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A Context-Driven Subgraph Model for Literature-Based Discovery
In: Kno.e.sis Publications (2014)
Abstract: Literature-Based Discovery (LBD) refers to the process of uncovering hidden connections that are implicit in scientific literature. Numerous hypotheses have been generated from scientific literature using the LBD paradigm, which influenced innovations in diagnosis, treatment, preventions and overall public health. However, much of the existing research on discovering hidden connections among concepts have used distributional statistics and graph-theoretic measures to capture implicit associations. Such metrics do not explicitly capture the semantics of hidden connections. Rather, they only allude to the existence of meaningful underlying associations. To gain in-depth insights into the meaning of hidden (and other) connections, complementary methods have often been employed. Some of these methods include: 1) the use of domain expertise for concept filtering and knowledge exploration, 2) leveraging structured background knowledge for context and to supplement concept filtering and 3) developing heuristics a priori to help eliminate spurious connections. While effective in some situations, the practice of relying on domain expertise, structured background knowledge and heuristics to complement distributional and graph-theoretic approaches, has serious limitations. The main issue is that the intricate context of complex associations is not always known a priori and cannot easily be computed without under- standing the underlying semantics of the associations. Complex associations should not be overlooked, since they are often needed to elucidate the mechanisms of interaction and causality relationships among concepts. Moreover, they can capture the broader aspects of a biomedical sub-domain by segregating associations along different thematic dimensions, such as Metabolic Function, Pharmaceutical Treatment and Neurological Activity. This dissertation proposes an innovative context-driven, automatic subgraph creation method for finding hidden and complex associations among concepts, along multiple thematic dimensions. It outlines definitions for context and shared context, based on implicit and explicit (or formal) semantics, which compensate for deficiencies in statistical and graph-based metrics. It also eliminates the need for heuristics a priori. An evidence-based evaluation of the proposed framework showed that 8 out of 9 existing scientific discoveries could be recovered using this approach. Additionally, insights into the meaning of associations could be obtained using provenance provided by the system. In a statistical evaluation to determine the interestingness of the generated subgraphs, it was observed that an arbitrary association is mentioned in only approximately 4 articles in MEDLINE, on average. These results suggest that leveraging implicit and explicit context, as defined in this dissertation, is an advancement of the state-of-the-art in LBD research.
Keyword: Bioinformatics; Communication; Communication Technology and New Media; Computer Sciences; Databases and Information Systems; Graph Mining; Life Sciences; Literature-Based Discovery (LBD); OS and Networks; Path Clustering; Physical Sciences and Mathematics; Science and Technology Studies; Semantic Predications; Semantic Relatedness; Social and Behavioral Sciences
URL: https://corescholar.libraries.wright.edu/knoesis/972
http://www.slideshare.net/knoesis/delroy-camerons-dissertation-defense-a-contenxtdriven-subgraph-model-for-literaturebased-discovery
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2
iExplore: Interactive Browsing and Exploring Biomedical Knowledge
In: Amit P. Sheth (2014)
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3
FACES: Diversity-Aware Entity Summarization using Incremental Hierarchical Conceptual Clustering
In: Amit P. Sheth (2014)
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4
A Graph-Based Recovery and Decomposition of Swanson’s Hypothesis using Semantic Predications
In: Krishnaprasad Thirunarayan (2014)
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5
Show Me What You Mean! Exploiting Domain Semantics in Ontology Visualization
In: Amit P. Sheth (2014)
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6
Semantics-Based Information Brokering
In: Amit P. Sheth (2014)
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7
Semantics for the Semantic Web: The Implicit, the Formal and the Powerful
In: Amit P. Sheth (2014)
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8
Context-Driven Automatic Subgraph Creation for Literature-Based Discovery
In: Amit P. Sheth (2014)
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9
SWETO: Large-Scale Semantic Web Test-bed
In: Amit P. Sheth (2014)
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10
Identifying Seekers and Suppliers in Social Media Communities to Support Crisis Coordination
In: Amit P. Sheth (2014)
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11
Updating Relational Views Using Knowledge at View Definition and View Update Time
In: Amit P. Sheth (2014)
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12
Semantic Visualization: Interfaces for Exploring and Exploiting Ontology, Knowledgebase, Heterogeneous Content and Complex Relationships
In: Amit P. Sheth (2014)
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13
What Kind of #Conversation is Twitter? Mining #Psycholinguistic Cues for Emergency Coordination
In: Amit P. Sheth (2014)
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14
FACES: Diversity-Aware Entity Summarization using Incremental Hierarchical Conceptual Clustering
In: Krishnaprasad Thirunarayan (2014)
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15
Identifying Seekers and Suppliers in Social Media Communities to Support Crisis Coordination
In: Kno.e.sis Publications (2014)
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16
ρ-Queries: Enabling Querying for Semantic Associations on the Semantic Web
In: Amit P. Sheth (2014)
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17
Online Information Searching for Cardiovascular Diseases: An Analysis of Mayo Clinic Search Query Logs
In: Kno.e.sis Publications (2014)
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18
Comparative Analysis of Online Health Queries Originating from Personal Computers and Smart Devices on a Consumer Health Information Portal
In: Amit P. Sheth (2014)
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19
Expressive Extensions to Inheritance Networks
In: Krishnaprasad Thirunarayan (2014)
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20
Visualization of Events in a Spatially and Multimedia Enriched Virtual Environment
In: Amit P. Sheth (2014)
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