Beyond the EU: DORA and NIS 2 Directive's Global Impact
Swanson rfo-pres-grp-mtg
1. A Graph-Based Decomposition of
Swanson’s Hypothesis using
Semantic Predications
Delroy Cameron, Olivier Bodenreider, HimaYalamanchili,
TuDanh, SreeramVallabhaneni, KrishnaprasadThirunarayan,
Amit P. Sheth and Thomas C. Rindflesch
02/17/2012
6. 6
LITERATURE-BASED DISCOVERY(LBD)
Finding explicit connections
Undiscovered public knowledge2
Noninteracting literatures
ABC Model
A B C
2Swanson DR.Undiscovered public knowledge.Library Quarterly 1986;56(1):103–18.
7. 7
PROBLEM
IR-based techniques
Lack context B C
A B3
Platelet Raynaud
DFO INHIBITS CAUSES
Aggregation Syndrome
ABC Model INHIBITS
Lack coverage Prostaglandin B2
AnC3 Model, n={B1, B2…Bm}
STIMULATES ISA
Epoprostenol B1
3Wilkowski B, Fiszman M, Miller C, Hristovski D, Arabandi S, Rosemblat G, Rindflesch T. Discovery browsing with semantic predications and graph theory. AMIA AnnuSymp Proc 2011
8. 8
PROBLEM-SOLUTION
AnC Model
Raynaud
Multiple Paths3 DFO STIMULATES Epoprostenol TREATS Syndrome
Subgraphs3
STIMULATE ISA
Background knowledge* S TREATS
PRODUCES Raynaud
DFO Prostaglandin Syndrome
INHIBITS CAUSES
Platelet
Aggregation
3Wilkowski B, Fiszman M, Miller C, Hristovski D, Arabandi S, Rosemblat G, Rindflesch T. Discovery browsing with semantic predications and graph theory. AMIA AnnuSymp Proc 2011
9. 9
CONTRIBUTION
Graph-based Framework for LBD
Semantic predications
From ABC Model to AnC Model Question Answering
Construct expressive subgraphs
Background knowledge*
Literature-based Discovery
Evaluate/Assess
Recover Swanson’s Hypothesis Information Retrieval
Decompose Swanson’s Hypothesis*
10. RELATED WORK (Semantics-based) 10
ABC AnC Graph Background
Subgraphs
Model Model Theory knowledge
Hristovski
[14,15,26] ✔ ✔
(BITOLA)
Pratt
[13, 22] ✔ ✔
(LitLinker)
Ahlers [16] ✔
Cohen [23]
✔ ✔
(Epiphanet)
Wilkowski [17] ✔ ✔ ✔
Cameron* ✔ ✔ ✔ ✔
11. 11
IMPACT
Interdisciplinary Research
Mechanisms of operation
Causality Relationships
Semantic Integration of Heterogeneous Data
Experimental Data
Scientific Literature
Structured Data
12. 12
APPROACH
Corpus
1. Literature Preprocessing
2. Predication Extraction (SemRep)
3. Predications Graph Creation
4. Path generation
Extend ABC Model to AnC Model
5. Subgraph Construction Path Generation
Multiple Paths
Background Knowledge
13. 13
Path Generation
Reachability
“the notion of being able to get from one vertex in a
directed graph to some other vertex”
DFO Transitive Reachability
A
Closure = Relation
C
RS
14. 14
Subgraph Creation
Original Swanson Associations
Thoroughly read Paper1
Three (3) Primary Associations
o Eight (8) Supplementary Associations
o Eight (8) Secondary Associations
Subgraph Construction (manual)
Classifying Paths from Reachability Relation
Human Cognition as Background Knowledge
1Swanson D. Fish oil, raynaud’s syndrome, and undiscovered public knowledge. PerspectBiol Med 1986;30(1):7–18.
21. Platelet Aggregation (path#4) Supplementary
Dietary Fish Oil->INHIBITS->triglyceride->ISA->Blood Lipid->AFFECTS->Blood Viscosity->CAUSES ->Raynaud Syndrome
Essential
Lipid
Fatty Acid
Six Relevant Paths
ISA INHIBIT ISA
Fatty Acid Triglyceride
ISA INHIBITS AFFECTS
Blood Raynaud
DFO DISRUPTS CAUSES
Viscosity Syndrome
22. 22
Experimental Results
Association Type Experiment I Experiment II
Primary (3) 3 2*(1VR missing)
Supplementary (8) 4 (2VR, 2BV missing) 4*(2VR, 2BV missing)
Secondary (8) 7 (1VR missing) 5* (3VR missing)
* - Not sufficiently detailed
23. RELATED WORK (Semantics-based) 23
ABC AnC Graph Background
Subgraphs
Model Model Theory knowledge
Hristovski
[14,15,26] ✔ ✔
(BITOLA)
Pratt
[13, 22] ✔ ✔
(LitLinker)
Ahlers [16] ✔
Cohen [23]
✔ ✔
(Epiphanet)
Wilkowski [17] ✔ ✔ ✔
Cameron* ✔ ✔ ✔ ✔
24. 24
FUTURE WORK
Scalability
Path Clustering
o Structural Features (Centrality, Geodesic)
o Semantic Features (Similarity, Relatedness)
Semantic Integration of Background Knowledge
o Heuristics (knowledge abstraction,[CameronBIBM2011])
Inconsistencies
Predication Extraction (SemRep)
Corpus (Richness)
25. 25
CONCLUSION
Graph-based Framework (GFB) for LBD
Semantic predications
Extend ABC Model to AnC Model
Construct expressive subgraphs
Background knowledge*
Evaluate/Assess
Recover Swanson’s Hypothesis
Decompose Swanson’s Hypothesis*
26. The future of LBD requires
the
Semantic Integration
of
subgraphs and background knowledge
Swanson - PhD in Physics from UC Berkeley (1947) -Professor University of ChicagoSmalheiser – MD, PhD in Neuroscience & Psychiatry - University of Illinois @ Chicago
J. Dyerberg Eskimo study - no thrombosis - no atherosclerosis (hardening of walls of arteries)
Take a close look at the paths again guys.It looks like Epoprostenol plays a central role reducing platelet aggregation, reducing blood viscosity and also causing vascular reactivity.Are we onto something here??Can we say that we have found that DFO ameliorates RS as a result of the effect of Epoprostenol on platelet aggregation, blood viscosity and vascular reactivity??
Take a close look at the paths again guys.It looks like Epoprostenol plays a central role reducing platelet aggregation, reducing blood viscosity and also causing vascular reactivity.Are we onto something here??Can we say that we have found that DFO ameliorates RS as a result of the effect of Epoprostenol on platelet aggregation, blood viscosity and vascular reactivity??
