The  robot scientist Planned search over an  well-defined (axiomatic) space  leading to knowledge discovery. Knowledge discovery by humans is done in  non-axiomatic ill-defined spaces over multi-modal data . Scientific literature is ill-defined and loosely structured source of data used in scientific investigations. Assigning structure and interpretation to text (Semantics) Syntax    Structure    Semantics
Knowledge Discovery = Extraction + Heuristic Aggregation Undiscovered Public  Knowledge
Information Extraction & Text Mining This MEK dependency was observed in BRAF mutant cells regardless of tissue lineage, and correlated with both downregulation of cyclin D1 protein expression and the induction of G1 arrest. *MEK dependency  ISA  Dependency_on_an_Organic_chemical  *BRAF mutant cells  ISA  Cell_type *downregulation of cyclin D1 protein expression  ISA  Biological_process *tissue lineage  ISA  Biological_concept *induction of G1 arrest  ISA  Biological_process Information Extraction = segmentation+classification+association+mining Text mining = entity identification+named relationship extraction+discovering association chains…. Segmentation Classification Named Relationship Extraction MEK dependency observed in BRAF mutant cells downregulation of  cyclin D1 protein expression correlated with induction of G1 arrest correlated with
Overview ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Knowledge Discovery over text Extraction of  Semantics  from text Semantic Metadata  Guided  Knowledge Explorations  Assigning interpretation to text  Semantic Metadata  Guided  Knowledge Discovery Triple-based Semantic  Search Semantic browser Subgraph discovery Semantic metadata  in the form of semi-structured data Text
Ontology-enabled Information Extraction Cartic Ramakrishnan , Krys Kochut, Amit P. Sheth: A Framework for Schema-Driven  Relationship Discovery from Unstructured Text.  International Semantic Web Conference 2006 : 583-596
Comparison with standard IE ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Information Extraction via Ontology assisted  text mining – Relationship extraction Biologically  active substance Lipid Disease or Syndrome affects causes affects causes complicates Fish Oils Raynaud’s Disease ??????? instance_of instance_of UMLS  Semantic Network MeSH PubMed 9284  documents 4733  documents 5  documents
Background knowledge and Data used ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Method – Parse Sentences in PubMed SS-Tagger (University of Tokyo) SS-Parser (University of Tokyo) (TOP (S (NP (NP (DT An) (JJ excessive) (ADJP (JJ endogenous) (CC or) (JJ exogenous) ) (NN stimulation) ) (PP (IN by) (NP (NN estrogen) ) ) ) (VP (VBZ induces) (NP (NP (JJ adenomatous) (NN hyperplasia) ) (PP (IN of) (NP (DT the) (NN endometrium) ) ) ) ) ) )  ,[object Object],[object Object],[object Object],[object Object],[object Object]
Method – Identify entities and relationships in Parse Tree TOP NP VP S NP VBZ induces NP PP NP IN of DT the NN endometrium JJ adenomatous NN hyperplasia NP PP IN by NN estrogen DT the JJ excessive ADJP NN stimulation JJ endogenous JJ exogenous CC or MeSHID D004967 MeSHID D006965 MeSHID D004717 UMLS ID T147 Modifiers Modified entities Composite Entities
Representation – Resulting RDF Modifiers Modified entities Composite Entities
Preliminary Results ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Paths between Migraine and Magnesium Paths are considered interesting if they have one or more named relationship Other than   hasPart  or  hasModifiers  in them
An example of such a path ,[object Object],[object Object],[object Object],[object Object]
Interesting Observations from this preliminary work
Observations – Sentence characteristics and  Parsing ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],(TOP (S (NP (NP (DT An) (JJ excessive) (ADJP (JJ endogenous) (CC or) (JJ exogenous) ) (NN stimulation) ) (PP (IN by) (NP (NN estrogen) ) ) ) (VP (VBZ induces) (NP (NP (JJ adenomatous) (NN hyperplasia) ) (PP (IN of) (NP (DT the) (NN endometrium) ) ) ) ) ) )
Observations – Complex entities with nesting and overlapping structure ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Possible Strategies ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Unsupervised Joint Extraction of Compound Entities and Relationship Cartic Ramakrishnan , Pablo N. Mendes, Shaojun Wang and Amit P. Sheth  "Unsupervised Discovery of Compound Entities for Relationship Extraction" EKAW 2008 - 16th International Conference on Knowledge Engineering and Knowledge Management Knowledge Patterns
Joint Extraction approach ,[object Object],amod  = adjectival modifier nsubjpass = nominal subject in passive voice governor dependent
Stanford Dependency Hierarchy
Hierarchy used to generalize the rules ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Algorithm Relationship head Subject head Object head Object head
Preliminary results
Extracted Triples
Analysis of compound entities ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Predicting the constituents to compound entities ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
What is Mutual information? ,[object Object],[object Object]
Dependency-based mutual information ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],rel(w i ,w j ) rel(w j ,w i ) rel(w i ,*) rel(*, w i )
Predicting constituents ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Results ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Evaluations ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Evaluation ,[object Object],[object Object],[object Object],[object Object]
Demo of Evaluation tool ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Evaluation conducted using this tool ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Results of Manual Evaluation
Applications ,[object Object],[object Object]
Semantic Metadata Guided Knowledge Explorations and Discovery
Supporting Knowledge Discovery
Discovery complex connection patterns ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Schema-driven edge weight assignment company Entertainment company Manufacturing company Oil company Automotive company Electronics company Sporting goods company Ford Motors Cartic’s  Company 0.67 0.33 <0.5 Schema Instances 1.0 1.0 1.0 1.0 1.0 1.0 0.33
Heuristics used to bias edge weights ,[object Object]
Algorithm ,[object Object],[object Object],[object Object],[object Object],[object Object]
Algorithm ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Results
Overview ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Past work ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Other major papers influencing my work ,[object Object],[object Object],[object Object],[object Object]
Overview ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Hypothesis Driven  retrieval of Scientific Literature  PubMed Keyword query: Migraine[MH] + Magnesium[MH] Complex  Query Supporting Document  sets retrieved Migraine Stress Patient affects isa Magnesium Calcium Channel  Blockers inhibit
Strength of a connection ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Mechanistic Models
Publications ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Publications ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Publications ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Experiences  ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Acknowledgements ,[object Object],[object Object],[object Object],[object Object]
On a lighter note

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Cartic Ramakrishnan's dissertation defense

  • 1. Extracting, representing and mining Semantic Metadata from text: Facilitating Knowledge Discovery in Biomedicine Cartic Ramakrishnan Advisor: Dr. Amit Sheth Committee Members: Dr. Michael Raymer Dr. Guozhu Dong Dr. Thaddeus Tarpey Dr. Vasant Honavar Dr. Shaojun Wang
  • 2.
  • 3.
  • 4.
  • 5. Element of surprise – Swanson’s discoveries Magnesium Migraine PubMed ? Stress Spreading Cortical Depression Calcium Channel Blockers Swanson’s Discoveries Associations Discovered based on keyword searches followed by manually analysis of text to establish possible relevant relationships 11 possible associations found
  • 6. Knowledge Discovery in AI- The robot scientist Planned search over an well-defined (axiomatic) space leading to knowledge discovery. Knowledge discovery by humans is done in non-axiomatic ill-defined spaces over multi-modal data . Scientific literature is ill-defined and loosely structured source of data used in scientific investigations. Assigning structure and interpretation to text (Semantics) Syntax  Structure  Semantics
  • 7. Knowledge Discovery = Extraction + Heuristic Aggregation Undiscovered Public Knowledge
  • 8. Information Extraction & Text Mining This MEK dependency was observed in BRAF mutant cells regardless of tissue lineage, and correlated with both downregulation of cyclin D1 protein expression and the induction of G1 arrest. *MEK dependency ISA Dependency_on_an_Organic_chemical *BRAF mutant cells ISA Cell_type *downregulation of cyclin D1 protein expression ISA Biological_process *tissue lineage ISA Biological_concept *induction of G1 arrest ISA Biological_process Information Extraction = segmentation+classification+association+mining Text mining = entity identification+named relationship extraction+discovering association chains…. Segmentation Classification Named Relationship Extraction MEK dependency observed in BRAF mutant cells downregulation of cyclin D1 protein expression correlated with induction of G1 arrest correlated with
  • 9.
  • 10. Knowledge Discovery over text Extraction of Semantics from text Semantic Metadata Guided Knowledge Explorations Assigning interpretation to text Semantic Metadata Guided Knowledge Discovery Triple-based Semantic Search Semantic browser Subgraph discovery Semantic metadata in the form of semi-structured data Text
  • 11. Ontology-enabled Information Extraction Cartic Ramakrishnan , Krys Kochut, Amit P. Sheth: A Framework for Schema-Driven Relationship Discovery from Unstructured Text. International Semantic Web Conference 2006 : 583-596
  • 12.
  • 13. Information Extraction via Ontology assisted text mining – Relationship extraction Biologically active substance Lipid Disease or Syndrome affects causes affects causes complicates Fish Oils Raynaud’s Disease ??????? instance_of instance_of UMLS Semantic Network MeSH PubMed 9284 documents 4733 documents 5 documents
  • 14.
  • 15.
  • 16. Method – Identify entities and relationships in Parse Tree TOP NP VP S NP VBZ induces NP PP NP IN of DT the NN endometrium JJ adenomatous NN hyperplasia NP PP IN by NN estrogen DT the JJ excessive ADJP NN stimulation JJ endogenous JJ exogenous CC or MeSHID D004967 MeSHID D006965 MeSHID D004717 UMLS ID T147 Modifiers Modified entities Composite Entities
  • 17. Representation – Resulting RDF Modifiers Modified entities Composite Entities
  • 18.
  • 19. Paths between Migraine and Magnesium Paths are considered interesting if they have one or more named relationship Other than hasPart or hasModifiers in them
  • 20.
  • 21. Interesting Observations from this preliminary work
  • 22.
  • 23.
  • 24.
  • 25. Unsupervised Joint Extraction of Compound Entities and Relationship Cartic Ramakrishnan , Pablo N. Mendes, Shaojun Wang and Amit P. Sheth &quot;Unsupervised Discovery of Compound Entities for Relationship Extraction&quot; EKAW 2008 - 16th International Conference on Knowledge Engineering and Knowledge Management Knowledge Patterns
  • 26.
  • 28.
  • 29. Algorithm Relationship head Subject head Object head Object head
  • 32.
  • 33.
  • 34.
  • 35.
  • 36.
  • 37.
  • 38.
  • 39.
  • 40.
  • 41.
  • 42. Results of Manual Evaluation
  • 43.
  • 44. Semantic Metadata Guided Knowledge Explorations and Discovery
  • 46.
  • 47. Schema-driven edge weight assignment company Entertainment company Manufacturing company Oil company Automotive company Electronics company Sporting goods company Ford Motors Cartic’s Company 0.67 0.33 <0.5 Schema Instances 1.0 1.0 1.0 1.0 1.0 1.0 0.33
  • 48.
  • 49.
  • 50.
  • 52.
  • 53.
  • 54.
  • 55.
  • 56. Hypothesis Driven retrieval of Scientific Literature PubMed Keyword query: Migraine[MH] + Magnesium[MH] Complex Query Supporting Document sets retrieved Migraine Stress Patient affects isa Magnesium Calcium Channel Blockers inhibit
  • 57.
  • 59.
  • 60.
  • 61.
  • 62.
  • 63.
  • 64. On a lighter note