Predicting Emergent Behavior in Cardiac Tissue: A Grand Challenge - PowerPoint PPT Presentation
Predicting Emergent Behavior in Cardiac Tissue: A Grand Challenge Radu Grosu SUNY at Stony Brook Joint work with Ezio Bartocci, Gregory Batt, Flavio H. Fenton, James Glimm, Colas Le Guernic, and Scott A. Smolka Excitable Cells Generate
MRM: Currents Equations Constant u ( u , v , w , s ) ( D u ) ( J fi ( u , v ) J si ( u , w , s ) J so ( u )) Resistanc e H ( u , v ) ( u v )( u u u ) v / fi J fi ( u , v ) J si ( u , w , s ) H ( u , w ) ws / si H ( u , w ) u / o ( u ) H ( u , w ) / so ( u ) J so ( u )
MRM: Currents Equations u ( u , v , w , s ) ( D u ) ( J fi ( u , v ) J si ( u , w , s ) J so ( u )) H ( u , v ) ( u v )( u u u ) v / fi J fi ( u , v ) Piecewise Nonlinear J si ( u , w , s ) H ( u , w ) ws / si H ( u , w ) u / o ( u ) H ( u , w ) / so ( u ) J so ( u )
MRM: Currents Equations u ( u , v , w , s ) ( D u ) ( J fi ( u , v ) J si ( u , w , s ) J so ( u )) H ( u , v ) ( u v )( u u u ) v / fi J fi ( u , v ) J si ( u , w , s ) H ( u , w ) ws / si Piecewise H ( u , w ) u / o ( u ) H ( u , w ) / so ( u ) J so ( u ) Bilinear
MRM: Currents Equations u ( u , v , w , s ) ( D u ) ( J fi ( u , v ) J si ( u , w , s ) J so ( u )) H ( u , v ) ( u v )( u u u ) v / fi J fi ( u , v ) J si ( u , w , s ) H ( u , w ) ws / si H ( u , w ) u / o ( u ) H ( u , w ) / so ( u ) J so ( u ) Piecewise Sigmoidal Resistanc Resistanc e e
MRM: Currents Equations u ( u , v , w , s ) ( D u ) ( J fi ( u , v ) J si ( u , w , s ) J so ( u )) H ( u , v ) ( u v )( u u u ) v / fi J fi ( u , v ) J si ( u , w , s ) H ( u , w ) ws / si H ( u , w ) u / o ( u ) H ( u , w ) / so ( u ) J so ( u ) Piecewise Nonlinear
MRM: Gates ODEs u ( u , v , w , s ) ( D u ) ( J fi ( u , v ) J si ( u , w , s ) J so ( u )) H ( u , v ,0,1) ( u v )( u u u ) v / fi J fi ( u , v ) J si ( u , w , s ) H ( u , w ,0,1) ws / si H ( u , w ,0,1) u / o ( u ) H ( u , w ,0,1) / so ( u ) J so ( u ) H ( u , v ) ( v v ) / v ( u ) H ( u , v ) v / v v ( u , v ) w ( u , w ) H ( u , w )( w w ) / w ( u ) H ( u , w ) w / w & ( S ( u , u s , k s ) s ) / s ( u ) & s ( u , s ) H ( u v )( u v )( u u u ) v / fi J fi
MRM: Gates ODEs u ( u , v , w , s ) ( D u ) ( J fi ( u , v ) J si ( u , w , s ) J so ( u )) H ( u , v ,0,1) ( u v )( u u u ) v / fi J fi ( u , v ) J si ( u , w , s ) H ( u , w ,0,1) ws / si Piecewise H ( u , w ,0,1) u / o ( u ) H ( u , w ,0,1) / so ( u ) J so ( u ) Resistance H ( u , v ) ( v v ) / v ( u ) H ( u , v ) v / v v ( u , v ) w ( u , w ) H ( u , w )( w w ) / w ( u ) H ( u , w ) w / w & ( S ( u , u s , k s ) s ) / s ( u ) & s ( u , s ) H ( u v )( u v )( u u u ) v / fi J fi Piecewise Resistance
MRM: Gates ODEs u ( u , v , w , s ) ( D u ) ( J fi ( u , v ) J si ( u , w , s ) J so ( u )) H ( u , v ,0,1) ( u v )( u u u ) v / fi J fi ( u , v ) J si ( u , w , s ) H ( u , w ,0,1) ws / si H ( u , w ,0,1) u / o ( u ) H ( u , w ,0,1) / so ( u ) J so ( u ) H ( u , v ) ( v v ) / v ( u ) H ( u , v ) v / v v ( u , v ) w ( u , w ) H ( u , w )( w w ) / w ( u ) H ( u , w ) w / w & ( S ( u , u s , k s ) s ) / s ( u ) & s ( u , s ) Sigmoidal Resistance H ( u v )( u v )( u u u ) v / fi J fi Sigmoid
MRM: Voltage-Controlled Resistances/SSV H ( u , o ) v 2 v ( u ) H ( u , o ) v 1 Piecewis e s ( u ) H ( u , w ) s 1 H ( u , w ) s 2 Constant o ( u ) H ( u , o ) o 1 H ( u , o ) o 2 w ( u )
MRM: Voltage-Controlled Resistances/SSV H ( u , o ) v 2 v ( u ) H ( u , o ) v 1 s ( u ) H ( u , w ) s 1 H ( u , w ) s 2 o ( u ) H ( u , o ) o 1 H ( u , o ) o 2 w ( u ) w 1 ) S ( u , u s , k w Sigmoidal w ( u ) w 1 ( w 2 ) so ( u ) so 1 ( so 2 so 1 ) S ( u , u s , k so ) w ( u )
MRM: Voltage-Controlled Resistances/SSV H ( u , o ) v 2 v ( u ) H ( u , o ) v 1 s ( u ) H ( u , w ) s 1 H ( u , w ) s 2 o ( u ) H ( u , o ) o 1 H ( u , o ) o 2 w ( u ) w 1 ) S ( u , u s , k w w ( u ) w 1 ( w 2 ) so ( u ) so 1 ( so 2 so 1 ) S ( u , u s , k so ) Piecewis Piecewise w ( u ) e v ( u ) H ( u , o ) Linear Constant w ( u ) H ( u , o ) (1 u / w ) H ( u , o ) w * H ( u , o ) o 1 H ( u , o ) o 2 so ( u )
MRM: Scaled Steps and Sigmoids , v 2 ) v ( u ) H ( u , o , v 1 Piecewis e s ( u ) H ( u , w , s 1 , s 2 ) Constant o ( u ) H ( u , o , o 1 , o 2 ) w ( u )
MRM: Scaled Steps and Sigmoids , v 2 ) v ( u ) H ( u , o , v 1 s ( u ) H ( u , w , s 1 , s 2 ) o ( u ) H ( u , o , o 1 , o 2 ) w ( u ) , w 2 ) w ( u ) S ( u , u s , k w , w 1 Sigmoidal so ( u ) S ( u , u s , k so , so 1 , so 2 ) w ( u )
Minimal Resistance Model (MRM) u v u v 0.3 u w 0. 13 u w u o 0.006 u o
Minimal Resistance Model (MRM) u v u v 0.3 0 u o u w 0. 13 u w u ( D u ) u / o 1 & u o 0.006 u o v (1 v ) / v 1 & w (1 u / w w ) / w & ( u ) s ( S ( u , u s , k s ) s ) / s 1 &
Minimal Resistance Model (MRM) o u w u ( D u ) u / o 2 & v v / v 2 & * w ) / w w ( w & ( u ) u v u v 0.3 0 u o s ( S ( u , u s , k s ) s ) / s 1 & u w 0. 13 u w u ( D u ) u / o 1 & u o 0.006 u o v (1 v ) / v 1 & w (1 u / w w ) / w & ( u ) s ( S ( u , u s , k s ) s ) / s 1 &
Minimal Resistance Model (MRM) w u v u ( D u ) ws / si 1/ so ( u ) & o u w v v / v 2 & u ( D u ) u / o 2 & w w / w & v v / v 2 s ( S ( u , u s , k s ) s ) / s 2 & & * w ) / w w ( w & ( u ) u v u v 0.3 0 u o s ( S ( u , u s , k s ) s ) / s 1 & u w 0. 13 u w u ( D u ) u / o 1 & u o 0.006 u o v (1 v ) / v 1 & w (1 u / w w ) / w & ( u ) s ( S ( u , u s , k s ) s ) / s 1 &
Minimal Resistance Model (MRM) v u < u s u ( D u ) ( u v )( u u u ) v / fi ws / fi 1/ so ( u ) & v v / v & w w / w & s ( S ( u , u s , k s ) s ) / , s 2 & w u v u ( D u ) ws / si 1/ so ( u ) & o u w v v / v 2 & u ( D u ) u / o 2 & w w / w & v v / v 2 s ( S ( u , u s , k s ) s ) / s 2 & & * w ) / w w ( w & ( u ) u v u v 0.3 0 u o s ( S ( u , u s , k s ) s ) / s 1 & u w 0. 13 u w u ( D u ) u / o 1 & u o 0.006 u o v (1 v ) / v 1 & w (1 u / w w ) / w & ( u ) s ( S ( u , u s , k s ) s ) / s 1 &
Sigmoid Closure Property Theorem: For ab > 0, scaled sigmoids are closed under the reciprocal operation: ln( a b ) 2 k , 1 b , 1 S ( u , k , , a , b ) 1 S ( u , k , a )
Sigmoid Closure Property ln( a b ) 2 k , 1 b , 1 S ( u , k , , a , b ) 1 S ( u , k , a ) S ( u , k , , a , b ) Proof: b b a S ( u , k , , a , b ) 1 ( a b-a ) 1 1 e 2 k u a
Sigmoid Reciprocal Closure ln( a b ) 2 k , 1 b , 1 S ( u , k , , a , b ) 1 S ( u , k , a ) S ( u , k , , a , b ) 1 1 Proof: a 1 a 1 S ( u , k , , a , b ) 1 1 a 1 1 b a 2 k ( u ( ln a ln b b )) 1 e 2 k 1 b ln( a / b ) / 2 k
From Resistances to Conductances Removing Divisions using Sigmoid Reciprocal: 1/ w S ( u , k w S ( u , k w , w 2 ) , u ' w , w 1 1 , w 2 1 ) w , u w , w 1 g w v u s u u u w u ' w u 0.03 0.04 0.9087 0.3 1.55
From Resistances to Conductances Removing Divisions using Sigmoid Reciprocal: 1/ w S ( u , k w S ( u , k w , w 2 ) , u ' w , w 1 1 , w 2 1 ) w , u w , w 1 g w g so 1/ s 0 S ( u , k so , u ' so , 1 so 1 , 1 so S ( u , k so , u so , so 1 , so 2 ) so 2 ) u so v u s u u u ' so u w u ' w u 0.65 0.03 0.04 0.9087 1.48 0.3 1.55
From Resistances to Conductances 1/ w S ( u , k w S ( u , k w , w 2 ) , u ' w , w 1 1 , w 2 1 ) w , u w , w 1 g w g so 1/ s 0 S ( u , k so , u ' so , 1 so 1 , 1 so S ( u , k so , u so , so 1 , so 2 ) so 2 ) Removing Divisions using Step Reciprocal: 1/ v H ( u , o , v 1 H ( u , o , v 1 , v 2 ) 1 , v 2 1 ) v g v g o 1/ o H ( u , o , 1 o 1 , 1 o H ( u , o , o 1 , o 2 ) o 2 ) * ) v H ( u , o ,0,1) w H ( u , o ,0,1) (1 ug w ) H ( u , o ,0,w u so v o u s u u u ' so u w u ' w u 0.006 0.65 0.03 0.04 0.9087 1.48 0.3 1.55
From Resistances to Conductances 1/ w S ( u , k w S ( u , k w , w 2 ) , u ' w , w 1 1 , w 2 1 ) w , u w , w 1 g w g so 1/ s 0 S ( u , k so , u ' so , 1 so 1 , 1 so S ( u , k so , u so , so 1 , so 2 ) so 2 ) Removing Divisions using Step Reciprocal: 1/ v H ( u , o , v 1 H ( u , o , v 1 , v 2 ) 1 , v 2 1 ) v g v g o 1/ o H ( u , o , 1 o 1 , 1 o H ( u , o , o 1 , o 2 ) o 2 ) s H ( u , w , s 1 , s 2 ) g s 1/ s H ( u , w , s 1 1 , s 2 1 ) * ) v H ( u , o ,0,1) w H ( u , o ,0,1) (1 ug w ) H ( u , o ,0,w u so v o w u s u u u ' so u w u ' w u 0.006 0.13 0.65 0.03 0.04 0.9087 1.48 0.3 1.55
Minimal Conductance Model (MCM) v u < u s u ( D u ) ( u v )( u u u ) v g fi ws g si g so ( u ) & v v g v & w w g w & s ( S ( u , u s , k s ,0,1) s ) g s 2 & w u v u ( D u ) ws g si g so ( u ) & o u w v v g v 2 & u ( D u ) u g o 2 & w w g w & v v g v 2 s ( S ( u , u s , k s ,0,1) s ) g s 2 & & * w ) g w ( u ) w ( w & u v u v 0.3 0 u o s ( S ( u , u s , k s ,0,1) s ) g s 1 & u w 0. 13 u w u ( D u ) u g o 1 & v (1 v ) g v 1 u o 0.006 u o & ( u ) w (1 u g w w ) g w & s ( S ( u , u s , k s ,0,1) s ) g s 1 &
Gene Regulatory Networks (GRN) GRN canonical sigmoidal form: n j m i S ( u k , k k u i , k , a k , b k ) b i u i a ij j 1 k 1
Gene Regulatory Networks (GRN) GRN canonical sigmoidal form: n j m i S ( u k , k k u i , k , a k , b k ) b i u i a ij j 1 k 1 where: a ij : are activation / inhibition constants b i : are decay constants S (..) : are on / off sigmoidal functions
Gene Regulatory Networks (GRN) GRN canonical sigmoidal form: n j m i S ( u k , k k u i , k , a k , b k ) b i u i a ij j 1 k 1 where: a ij : are activation / inhibition constants b i : are decay constants S (..) : are on / off sigmoidal functions Note: steps and ramps are sigmoid approximations
Optimal Polygonal Approximation Given: One nonlinear curve and desired # segments Find: Optimal polygonal approximation
Optimal Polygonal Approximation Example: What is the optimal polygonal approxima- tion of the blue curve with 3 segments ?
Optimal Polygonal Approximation Example: What is the optimal polygonal approxima- tion of the blue curve with 3 segments ?
Optimal Polygonal Approximation Example: What is the optimal polygonal approxima- tion of the blue curve with 3 segments ?
Optimal Polygonal Approximation Example: What is the optimal polygonal approxima- tion of the blue curve with 3 segments ?
Optimal Polygonal Approximation Example: What is the optimal polygonal approxima- tion of the blue curve with 3 segments ?
Optimal Polygonal Approximation Dynamic Programming Algorithm • Complexity: O(P 2 ) • P: # points of the curve M. Salotti, Pattern Recognition Letters 22 (2001), Pag 215-221
Optimal Polygonal Approximation Dynamic Programming Algorithm • Complexity: O(P 2 ) • P: # points of the curve M. Salotti, Pattern Recognition Letters 22 (2001), Pag 215-221
Optimal Polygonal Approximation Dynamic Programming Algorithm • Complexity: O(P 2 ) • P: # points of the curve M. Salotti, Pattern Recognition Letters 22 (2001), Pag 215-221
Optimal Polygonal Approximation Dynamic Programming Algorithm • Complexity: O(P 2 ) • P: # points of the curve M. Salotti, Pattern Recognition Letters 22 (2001), Pag 215-221
Optimal Polygonal Approximation Dynamic Programming Algorithm • Complexity: O(P 2 ) • P: # points of the curve M. Salotti, Pattern Recognition Letters 22 (2001), Pag 215-221
Globally-Optimal Polygonal Approximation Given: Set of nonlinear curves and desired # of segments Find: Globally optimal polygonal approximation
Globally-Optimal Polygonal Approximation Example: What is the optimal polygonal approxima- tion of the curves below with 5 segments ?
Globally-Optimal Polygonal Approximation Example: What is the optimal polygonal approxima- tion of the curves below with 5 segments ? Combining the two we obtain 8 segments and not 5 segments
Globally-Optimal Polygonal Approximation Example: What is the optimal polygonal approxima- tion of the curves below with 5 segments ? Solution: modify the OPAA to minimize the maximum error of a set of curves simultaneously.
Deriving the Piecewise Multi-Affine Model ( v u < u u ) u e ( u v )( u u u ) v g fi ws g si g so ( u ) & v v g v & w w g w & s S ( u , k s , u s ,0,1) g s 2 s g s 2 & w u v u v u e ws g si g so ( u ) & v v g v 2 & u v w w g w & s S ( u , k s , u s ,0,1) g s 2 s g s 2 & o u w u w u e u g o 2 & v v g v 2 & u w * w ) g w ( u ) w ( w & s S ( u , k s , u s ) g s 1 s g s 1 & 0 u o u o u e u g o 1 & v (1 v ) g v 1 & u o w (1 u g w w ) g w ( u ) & s S ( u , k s , u s ) g s 1 s g s 1 &
Deriving the Piecewise Multi-Affine Model ( v u < u u ) u e ( u v )( u u u ) v g fi ws g si g so ( u ) & v v g v & w w g w & s S ( u , k s , u s ,0,1) g s 2 s g s 2 & w u v u v u e ws g si g so ( u ) & v v g v 2 & u v w w g w & s S ( u , k s , u s ,0,1) g s 2 s g s 2 & o u w u w u e u g o 2 & v v g v 2 & u w * w ) g w ( u ) w ( w & s S ( u , k s , u s ) g s 1 s g s 1 & 0 u o u o u e u g o 1 & v (1 v ) g v 1 & u o w (1 u g w w ) g w ( u ) & s S ( u , k s , u s ) g s 1 s g s 1 &
Deriving the Piecewise Multi-Affine Model ( v u < u u ) u e ( u v )( u u u ) v g fi ws g si g so ( u ) & v v g v & w w g w & s S ( u , k s , u s ,0,1) g s 2 s g s 2 & w u v u v u e ws g si g so ( u ) & v v g v 2 & u v w w g w & s S ( u , k s , u s ,0,1) g s 2 s g s 2 & o u w u w u e u g o 2 & v v g v 2 & u w * w ) g w ( u ) w ( w & s S ( u , k s , u s ) g s 1 s g s 1 & 0 u o u o u e u g o 1 & v (1 v ) g v 1 & u o w (1 u g w w ) g w ( u ) & s S ( u , k s , u s ) g s 1 s g s 1 &
Deriving the Piecewise Multi-Affine Model ( v u < u u ) u e ( u v )( u u u ) v g fi ws g si g so ( u ) & v v g v & w w g w & s S ( u , k s , u s ) g s 2 s g s 2 & w u v u v u e ws g si g so ( u ) & v v g v 2 & u v w w g w & s S ( u , k s , u s ) g s 2 s g s 2 & o u w u w u e u g o 2 & v v g v 2 & u w * w ) g w ( u ) w ( w & s S ( u , k s , u s ) g s 1 s g s 1 & 0 u o u o u e u g o 1 & v (1 v ) g v 1 & u o w (1 u g w w ) g w ( u ) & s S ( u , k s , u s ) g s 1 s g s 1 &
Deriving the Piecewise Multi-Affine Model ( v u < u u ) u e ( u v )( u u u ) v g fi ws g si g so ( u ) & v v g v & w w g w & s S ( u , k s , u s ) g s 2 s g s 2 & w u v u v u e ws g si g so ( u ) & v v g v 2 & u v w w g w & s S ( u , k s , u s ) g s 2 s g s 2 & o u w u w u e u g o 2 & v v g v 2 & u w * w ) g w ( u ) w ( w & s S ( u , k s , u s ) g s 1 s g s 1 & 0 u o u o u e u g o 1 & v (1 v ) g v 1 & u o w (1 u g w w ) g w ( u ) & s S ( u , k s , u s ) g s 1 s g s 1 &
Deriving the Piecewise Multi-Affine Model 12 v < u u u 26 25 25 u e v g fi ws g si & R ( u , i , i 1 , u fi i , u fi i 1 ) R ( u , i , i 1 , u so i , u so i 1 ) g so i 12 i 12 v v g v & w w g w & 25 s ( s ) g s 2 & R ( u , i , i 1 , u s i , u s i 1 ) i 12 8 w u v 12 11 u e ws g si & R ( u , i , i 1 , u so i , u so i 1 ) g so u v i 8 v v g v 2 & u v w w g w & 11 s ( s ) g s 2 & R ( u , i , i 1 , u s i , u s i 1 ) i 8 2 o u w 8 u e u g o 2 & u w v v g v 2 & * w ) u w 7 w ( w & R ( u , i , i 1 , u w i , u w i 1 ) g w b i 2 7 s ( s ) g s 1 & R ( u , i , i 1 , u s i , u s i 1 ) i 2 0 0 u o 2 u o u e u g o 1 & v (1 v ) g v 1 & u o , u w i 1 ) , u w i 1 )) g w a 1 w ( wR ( u , i , i 1 , u w i & ( R ( u , i , i 1 , u w i i 0 1 s ( s ) g s 1 & R ( u , i , i 1 , u s i , u s i 1 ) i 0
2D Comparison
Analysis Problem • Find parameter ranges reproducing non-excitability: – Restated as an LTL formula: G ( u v )
Analysis Problem G ( u v ) • Initial region: u [0, 1 ] s [0,0.01] v [0.95,1] w [0.95,1]
Analysis Problem G ( u v ) u [0, 1 ] s [0,0.01] v [0.95,1] w [0.95,1] • Uncertain parameter ranges: g o 1 [1,180] g o 2 [0,10] g si [0.1,100] g so [0.9,50]
Analysis Problem G ( u v ) u [0, 1 ] s [0,0.01] v [0.95,1] w [0.95,1] g o 1 [1,180] g o 2 [0,10] g si [0.1,100] g so [0.9,50] e 1 • Stimulus:
State Space Partition v 1.00 0.95 u 0.00 0 1 2 3 7 8 9 11 12 13 25 26 • Hyperrectangles: 4 dimensional (uv-projection) – Arrows: indicate the vector field
Embedding Transition System T X (p) v 1.00 0.95 x ' x u 0.00 0 1 2 3 7 8 9 11 12 13 25 26 T X ( p ) x ' iff there is a solution and time such that: x ( 0 ) x , ( ) x ' t [ 0 , ]. ( t ) rect ( x ) rect ( x ') rect ( x ) is adjacent to rect ( x ')
The Discrete Abstraction T R (p) v 1.00 0.95 u 0.00 0 1 2 3 7 8 9 11 12 13 25 26 x : R ( p ) x ' iff rect ( x ) rect ( x ') T R ( p ) is the quotiont of T X ( p ) with respect to : R ( p )
The Discrete Abstraction T R (p) v 1.00 0.95 u 0.00 0 1 2 3 7 8 9 11 12 13 25 26 x : R ( p ) x ' iff rect ( x ) rect ( x ') T R ( p ) is the quotiont of T X ( p ) with respect to : R ( p ) Theorem: p . T X ( p ) T R ( p )
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