An immune network approach to learning qualitative models of biological pathways

ACKNOWLEDGMENT GMC is supported by the CRISP project (Combinatorial Responses In Stress Pathways) funded by the BBSRC (BB/F00513X/1) under the Systems Approaches to Biological Research (SABR) Initiative. WP and GMC are also supported by the partnership fund from dot.rural, RCUK Digital Economy research.Postprin

Bayesian Verification under Model Uncertainty

Machine learning enables systems to build and update domain models based on runtime observations. In this paper, we study statistical model checking and runtime verification for systems with this ability. Two challenges arise: (1) Models built from limited runtime data yield uncertainty to be dealt with. (2) There is no definition of satisfaction w.r.t. uncertain hypotheses. We propose such a definition of subjective satisfaction based on recently introduced satisfaction functions. We also propose the BV algorithm as a Bayesian solution to runtime verification of subjective satisfaction under model uncertainty. BV provides user-definable stochastic bounds for type I and II errors. We discuss empirical results from an example application to illustrate our ideas.Comment: Accepted at SEsCPS @ ICSE 201

Learning and Designing Stochastic Processes from Logical Constraints

Stochastic processes offer a flexible mathematical formalism to model and reason about systems. Most analysis tools, however, start from the premises that models are fully specified, so that any parameters controlling the system's dynamics must be known exactly. As this is seldom the case, many methods have been devised over the last decade to infer (learn) such parameters from observations of the state of the system. In this paper, we depart from this approach by assuming that our observations are {\it qualitative} properties encoded as satisfaction of linear temporal logic formulae, as opposed to quantitative observations of the state of the system. An important feature of this approach is that it unifies naturally the system identification and the system design problems, where the properties, instead of observations, represent requirements to be satisfied. We develop a principled statistical estimation procedure based on maximising the likelihood of the system's parameters, using recent ideas from statistical machine learning. We demonstrate the efficacy and broad applicability of our method on a range of simple but non-trivial examples, including rumour spreading in social networks and hybrid models of gene regulation

Data-driven and Model-based Verification: a Bayesian Identification Approach

This work develops a measurement-driven and model-based formal verification approach, applicable to systems with partly unknown dynamics. We provide a principled method, grounded on reachability analysis and on Bayesian inference, to compute the confidence that a physical system driven by external inputs and accessed under noisy measurements, verifies a temporal logic property. A case study is discussed, where we investigate the bounded- and unbounded-time safety of a partly unknown linear time invariant system