Parallel parameter synthesis from hybrid logic HUCTL formulas

Student: Samuel Pastva

Supervisor: Luboš Brim

Big Picture: Systems Biology

Discrete Bifurcation Analysis using Behaviour Patterns

Custom hybrid temporal logic HUCTL

Parameter Synthesis Problem

How parameters effect the presence of patterns? 

Given a HUCTL pattern P (specification) and a parametrised model M, find parameter values for which P is present in M (M satisfies P)

• Semi-symbolic approach: State space is explicit, but parameter space is symbolic.
• State space is distributed into a set of fragments connected using border states.
• Appropriate solver is used to compare and minimise parameter constraints during computation.

Algorithm

Architecture

Implementation

Pithya: Parameter Investigation Tool

Kotlin on JVM, R Shiny server, Gradle, ANTLR, Z3, Reactive Streams on backend and frontend, Test coverage 80%+

Case study

Model: Two dimensional repressilator (discretization of an ODE model)

Behaviour: One vs. Two terminal strongly connected components

Conclusions

• Studying real world systems requires advanced algorithmic techniques.
• HUCTL can be used to describe general patterns of model behaviour.
• Patterns change with respect to parameters => Bifurcation.
• Parameter synthesis computes pattern validity regions.
• Semi-symbolic paralel algorithm for parameter synthesis.
• Implemented in tool PITHYA design for analysis of biological ODE models.