from sensitive to formal barbaric systems biology
play

From Sensitive to Formal Barbaric Systems Biology Oded Maler - PowerPoint PPT Presentation

From Sensitive to Formal Barbaric Systems Biology Oded Maler Memorial Alexandre Donz Decyphir SAS, Moirans, France HSB19, April 6th 2019 Alexandre Donz HSB19 1 / 46 A Tribute To Oded? Disclaimer: several ways this talk is (sort


  1. Proving correctness? Correctness is a subjective notion until it is defined formally . For this we need: ◮ a description of the systems behaviors ◮ a specification language to describe desired (good) and unwanted (bad) properties Coffee machine example ◮ a good property is: if I insert a coin and push ’coffee’, I get coffee ◮ a bad one: I get a tea (and no change) The system is declared correct iff all the behaviors of the system satisfies all the good properties and none of the bad ones Alexandre Donzé Introduction HSB’19 7 / 46

  2. Proving correctness? Correctness is a subjective notion until it is defined formally . For this we need: ◮ a description of the systems behaviors ◮ a specification language to describe desired (good) and unwanted (bad) properties Coffee machine example ◮ a good property is: if I insert a coin and push ’coffee’, I get coffee ◮ a bad one: I get a tea (and no change) The system is declared correct iff all the behaviors of the system satisfies all the good properties and none of the bad ones Alexandre Donzé Introduction HSB’19 7 / 46

  3. Proving correctness? Correctness is a subjective notion until it is defined formally . For this we need: ◮ a description of the systems behaviors ◮ a specification language to describe desired (good) and unwanted (bad) properties Coffee machine example ◮ a good property is: if I insert a coin and push ’coffee’, I get coffee ◮ a bad one: I get a tea (and no change) The system is declared correct iff all the behaviors of the system satisfies all the good properties and none of the bad ones Alexandre Donzé Introduction HSB’19 7 / 46

  4. Reactive Systems and Temporal Logics A key issue is the appropriate choice of language to describe properties: ◮ Enough expressivity ◮ Ease of writing specification Temporal logics popularized in 1978 by Amir Pnueli when programs shifted from simple input-output relations to reactive programs, A typical reactive program is an operating system: ◮ a good property is always when the mouse is moved, the cursors moves ◮ a bad one: always eventually a blue screen appears and nothing happens A good property such as the one above is a liveness property . Living systems are typically reactive programs.. Alexandre Donzé Introduction HSB’19 8 / 46

  5. Reactive Systems and Temporal Logics A key issue is the appropriate choice of language to describe properties: ◮ Enough expressivity ◮ Ease of writing specification Temporal logics popularized in 1978 by Amir Pnueli when programs shifted from simple input-output relations to reactive programs, A typical reactive program is an operating system: ◮ a good property is always when the mouse is moved, the cursors moves ◮ a bad one: always eventually a blue screen appears and nothing happens A good property such as the one above is a liveness property . Living systems are typically reactive programs.. Alexandre Donzé Introduction HSB’19 8 / 46

  6. Reactive Systems and Temporal Logics A key issue is the appropriate choice of language to describe properties: ◮ Enough expressivity ◮ Ease of writing specification Temporal logics popularized in 1978 by Amir Pnueli when programs shifted from simple input-output relations to reactive programs, A typical reactive program is an operating system: ◮ a good property is always when the mouse is moved, the cursors moves ◮ a bad one: always eventually a blue screen appears and nothing happens A good property such as the one above is a liveness property . Living systems are typically reactive programs.. Alexandre Donzé Introduction HSB’19 8 / 46

  7. From Verification to Synthesis Verification of mis-conceived systems can be tedious and frustrating. Rather than chasing bugs, can’t we prevent them from happening in the first place ? Synthesis is the ultimate goal of Formal Verification: Building correct-by-construction systems directly from specifications For synthesized systems, verification is unnecessary. Alexandre Donzé Introduction HSB’19 9 / 46

  8. Synthesis in the Wild Synthesis is a difficult problem: decades of research, actually applied for hardly a couple of years to produce small digital circuits Attempts to apply synthesis in even more challenging context: software, analog circuits , control engineering, biology, etc Is this reasonnable/useful ? In most cases, no. A common syndrome: When you have a hammer, everything looks like a nail Still, genuine belief that diffusing formal methods to other, more primitive scientific domains, if done in an humble and intelligent way, can do some good Alexandre Donzé Introduction HSB’19 10 / 46

  9. Synthesis in the Wild Synthesis is a difficult problem: decades of research, actually applied for hardly a couple of years to produce small digital circuits Attempts to apply synthesis in even more challenging context: software, analog circuits , control engineering, biology, etc Is this reasonnable/useful ? In most cases, no. A common syndrome: When you have a hammer, everything looks like a nail Still, genuine belief that diffusing formal methods to other, more primitive scientific domains, if done in an humble and intelligent way, can do some good Alexandre Donzé Introduction HSB’19 10 / 46

  10. Synthesis in the Wild Synthesis is a difficult problem: decades of research, actually applied for hardly a couple of years to produce small digital circuits Attempts to apply synthesis in even more challenging context: software, analog circuits , control engineering, biology, etc Is this reasonnable/useful ? In most cases, no. A common syndrome: When you have a hammer, everything looks like a nail Still, genuine belief that diffusing formal methods to other, more primitive scientific domains, if done in an humble and intelligent way, can do some good Alexandre Donzé Introduction HSB’19 10 / 46

  11. Parameter Synthesis 1 Parametric Systems Sensitive Systematic (aka Barbaric) Simulation Parameter Synthesis with Formal Specifications 2 Signal Temporal Logic Property parameters Model parameters Some Results and Concluding Remarks 3 Alexandre Donzé Parameter Synthesis HSB’19 11 / 46

  12. Parametric Systems Definition (Parametric System) An object mapping a finite set of values (parameters) to a set of signals p = ( p 1 , · · · , p n ) System S x [ t ] : ◮ p , t , x [ t ] in R domain, t �→ x [ t ] continuous “almost everywhere” ◮ Typically (for us): S is a (hybrid) system of ordinary differential equations ◮ But most of what we do works for black box parametric systems Alexandre Donzé Parameter Synthesis HSB’19 12 / 46

  13. Parametric Systems Definition (Parametric System) An object mapping a finite set of values (parameters) to a set of signals p = ( p 1 , · · · , p n ) System S x [ t ] : ◮ p , t , x [ t ] in R domain, t �→ x [ t ] continuous “almost everywhere” ◮ Typically (for us): S is a (hybrid) system of ordinary differential equations ◮ But most of what we do works for black box parametric systems Alexandre Donzé Parameter Synthesis HSB’19 12 / 46

  14. Parametric Systems Definition (Parametric System) An object mapping a finite set of values (parameters) to a set of signals p = ( p 1 , · · · , p n ) System S x [ t ] : ◮ p , t , x [ t ] in R domain, t �→ x [ t ] continuous “almost everywhere” ◮ Typically (for us): S is a (hybrid) system of ordinary differential equations ◮ But most of what we do works for black box parametric systems Alexandre Donzé Parameter Synthesis HSB’19 12 / 46

  15. Parametric Systems Definition (Parametric System) An object mapping a finite set of values (parameters) to a set of signals p = ( p 1 , · · · , p n ) System S x [ t ] : ◮ p , t , x [ t ] in R domain, t �→ x [ t ] continuous “almost everywhere” ◮ Typically (for us): S is a (hybrid) system of ordinary differential equations ◮ But most of what we do works for black box parametric systems Alexandre Donzé Parameter Synthesis HSB’19 12 / 46

  16. Example: acute inflamatory response to pathogen dP 1 − P k pm s m P k pg P � � = µ m + k mp P − k pm f ( N A ) P, − dt p ∞ dN A s nr R = µ nr + R − µ n N A , dt dD = k dn f s ( f ( N A )) − µ d D, dt s c + k cn f ( N A + k cmd D ) dC A = 1 + f ( N A + k cmd D ) − µ c C A , dt Parameters ◮ “Initial” conditions: P ( t = 0) , N A ( t = 0) , D ( t = 0) , C A ( t = 0) . ◮ Others: k pg , p ∞ , k pm , s m , µ m , s nr , . . . Depending on their values, three possible outcomes ◮ Health: pathogen and damage are driven to a low steady state ◮ Aseptic death: pathogen is eliminated but not tissue damage ◮ Septic death: tissue damage and pathogen remain high Alexandre Donzé Parameter Synthesis HSB’19 13 / 46

  17. Example: acute inflamatory response to pathogen dP 1 − P k pm s m P k pg P � � = µ m + k mp P − k pm f ( N A ) P, − dt p ∞ dN A s nr R = µ nr + R − µ n N A , dt dD = k dn f s ( f ( N A )) − µ d D, dt s c + k cn f ( N A + k cmd D ) dC A = 1 + f ( N A + k cmd D ) − µ c C A , dt Parameters ◮ “Initial” conditions: P ( t = 0) , N A ( t = 0) , D ( t = 0) , C A ( t = 0) . ◮ Others: k pg , p ∞ , k pm , s m , µ m , s nr , . . . Depending on their values, three possible outcomes ◮ Health: pathogen and damage are driven to a low steady state ◮ Aseptic death: pathogen is eliminated but not tissue damage ◮ Septic death: tissue damage and pathogen remain high Alexandre Donzé Parameter Synthesis HSB’19 13 / 46

  18. Example: acute inflamatory response to pathogen dP 1 − P k pm s m P k pg P � � = µ m + k mp P − k pm f ( N A ) P, − dt p ∞ dN A s nr R = µ nr + R − µ n N A , dt dD = k dn f s ( f ( N A )) − µ d D, dt s c + k cn f ( N A + k cmd D ) dC A = 1 + f ( N A + k cmd D ) − µ c C A , dt Parameters ◮ “Initial” conditions: P ( t = 0) , N A ( t = 0) , D ( t = 0) , C A ( t = 0) . ◮ Others: k pg , p ∞ , k pm , s m , µ m , s nr , . . . Depending on their values, three possible outcomes ◮ Health: pathogen and damage are driven to a low steady state ◮ Aseptic death: pathogen is eliminated but not tissue damage ◮ Septic death: tissue damage and pathogen remain high Alexandre Donzé Parameter Synthesis HSB’19 13 / 46

  19. Healthy outcome Pathogen Damage Alexandre Donzé Parameter Synthesis HSB’19 14 / 46

  20. Aseptic death outcome Pathogen Damage Alexandre Donzé Parameter Synthesis HSB’19 14 / 46

  21. Septic death outcome Pathogen Damage Alexandre Donzé Parameter Synthesis HSB’19 14 / 46

  22. The problem with parameters We don’t know them. Alexandre Donzé Parameter Synthesis HSB’19 15 / 46

  23. The problem with parameters We don’t know them. Traditional approach to solve this ◮ Calibration: Find p such that � S ( p ) − x measured � is minimized. ◮ Usually some optimization problem. Alexandre Donzé Parameter Synthesis HSB’19 15 / 46

  24. The problem with parameters We don’t know them. Traditional approach to solve this ◮ Calibration: Find p such that � S ( p ) − x measured � is minimized. ◮ Usually some optimization problem. Validation (hard) ◮ S ( p ) predicts x measured before it’s measured ◮ (and not just once by luck) ◮ Robustness: S ( p + ǫ ) is not vastly different from S ( p ) ◮ ? Alexandre Donzé Parameter Synthesis HSB’19 15 / 46

  25. Formal methods and parameter synthesis Verification System | = ? Specifications Synthesis ◮ Parameter synthesis reduces synthesis to finding “a few” valid values for parameters ◮ We consider: ◮ System parameters: for which values is the spec. satisfied ? ◮ Specification parameters: what is the spec. actually satisfied ? In the following we focus on reachability specifications Alexandre Donzé Parameter Synthesis HSB’19 16 / 46

  26. Formal methods and parameter synthesis Verification System | = ? Specifications Synthesis ◮ Parameter synthesis reduces synthesis to finding “a few” valid values for parameters ◮ We consider: ◮ System parameters: for which values is the spec. satisfied ? ◮ Specification parameters: what is the spec. actually satisfied ? In the following we focus on reachability specifications Alexandre Donzé Parameter Synthesis HSB’19 16 / 46

  27. Formal methods and parameter synthesis Verification System | = ? Specifications Synthesis ◮ Parameter synthesis reduces synthesis to finding “a few” valid values for parameters ◮ We consider: ◮ System parameters: for which values is the spec. satisfied ? ◮ Specification parameters: what is the spec. actually satisfied ? In the following we focus on reachability specifications Alexandre Donzé Parameter Synthesis HSB’19 16 / 46

  28. Formal methods and parameter synthesis Verification System | = ? Specifications Synthesis ◮ Parameter synthesis reduces synthesis to finding “a few” valid values for parameters ◮ We consider: ◮ System parameters: for which values is the spec. satisfied ? ◮ Specification parameters: what is the spec. actually satisfied ? In the following we focus on reachability specifications Alexandre Donzé Parameter Synthesis HSB’19 16 / 46

  29. Parameter Synthesis 1 Parametric Systems Sensitive Systematic (aka Barbaric) Simulation Parameter Synthesis with Formal Specifications 2 Signal Temporal Logic Property parameters Model parameters Some Results and Concluding Remarks 3 Alexandre Donzé Parameter Synthesis HSB’19 17 / 46

  30. Reachability analysis and systematic simulation Reachable set Note x ( t, p ) the simulation trace obtained using p . We define Reach ( T, P ) = { x ( t, p ) such that t ≤ T, p ∈ P} Lots of very sophisticated, non-scalable techniques developed to compute it using computer geometry, numerical and symbolic analysis, formal methods, etc. Systematic simulation ◮ Estimates Reach ( T, P ) by computing bunch of trajectories from P ◮ Also known as Barbaric reachability ◮ It works by 1. Sampling the parameter set P . 2. Computing and visualizing the simulation traces. Alexandre Donzé Parameter Synthesis HSB’19 18 / 46

  31. Reachability analysis and systematic simulation Reachable set Note x ( t, p ) the simulation trace obtained using p . We define Reach ( T, P ) = { x ( t, p ) such that t ≤ T, p ∈ P} Lots of very sophisticated, non-scalable techniques developed to compute it using computer geometry, numerical and symbolic analysis, formal methods, etc. Systematic simulation ◮ Estimates Reach ( T, P ) by computing bunch of trajectories from P ◮ Also known as Barbaric reachability ◮ It works by 1. Sampling the parameter set P . 2. Computing and visualizing the simulation traces. Alexandre Donzé Parameter Synthesis HSB’19 18 / 46

  32. Reachability analysis and systematic simulation Reachable set Note x ( t, p ) the simulation trace obtained using p . We define Reach ( T, P ) = { x ( t, p ) such that t ≤ T, p ∈ P} Lots of very sophisticated, non-scalable techniques developed to compute it using computer geometry, numerical and symbolic analysis, formal methods, etc. Systematic simulation ◮ Estimates Reach ( T, P ) by computing bunch of trajectories from P ◮ Also known as Barbaric reachability ◮ It works by 1. Sampling the parameter set P . 2. Computing and visualizing the simulation traces. Alexandre Donzé Parameter Synthesis HSB’19 18 / 46

  33. Reachability analysis and systematic simulation Reachable set Note x ( t, p ) the simulation trace obtained using p . We define Reach ( T, P ) = { x ( t, p ) such that t ≤ T, p ∈ P} Lots of very sophisticated, non-scalable techniques developed to compute it using computer geometry, numerical and symbolic analysis, formal methods, etc. Systematic simulation ◮ Estimates Reach ( T, P ) by computing bunch of trajectories from P ◮ Also known as Barbaric reachability ◮ It works by 1. Sampling the parameter set P . 2. Computing and visualizing the simulation traces. Alexandre Donzé Parameter Synthesis HSB’19 18 / 46

  34. Sampling Parameter Sets In Breach, parameter sets P are defined as boxes (hyper-rectangles) A parameter set can be refined into subsets by ◮ grid refinement, usually if P is of low dimension ◮ quasi-random refinement if P is high-dimensional Additionally, the GUI allows to change parameters interactively with automatic recomputation of trajectories Alexandre Donzé Parameter Synthesis HSB’19 19 / 46

  35. Grid Refinement Alexandre Donzé Parameter Synthesis HSB’19 20 / 46

  36. Grid Refinement Alexandre Donzé Parameter Synthesis HSB’19 20 / 46

  37. Quasi-random Refinement Alexandre Donzé Parameter Synthesis HSB’19 21 / 46

  38. Quasi-random Refinement Alexandre Donzé Parameter Synthesis HSB’19 21 / 46

  39. Quasi-random Refinement Quasi-random provides better repartition than uniform-random sampling Alexandre Donzé Parameter Synthesis HSB’19 21 / 46

  40. Plotting simulation traces Alexandre Donzé Parameter Synthesis HSB’19 22 / 46

  41. Barbarians can be sensitive Sensitivity functions s ij ( t ) = ∂ x i ∂ p j ( t ) can also be computed by CVodes solver Note S ( t, p ) = ( s ij ( t )) i,j is called the sensitivity matrix. Provides for a cheap estimate of Reach ( t, P ) by the affine transform of P : 1 Reach ( t, P ) ≃ x ( t, p 0 ) + S ( t, p 0 ) · ( P − p 0 ) 1 ( Systematic Simulation Using Sensitivity Analysis Donzé, Maler, HSCC’07) Alexandre Donzé Parameter Synthesis HSB’19 23 / 46

  42. Reachability using sensitivity P Reach ( t, P ) ◮ Works well for low dimensional P ◮ Otherwise, averaging s ij ( t ) over samplings of P provides estimates of global sensitivity / robustness Alexandre Donzé Parameter Synthesis HSB’19 24 / 46

  43. Reachability using sensitivity P ◮ Works well for low dimensional P ◮ Otherwise, averaging s ij ( t ) over samplings of P provides estimates of global sensitivity / robustness Alexandre Donzé Parameter Synthesis HSB’19 24 / 46

  44. Reachability using sensitivity P ◮ Works well for low dimensional P ◮ Otherwise, averaging s ij ( t ) over samplings of P provides estimates of global sensitivity / robustness Alexandre Donzé Parameter Synthesis HSB’19 24 / 46

  45. Reachability using sensitivity P ◮ Works well for low dimensional P ◮ Otherwise, averaging s ij ( t ) over samplings of P provides estimates of global sensitivity / robustness Alexandre Donzé Parameter Synthesis HSB’19 24 / 46

  46. Reachability using sensitivity P ◮ Works well for low dimensional P ◮ Otherwise, averaging s ij ( t ) over samplings of P provides estimates of global sensitivity / robustness Alexandre Donzé Parameter Synthesis HSB’19 24 / 46

  47. Results on the acute inflammatory response model Circles lead to health, crosses to death... 0.8 0.7 0.6 0.5 ca 0.4 0.3 0.2 0.1 0 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2 p Considered parameters are the initial concentrations of pathogen and anti-inflammatory agents Alexandre Donzé Parameter Synthesis HSB’19 25 / 46

  48. Parameter Synthesis 1 Parametric Systems Sensitive Systematic (aka Barbaric) Simulation Parameter Synthesis with Formal Specifications 2 Signal Temporal Logic Property parameters Model parameters Some Results and Concluding Remarks 3 Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 26 / 46

  49. Temporal logics in a nutshell Temporal logics specify patterns that timed behaviors of systems may or may not satisfy. The most intuitive is the Linear Temporal Logic (LTL), dealing with discrete sequences of states. Based on logic operators ( ¬ , ∧ , ∨ ) and temporal operators: “next”, “always” (alw), “eventually” (ev) and “until” ( U ) Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 27 / 46

  50. Linear Temporal Logic An LTL formula ϕ is evaluated on a sequence, e.g., w = aaabbaaa . . . At each step of w , we can define a truth value of ϕ , noted χ ϕ ( w, i ) LTL atoms are symbols: a , b : i = 0 1 2 3 4 5 6 7 . . . w = a a a b b a a a . . . χ a ( w, i ) = 1 1 1 0 0 1 1 1 . . . χ b ( w, i ) = 0 0 0 1 1 0 0 0 . . . Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 28 / 46

  51. LTL, temporal operators � (“next”), alw (“globally”), ev (“eventually”) and U (“until”). They are evaluated at each step wrt the future of sequences w = a a a b b a a a . . . χ � b ( w, i ) = � b ( next ) 0 0 1 1 0 0 0 ? . . . χ alw a ( w, i ) = alw a ( always ) 0 0 0 0 0 1? 1? 1? . . . χ ev b ( w, i ) = ev b ( eventually ) 1 1 1 1 1 0? 0? 0? . . . χ a U⌊ ( w, i ) = a U ⌊ ( until ) 1 1 1 0 0 0? 0? 0? . . . Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 29 / 46

  52. LTL, temporal operators � (“next”), alw (“globally”), ev (“eventually”) and U (“until”). They are evaluated at each step wrt the future of sequences w = a a a b b a a a . . . χ � b ( w, i ) = � b ( next ) 0 0 1 1 0 0 0 ? . . . χ alw a ( w, i ) = alw a ( always ) 0 0 0 0 0 1? 1? 1? . . . χ ev b ( w, i ) = ev b ( eventually ) 1 1 1 1 1 0? 0? 0? . . . χ a U⌊ ( w, i ) = a U ⌊ ( until ) 1 1 1 0 0 0? 0? 0? . . . Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 29 / 46

  53. LTL, temporal operators � (“next”), alw (“globally”), ev (“eventually”) and U (“until”). They are evaluated at each step wrt the future of sequences w = a a a b b a a a . . . χ � b ( w, i ) = � b ( next ) 0 0 1 1 0 0 0 0? . . . χ alw a ( w, i ) = alw a ( always ) 0 0 0 0 0 1? 1? 1? . . . χ ev b ( w, i ) = ev b ( eventually ) 1 1 1 1 1 0? 0? 0? . . . χ a U⌊ ( w, i ) = a U ⌊ ( until ) 1 1 1 0 0 0? 0? 0? . . . Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 29 / 46

  54. LTL, temporal operators � (“next”), alw (“globally”), ev (“eventually”) and U (“until”). They are evaluated at each step wrt the future of sequences w = a a a b b a a a . . . χ � b ( w, i ) = � b ( next ) 0 0 1 1 0 0 0 ? . . . χ alw a ( w, i ) = alw a ( always ) 0 0 0 0 0 1? 1? 1? . . . χ ev b ( w, i ) = ev b ( eventually ) 1 1 1 1 1 0? 0? 0? . . . χ a U⌊ ( w, i ) = a U ⌊ ( until ) 1 1 1 0 0 0? 0? 0? . . . Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 29 / 46

  55. From LTL to STL Extension of LTL with real-time and real-valued constraints Ex: request-grant property LTL G( r => F g) Boolean predicates, discrete-time Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 30 / 46

  56. From LTL to STL Extension of LTL with real-time and real-valued constraints Ex: request-grant property LTL G( r => F g) Boolean predicates, discrete-time Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 30 / 46

  57. From LTL to STL Extension of LTL with real-time and real-valued constraints Ex: request-grant property LTL G( r => F g) Boolean predicates, discrete-time MTL G( r => F [0 ,. 5 s ] g ) Boolean predicates, real-time Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 30 / 46

  58. From LTL to STL Extension of LTL with real-time and real-valued constraints Ex: request-grant property LTL G( r => F g) Boolean predicates, discrete-time MTL G( r => F [0 ,. 5 s ] g ) Boolean predicates, real-time STL G( x [ t ] > 0 => F [0 ,. 5 s ] y [ t ] > 0 ) Predicates over real values , real-time Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 30 / 46

  59. STL examples Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 31 / 46

  60. STL examples The signal is never above 3.5 ϕ := alw ( x [ t ] < 3 . 5) 3.5 Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 31 / 46

  61. STL examples Between 2s and 6s the signal is between -2 and 2 ϕ := alw [2 , 6] ( | x [ t ] | < 2) 6 s 2 s 2 Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 31 / 46

  62. STL examples Always | x | > 0 . 5 ⇒ after 1 s, | x | settles under 0.5 for 1.5 s ϕ := alw ( x [ t ] > . 5 → ev [0 ,. 6] ( alw [0 , 1 . 5] x [ t ] < 0 . 5)) 0.5 0.5 0.5 ≤ 1 s 1.5 s ≤ 1 s 1.5 s ≤ 1 s 1.5 s Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 31 / 46

  63. STL Robust Semantics Given ϕ , x and t , the quantitative satisfaction function ρ is such that: ρ ϕ ( x, t ) > 0 ⇒ x, t � ϕ ρ ϕ ( x, t ) < 0 ⇒ x, t � ϕ ok ρ ϕ ( x, t ) > 0 x : [0 , T ] �→ R n STL Monitor ϕ ¬ ok Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 32 / 46

  64. Quantitative Satisfaction, Example Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 33 / 46

  65. Quantitative Satisfaction, Example Between 2s and 6s the signal is between -2.5 and 2.5 ϕ := alw [2 , 6] ( | x [ t ] | < 2 . 5) ρ = 0 . 7 Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 33 / 46

  66. Quantitative Satisfaction, Example Between 2s and 6s the signal is between -1 and -1 ϕ := alw [2 , 6] ( | x [ t ] | < 2 . 5) ρ = − 0 . 8 Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 33 / 46

  67. Quantitative Satisfaction, Example Always | x | > 0 . 5 ⇒ after 1 s, | x | settles under 0.5 for 1.5 s ϕ := alw ( x [ t ] > . 5 → ev [0 , 1 . ] ( alw [0 , 1 . 5] x [ t ] < 0 . 5)) ρ ? 0.5 0.5 0.5 ≤ 1 s 1.5 s ≤ 1 s 1.5 s ≤ 1 s 1.5 s Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 33 / 46

  68. Quantitative Satisfaction, Example Always | x | > 0 . 5 ⇒ after 1 s, | x | settles under 0.5 for 1.5 s ϕ := alw ( x [ t ] > . 5 → ev [0 , 1 . ] ( alw [0 , 1 . 5] x [ t ] < 0 . 5)) Robust satisfaction can be computed efficiently for general formulas ρ ? 0.5 0.5 0.5 ≤ 1 s 1.5 s ≤ 1 s 1.5 s ≤ 1 s 1.5 s Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 33 / 46

  69. Computing the robust satisfaction function (Donze, Ferrere, Maler, Efficient Robust Monitoring of STL Formula , CAV’13) ◮ The function ρ ϕ ( x, t ) is computed inductively on the structure of ϕ ◮ linear time complexity in size of x is preserved ◮ exponential worst case complexity in the size of ϕ ◮ Atomic transducers compute in linear time in the size of the input ◮ Key idea is to exploit efficient streaming algorithm (Lemire’s) computing the max and min over a moving window Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 34 / 46

  70. Parameter Synthesis 1 Parametric Systems Sensitive Systematic (aka Barbaric) Simulation Parameter Synthesis with Formal Specifications 2 Signal Temporal Logic Property parameters Model parameters Some Results and Concluding Remarks 3 Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 35 / 46

  71. Parametric-STL Formulas STL formula where numeric constants are left unspecified. “After 2s, the signal is never above 3” ϕ := ev [2 , ∞ ] ( x [ t ] < 3) Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 36 / 46

  72. Parametric-STL Formulas STL formula where numeric constants are left unspecified. “After 2s, the signal is never above 3” ϕ := ev [2 , ∞ ] ( x [ t ] < 3) 2 3 Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 36 / 46

  73. Parametric-STL Formulas STL formula where numeric constants are left unspecified. “After τ s, the signal is never above π ” ϕ := alw [ τ, ∞ ] ( x [ t ] < π ) τ ? π ? Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 36 / 46

  74. Parameter synthesis for PSTL ◮ In general, looking for “tight” valuations ◮ E.g., ϕ := alw � � x [ t ] > π → ev [0 ,τ 1 ] ( alw [0 ,τ 2 ] x [ t ] < π ) ◮ Valuation 1: π ← 1 . 5 , τ 1 ← 1 s , τ 2 ← 1 . 15 s ◮ Valuation 2 (tight): π ← . 5 , τ 1 ← 0 . 65 s , τ 2 ← 2 s Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 37 / 46

  75. Parameter synthesis for PSTL ◮ In general, looking for “tight” valuations ◮ E.g., ϕ := alw � � x [ t ] > π → ev [0 ,τ 1 ] ( alw [0 ,τ 2 ] x [ t ] < π ) ◮ Valuation 1: π ← 1 . 5 , τ 1 ← 1 s , τ 2 ← 1 . 15 s ◮ Valuation 2 (tight): π ← . 5 , τ 1 ← 0 . 65 s , τ 2 ← 2 s π τ 1 s τ 2 s Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 37 / 46

  76. Parameter synthesis for PSTL ◮ In general, looking for “tight” valuations ◮ E.g., ϕ := alw � � x [ t ] > π → ev [0 ,τ 1 ] ( alw [0 ,τ 2 ] x [ t ] < π ) ◮ Valuation 1: π ← 1 . 5 , τ 1 ← 1 s , τ 2 ← 1 . 15 s ◮ Valuation 2 (tight): π ← . 5 , τ 1 ← 0 . 65 s , τ 2 ← 2 s π τ 1 s τ 2 s Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 37 / 46

  77. Parameter synthesis for PSTL Challenges ◮ Multiple solutions: which one to chose ? ◮ Tightness implies to “optimize” the valuation v ( p i ) for each p i The problem can be simplified if the formula is monotonic in each p i , i.e., ◮ If the formula holds for p i , then it will hold for p ′ i > p i , or ◮ if the formula holds for p i , then it will hold for p ′ i < p i If the formula is not monotonic, parameters can be treated as a system parameters (next section). Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 38 / 46

  78. Monotonic validity domains ◮ The validity domain D of ϕ and x is the set of valuations v s.t. x | = ϕ ( v ) ◮ A tight valuation is a valuation in D close to its boundary ∂D ◮ In case of monoticity, ∂D has the structure of a Pareto front which can be estimated with generalized binary search heuristics � D ( x, ϕ ) ⊆ D ( x, ϕ ) p 1 Exact D ( x, ϕ ) p 2 Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 39 / 46

  79. Monotonic validity domains ◮ The validity domain D of ϕ and x is the set of valuations v s.t. x | = ϕ ( v ) ◮ A tight valuation is a valuation in D close to its boundary ∂D ◮ In case of monoticity, ∂D has the structure of a Pareto front which can be estimated with generalized binary search heuristics � D ( x, ϕ ) ⊆ D ( x, ϕ ) p 1 x p 2 Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 39 / 46

  80. Monotonic validity domains ◮ The validity domain D of ϕ and x is the set of valuations v s.t. x | = ϕ ( v ) ◮ A tight valuation is a valuation in D close to its boundary ∂D ◮ In case of monoticity, ∂D has the structure of a Pareto front which can be estimated with generalized binary search heuristics � D ( x, ϕ ) ⊆ D ( x, ϕ ) p 1 x p 2 Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 39 / 46

  81. Monotonic validity domains ◮ The validity domain D of ϕ and x is the set of valuations v s.t. x | = ϕ ( v ) ◮ A tight valuation is a valuation in D close to its boundary ∂D ◮ In case of monoticity, ∂D has the structure of a Pareto front which can be estimated with generalized binary search heuristics � D ( x, ϕ ) ⊆ D ( x, ϕ ) p 1 x p 2 Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 39 / 46

  82. Monotonic validity domains ◮ The validity domain D of ϕ and x is the set of valuations v s.t. x | = ϕ ( v ) ◮ A tight valuation is a valuation in D close to its boundary ∂D ◮ In case of monoticity, ∂D has the structure of a Pareto front which can be estimated with generalized binary search heuristics � D ( x, ϕ ) ⊆ D ( x, ϕ ) p 1 x p 2 Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 39 / 46

  83. Monotonic validity domains ◮ The validity domain D of ϕ and x is the set of valuations v s.t. x | = ϕ ( v ) ◮ A tight valuation is a valuation in D close to its boundary ∂D ◮ In case of monoticity, ∂D has the structure of a Pareto front which can be estimated with generalized binary search heuristics � D ( x, ϕ ) ⊆ D ( x, ϕ ) p 1 x x p 2 Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 39 / 46

  84. Monotonic validity domains ◮ The validity domain D of ϕ and x is the set of valuations v s.t. x | = ϕ ( v ) ◮ A tight valuation is a valuation in D close to its boundary ∂D ◮ In case of monoticity, ∂D has the structure of a Pareto front which can be estimated with generalized binary search heuristics � D ( x, ϕ ) ⊆ D ( x, ϕ ) p 1 x x x p 2 Alexandre Donzé Parameter Synthesis with Formal Specifications HSB’19 39 / 46

Download Presentation
Download Policy: The content available on the website is offered to you 'AS IS' for your personal information and use only. It cannot be commercialized, licensed, or distributed on other websites without prior consent from the author. To download a presentation, simply click this link. If you encounter any difficulties during the download process, it's possible that the publisher has removed the file from their server.

Recommend


More recommend