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ECML-PKDD2012 Workshop on Learning and Discovery in Symbolic Systems Biology Abducing Biological Regulatory Networks from Process Hitting models Maxime FOLSCHETTE 1 , 2 maxime.folschette@irccyn.ec-nantes.fr

  1. — ECML-PKDD’2012 — Workshop on Learning and Discovery in Symbolic Systems Biology Abducing Biological Regulatory Networks from Process Hitting models Maxime FOLSCHETTE 1 , 2 maxime.folschette@irccyn.ec-nantes.fr http://www.irccyn.ec-nantes.fr/~folschet/ Joint work with: Loïc PAULEVÉ 3 , Katsumi INOUE 2 , Morgan MAGNIN 1 , Olivier ROUX 1 1 MeForBio / IRCCyN / École Centrale de Nantes (Nantes, France) morgan.magnin@irccyn.ec-nantes.fr olivier.roux@irccyn.ec-nantes.fr 2 Inoue Laboratory / NII / Sokendai University (Tokyo, Japan) ki@nii.ac.jp 3 AMIB / LIX / École Polytechnique (Palaiseau, France) pauleve@lix.polytechnique.fr AtlanSTIC sojourn financed by NII & Centrale Initiatives

  2. Abducing BRNs from PH models ◦ Introduction Context and Aims Algebraic modeling to study complex dynamical biological systems: Maxime FOLSCHETTE 2/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  3. Abducing BRNs from PH models ◦ Introduction Context and Aims Algebraic modeling to study complex dynamical biological systems: • Historical model: Biological Regulatory Network (René Thomas) • New developed model: Process Hitting ⇒ Allow efficient translation from Process Hitting to BRN ⇐ Maxime FOLSCHETTE 2/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  4. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 Sorts : components a , b , z Maxime FOLSCHETTE 3/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  5. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 Sorts : components a , b , z Processes : local states / levels of expression z 0 , z 1 , z 2 Maxime FOLSCHETTE 3/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  6. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 Sorts : components a , b , z Processes : local states / levels of expression z 0 , z 1 , z 2 States : sets of active processes � a 0 , b 1 , z 0 � Maxime FOLSCHETTE 3/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  7. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 Sorts : components a , b , z Processes : local states / levels of expression z 0 , z 1 , z 2 States : sets of active processes � a 0 , b 1 , z 0 � Actions : dynamics b 1 → z 0 � z 1 , a 0 → a 0 � a 1 , a 1 → z 1 � z 2 Maxime FOLSCHETTE 3/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  8. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 Sorts : components a , b , z Processes : local states / levels of expression z 0 , z 1 , z 2 States : sets of active processes � a 0 , b 1 , z 1 � Actions : dynamics b 1 → z 0 � z 1 , a 0 → a 0 � a 1 , a 1 → z 1 � z 2 Maxime FOLSCHETTE 3/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  9. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 Sorts : components a , b , z Processes : local states / levels of expression z 0 , z 1 , z 2 States : sets of active processes � a 1 , b 1 , z 1 � Actions : dynamics b 1 → z 0 � z 1 , a 0 → a 0 � a 1 , a 1 → z 1 � z 2 Maxime FOLSCHETTE 3/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  10. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 Sorts : components a , b , z Processes : local states / levels of expression z 0 , z 1 , z 2 States : sets of active processes � a 1 , b 1 , z 2 � Actions : dynamics b 1 → z 0 � z 1 , a 0 → a 0 � a 1 , a 1 → z 1 � z 2 Maxime FOLSCHETTE 3/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  11. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Maxime FOLSCHETTE 4/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  12. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Maxime FOLSCHETTE 4/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  13. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a 1 z 0 2 1 b 1 0 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Maxime FOLSCHETTE 4/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  14. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort ab Maxime FOLSCHETTE 4/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  15. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort ab Maxime FOLSCHETTE 4/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  16. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort ab Maxime FOLSCHETTE 4/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  17. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort ab Maxime FOLSCHETTE 4/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  18. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort ab Constraint: each configuration is represented by one process � a 1 , b 0 � Maxime FOLSCHETTE 4/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  19. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort ab Constraint: each configuration is represented by one process � a 1 , b 0 � Maxime FOLSCHETTE 4/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  20. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort ab Constraint: each configuration is represented by one process � a 1 , b 0 � Maxime FOLSCHETTE 4/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  21. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort ab Constraint: each configuration is represented by one process � a 1 , b 0 � ⇒ ab 10 Maxime FOLSCHETTE 4/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  22. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort to express a 1 ∧ b 0 ab Constraint: each configuration is represented by one process � a 1 , b 0 � ⇒ ab 10 Maxime FOLSCHETTE 4/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  23. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort to express a 1 ∧ b 0 ab Constraint: each configuration is represented by one process � a 1 , b 0 � ⇒ ab 10 Maxime FOLSCHETTE 4/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

  24. Abducing BRNs from PH models ◦ Frameworks Definitions ◦ The Process Hitting The Process Hitting modeling [PMR12-MSCS] a ab 1 z 11 0 2 10 1 b 01 1 0 00 0 How to introduce some cooperation between sorts? a 1 ∧ b 0 → z 1 � z 2 Solution: a cooperative sort to express a 1 ∧ b 0 ab Constraint: each configuration is represented by one process � a 1 , b 0 � ⇒ ab 10 Advantage: regular sort; drawbacks: complexity, temporal shift Maxime FOLSCHETTE 4/19 ECML-PKDD’2012 / LDSSB — 24/09/2012

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