252 research outputs found
A mass action model of a fibroblast growth factor signaling pathway and its simplification
We consider a kinetic law of mass action model for Fibroblast Growth Factor (FGF) signaling, focusing on the induction of the RAS-MAP kinase pathway via GRB2 binding. Our biologically simple model suffers a combinatorial explosion in the number of differential equations required to simulate the system. In addition to numerically solving the full model, we show that it can be accurately simplified. This requires combining matched asymptotics, the quasi-steady state hypothesis, and the fact subsets of the equations decouple asymptotically. Both the full and simplified models reproduce the qualitative dynamics observed experimentally and in previous stochastic models. The simplified model also elucidates both the qualitative features of GRB2 binding and the complex relationship between SHP2 levels, the rate SHP2 induces dephosphorylation and levels of bound GRB2. In addition to providing insight into the important and redundant features of FGF signaling, such work further highlights the usefulness of numerous simplification techniques in the study of mass action models of signal transduction, as also illustrated recently by Borisov and co-workers (Borisov et al. in Biophys. J. 89, 951–66, 2005, Biosystems 83, 152–66, 2006; Kiyatkin et al. in J. Biol. Chem. 281, 19925–9938, 2006). These developments will facilitate the construction of tractable models of FGF signaling, incorporating further biological realism, such as spatial effects or realistic binding stoichiometries, despite a more severe combinatorial explosion associated with the latter
A Study of the PDGF Signaling Pathway with PRISM
In this paper, we apply the probabilistic model checker PRISM to the analysis
of a biological system -- the Platelet-Derived Growth Factor (PDGF) signaling
pathway, demonstrating in detail how this pathway can be analyzed in PRISM. We
show that quantitative verification can yield a better understanding of the
PDGF signaling pathway.Comment: In Proceedings CompMod 2011, arXiv:1109.104
Towards the Automated Verification of Weibull Distributions for System Failure Rates
Weibull distributions can be used to accurately model failure
behaviours of a wide range of critical systems such as on-orbit satellite
subsystems. Markov chains have been used extensively to model reliability
and performance of engineering systems or applications. However,
the exponentially distributed sojourn time of Continuous-Time Markov
Chains (CTMCs) can sometimes be unrealistic for satellite systems that
exhibit Weibull failures. In this paper, we develop novel semi-Markov
models that characterise failure behaviours, based on Weibull failure
modes inferred from realistic data sources. We approximate and encode
these new models with CTMCs and use the PRISM probabilistic model
checker. The key bene t of this integration is that CTMC-based model
checking tools allow us to automatically and e ciently verify reliability
properties relevant to industrial critical systems
Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs
In this paper, we consider termination of probabilistic programs with
real-valued variables. The questions concerned are:
1. qualitative ones that ask (i) whether the program terminates with
probability 1 (almost-sure termination) and (ii) whether the expected
termination time is finite (finite termination); 2. quantitative ones that ask
(i) to approximate the expected termination time (expectation problem) and (ii)
to compute a bound B such that the probability to terminate after B steps
decreases exponentially (concentration problem).
To solve these questions, we utilize the notion of ranking supermartingales
which is a powerful approach for proving termination of probabilistic programs.
In detail, we focus on algorithmic synthesis of linear ranking-supermartingales
over affine probabilistic programs (APP's) with both angelic and demonic
non-determinism. An important subclass of APP's is LRAPP which is defined as
the class of all APP's over which a linear ranking-supermartingale exists.
Our main contributions are as follows. Firstly, we show that the membership
problem of LRAPP (i) can be decided in polynomial time for APP's with at most
demonic non-determinism, and (ii) is NP-hard and in PSPACE for APP's with
angelic non-determinism; moreover, the NP-hardness result holds already for
APP's without probability and demonic non-determinism. Secondly, we show that
the concentration problem over LRAPP can be solved in the same complexity as
for the membership problem of LRAPP. Finally, we show that the expectation
problem over LRAPP can be solved in 2EXPTIME and is PSPACE-hard even for APP's
without probability and non-determinism (i.e., deterministic programs). Our
experimental results demonstrate the effectiveness of our approach to answer
the qualitative and quantitative questions over APP's with at most demonic
non-determinism.Comment: 24 pages, full version to the conference paper on POPL 201
Stochastic Invariants for Probabilistic Termination
Termination is one of the basic liveness properties, and we study the
termination problem for probabilistic programs with real-valued variables.
Previous works focused on the qualitative problem that asks whether an input
program terminates with probability~1 (almost-sure termination). A powerful
approach for this qualitative problem is the notion of ranking supermartingales
with respect to a given set of invariants. The quantitative problem
(probabilistic termination) asks for bounds on the termination probability. A
fundamental and conceptual drawback of the existing approaches to address
probabilistic termination is that even though the supermartingales consider the
probabilistic behavior of the programs, the invariants are obtained completely
ignoring the probabilistic aspect.
In this work we address the probabilistic termination problem for
linear-arithmetic probabilistic programs with nondeterminism. We define the
notion of {\em stochastic invariants}, which are constraints along with a
probability bound that the constraints hold. We introduce a concept of {\em
repulsing supermartingales}. First, we show that repulsing supermartingales can
be used to obtain bounds on the probability of the stochastic invariants.
Second, we show the effectiveness of repulsing supermartingales in the
following three ways: (1)~With a combination of ranking and repulsing
supermartingales we can compute lower bounds on the probability of termination;
(2)~repulsing supermartingales provide witnesses for refutation of almost-sure
termination; and (3)~with a combination of ranking and repulsing
supermartingales we can establish persistence properties of probabilistic
programs.
We also present results on related computational problems and an experimental
evaluation of our approach on academic examples.Comment: Full version of a paper published at POPL 2017. 20 page
Automated Security Analysis of IoT Software Updates
IoT devices often operate unsupervised in ever-changing environments for several years. Therefore, they need to be updated on a regular basis. Current approaches for software updates on IoT, like the recent SUIT proposal, focus on granting integrity and confidentiality but do not analyze the content of the software update, especially the IoT application which is deployed to IoT devices. To this aim, in this paper, we present IoTAV, an automated software analysis framework for systematically verifying the security of the applications contained in software updates w.r.t. a given security policy. Our proposal can be adopted transparently by current IoT software updates workflows. We prove the viability of IoTAV by testing our methodology on a set of actual RIOT OS applications. Experimental results indicate that the approach is viable in terms of both reliability and performance, leading to the identification of 26 security policy violations in 31 real-world RIOT applications
More Scalable LTL Model Checking via Discovering Design-Space Dependencies (D3)
Modern system design often requires comparing several models over a large design space. Different models arise out of a need to weigh different design choices, to check core capabilities of versions with varying features, or to analyze a future version against previous ones. Model checking can compare different models; however, applying model checking off-the-shelf may not scale due to the large size of the design space for today’s complex systems. We exploit relationships between different models of the same (or related) systems to optimize the model-checking search. Our algorithm, D3 , preprocesses the design space and checks fewer model-checking instances, e.g., using nuXmv. It automatically prunes the search space by reducing both the number of models to check, and the number of LTL properties that need to be checked for each model in order to provide the complete model-checking verdict for every individual model-property pair. We formalize heuristics that improve the performance of D3 . We demonstrate the scalability of D3 by extensive experimental evaluation, e.g., by checking 1,620 real-life models for NASA’s NextGen air traffic control system. Compared to checking each model-property pair individually, D3 is up to 9.4 × faster
Syntactic Markovian Bisimulation for Chemical Reaction Networks
In chemical reaction networks (CRNs) with stochastic semantics based on
continuous-time Markov chains (CTMCs), the typically large populations of
species cause combinatorially large state spaces. This makes the analysis very
difficult in practice and represents the major bottleneck for the applicability
of minimization techniques based, for instance, on lumpability. In this paper
we present syntactic Markovian bisimulation (SMB), a notion of bisimulation
developed in the Larsen-Skou style of probabilistic bisimulation, defined over
the structure of a CRN rather than over its underlying CTMC. SMB identifies a
lumpable partition of the CTMC state space a priori, in the sense that it is an
equivalence relation over species implying that two CTMC states are lumpable
when they are invariant with respect to the total population of species within
the same equivalence class. We develop an efficient partition-refinement
algorithm which computes the largest SMB of a CRN in polynomial time in the
number of species and reactions. We also provide an algorithm for obtaining a
quotient network from an SMB that induces the lumped CTMC directly, thus
avoiding the generation of the state space of the original CRN altogether. In
practice, we show that SMB allows significant reductions in a number of models
from the literature. Finally, we study SMB with respect to the deterministic
semantics of CRNs based on ordinary differential equations (ODEs), where each
equation gives the time-course evolution of the concentration of a species. SMB
implies forward CRN bisimulation, a recently developed behavioral notion of
equivalence for the ODE semantics, in an analogous sense: it yields a smaller
ODE system that keeps track of the sums of the solutions for equivalent
species.Comment: Extended version (with proofs), of the corresponding paper published
at KimFest 2017 (http://kimfest.cs.aau.dk/
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