A Semantic Web Platform for Improving the Automation and Reproducibility of Finite Element Bio-simulations

A Semantic Web Platform for
Automating the Interpretation of
Finite Element Bio-simulations
Dr. Ratnesh Sahay
Semantics in eHealth & Life Sciences (SeLS)
Insight Centre for Data Analytics
NUI Galway, Ireland
10-12-2014
SWAT4LS-2014, Berlin
Germany

Background – Hearing Loss
278 Million People
• Outer ear gets excited both by the sound waves propagate through the ear canal and strike the eardrum
• In the middle ear the ear drum vibrates generating pressure waves in the inner ear fluid chambers
• The inner ear turns pressure waves into electrical signals that our brain can understand
Slide 2

Background – Hearing Loss
• The ear drum vibrates generating pressure waves in the inner ear fluid chambers
• The inner ear turns pressure waves into electrical signals that our brain can understand
Infrastructure to integrate clinical knowledge, experimental data and inner ear models
Slide 3

Inner Ear - Bio Simulation Model & System
PAK - FM
Slide 4

SIFEM Project
Electrical Coupling Model
Micromechanics Model
Finite Element Model
Fluid Coupling Model
Slide 5

Goals
Automate the interpretation of finite element (FE)
biosimulations ...
Insight Centre for Data Analytics Slide 6

Motivational Scenario: Cochlear
mechanics

Characteristics of the FE Domain
• Difficult to represent
• Physics, geometrical models, topological relations, algoithmic,
mathematics

Dimensions of a FE Bio-simulation

Geometrical Model

Physics Model
• FE equilibrium for solid
• FE equilibrium for fluid

Numerical Models/Solvers
• Incremental-iterative implicit solution scheme

Experimental Data
• A

Lid-driven cavity flow
Physical Model
FEM Model
Solver
 If there a vortex close to
the lid?

Lid-driven cavity flow
Physical Model
FEM Model
Solver
 definition of a simulation
 If there a vortex close to
the lid?

Numerical Data Interpretation
description of the
simulation
Is translated into
Rules using references
to anatomical, physical
and data feature
elements
Multiple simulations
Feature extraction
Interpretation = rules
applied over data at
the symbolic level
Insight Centre for Data Analytics 02 May 2014 Slide 16

Data View
Data Selection
y
0.05

Feature Extraction
maximum
velocity is 0.93
at the lid
fast increase
(avg first derivative > 35)
Minima=(0.055,-0.20)
velocity starts
at 0 at the
bottom
slow decrease
followed by
Based on the TEDDY
ontology

Data Interpretation Statements
:DataView1 :hasDimensionY :VelocityX .
:DataView1 :hasDimensionX :DistanceFromTheCavityBase .
:DataView1 :x0 “0.0"^^xsd:double .
:DataView1 :y0 “0.0"^^xsd:double .
:DataView1 :hasMinimumX “-0.055"^^xsd:double .
:DataView1 :hasMinimumY “-0.20"^^xsd:double .
:DataView1 :hasFeature :PositiveSecondDerivative .
:DataView1 :hasBehaviour :BehaviourRegion1 .
:DataView1 :hasBehaviour :BehaviourRegion2 .
:BehaviourRegion1 :avgFirstDerivative “-3.63"^^xsd:double .
:BehaviourRegion1 :hasFeature EndRegion .
:BehaviourRegion1 :hasFeature :Decreases .
:BehaviourRegion1 :hasFeature :DecreasesSlowly .
:BehaviourRegion2 :avgFirstDerivative “33.35"^^xsd:double .
:BehaviourRegion2 :hasFeature EndRegion .
:BehaviourRegion2 :hasFeature :Increases .
:BehaviourRegion2 :hasFeature :IncreasesFast .
:BehaviourRegion1 :isFollowedBy :BehaviourRegion1 .
: LidSimulation Data Analysis Rule :hasInterpretation :ValidVelocityBehaviour .

Data Analysis Rules
IF( minima(velocity) is negative AND
decreases very slowly(velocity) AND
increases very fast (velocity) )
VALID VELOCITY BEHAVIOUR
SPARQL Rule
CONSTRUCT
{ :LidSimulation sif: hasInterpretation :ValidVelocityBehaviour }
WHERE {
?dataview rdf:type dao:DataView .
?dataview dao:hasFeature ?x .
...
}

Output Data Views

Feature Extraction
:DataView1 :hasDimensionY :BasilarMembraneMagnitude .
:DataView1 :hasDimensionX :DistanceFromTheCochleaBasis .
:DataView1 :hasFeature :isSingleWave .
:DataView1 :hasMaximumAmplitude “0.0031 "^^xsd:double.
:DataView1 :hasMaximumY “0.0020 e^-6 "^^xsd:double .
:DataView1 :hasMaximumX “14"^^xsd:double .
:DataView1 :hasMinimumY “-0.0011 e^-6 "^^xsd:double .
:DataView1 :hasMinimumX “17"^^xsd:double .

Conceptual Model Excerpt

Take-away message
• Contemporary science demands new infrastructures to
scale scientific discovery in a complex knowledge
environment.
• Numerical data is everywhere, not only in FE simulations.
• In this work we started exploring how to represent and
extract numerical data features to a conceptual level.

Future Directions
• Better integration of the proposed representation and data
analysis framework to the (TErminology for the Description of
DYnamics) TEDDY conceptual model [EMBL-EBI].
• Use of the feature set and rules as a heuristic method to
improve the simulation configuration space.

SIFEM TEAM
• Andre Freitas
• Kartik Asooja
• Joao B. Jares
• Stefan Decker
• Ratnesh Sahay
Th a n k Yo u !

A Semantic Web Platform for Improving the Automation and Reproducibility of Finite Element Bio-simulations

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