48 research outputs found
Explicit Model Checking of Very Large MDP using Partitioning and Secondary Storage
The applicability of model checking is hindered by the state space explosion
problem in combination with limited amounts of main memory. To extend its
reach, the large available capacities of secondary storage such as hard disks
can be exploited. Due to the specific performance characteristics of secondary
storage technologies, specialised algorithms are required. In this paper, we
present a technique to use secondary storage for probabilistic model checking
of Markov decision processes. It combines state space exploration based on
partitioning with a block-iterative variant of value iteration over the same
partitions for the analysis of probabilistic reachability and expected-reward
properties. A sparse matrix-like representation is used to store partitions on
secondary storage in a compact format. All file accesses are sequential, and
compression can be used without affecting runtime. The technique has been
implemented within the Modest Toolset. We evaluate its performance on several
benchmark models of up to 3.5 billion states. In the analysis of time-bounded
properties on real-time models, our method neutralises the state space
explosion induced by the time bound in its entirety.Comment: The final publication is available at Springer via
http://dx.doi.org/10.1007/978-3-319-24953-7_1
PRISM-PSY:Precise GPU-Accelerated Parameter Synthesis for Stochastic Systems
In this paper we present PRISM-PSY, a novel tool that performs
precise GPU-accelerated parameter synthesis for continuous-time
Markov chains and time-bounded temporal logic specifications. We redesign,
in terms of matrix-vector operations, the recently formulated algorithms
for precise parameter synthesis in order to enable effective dataparallel
processing, which results in significant acceleration on many-core
architectures. High hardware utilisation, essential for performance and
scalability, is achieved by state space and parameter space parallelisation:
the former leverages a compact sparse-matrix representation, and the latter
is based on an iterative decomposition of the parameter space. Our
experiments on several biological and engineering case studies demonstrate
an overall speedup of up to 31-fold on a single GPU compared to
the sequential implementation
A Comparison of Time- and Reward-Bounded Probabilistic Model Checking Techniques
In the design of probabilistic timed systems, requirements concerning behaviour that occurs within a given time or energy budget are of central importance. We observe that model-checking such requirements for probabilistic timed automata can be reduced to checking reward-bounded properties on Markov decision processes. This is traditionally implemented by unfolding the model according to the bound, or by solving a sequence of linear programs. Neither scales well to large models. Using value iteration in place of linear programming achieves scalability but accumulates approximation error. In this paper, we correct the value iteration-based scheme, present two new approaches based on scheduler enumeration and state elimination, and compare the practical performance and scalability of all techniques on a number of case studies from the literature. We show that state elimination can significantly reduce runtime for large models or high bounds
The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways
<p>Abstract</p> <p>Background</p> <p>There is general agreement amongst biologists about the need for good pathway diagrams and a need to formalize the way biological pathways are depicted. However, implementing and agreeing how best to do this is currently the subject of some debate.</p> <p>Results</p> <p>The modified Edinburgh Pathway Notation (mEPN) scheme is founded on a notation system originally devised a number of years ago and through use has now been refined extensively. This process has been primarily driven by the author's attempts to produce process diagrams for a diverse range of biological pathways, particularly with respect to immune signaling in mammals. Here we provide a specification of the mEPN notation, its symbols, rules for its use and a comparison to the proposed Systems Biology Graphical Notation (SBGN) scheme.</p> <p>Conclusions</p> <p>We hope this work will contribute to the on-going community effort to develop a standard for depicting pathways and will provide a coherent guide to those planning to construct pathway diagrams of their biological systems of interest.</p
Construction of a large scale integrated map of macrophage pathogen recognition and effector systems
<p>Abstract</p> <p>Background</p> <p>In an effort to better understand the molecular networks that underpin macrophage activation we have been assembling a map of relevant pathways. Manual curation of the published literature was carried out in order to define the components of these pathways and the interactions between them. This information has been assembled into a large integrated directional network and represented graphically using the modified Edinburgh Pathway Notation (mEPN) scheme.</p> <p>Results</p> <p>The diagram includes detailed views of the toll-like receptor (TLR) pathways, other pathogen recognition systems, NF-kappa-B, apoptosis, interferon signalling, MAP-kinase cascades, MHC antigen presentation and proteasome assembly, as well as selected views of the transcriptional networks they regulate. The integrated pathway includes a total of 496 unique proteins, the complexes formed between them and the processes in which they are involved. This produces a network of 2,170 nodes connected by 2,553 edges.</p> <p>Conclusions</p> <p>The pathway diagram is a navigable visual aid for displaying a consensus view of the pathway information available for these systems. It is also a valuable resource for computational modelling and aid in the interpretation of functional genomics data. We envisage that this work will be of value to those interested in macrophage biology and also contribute to the ongoing Systems Biology community effort to develop a standard notation scheme for the graphical representation of biological pathways.</p
Safety verification for deep neural networks with provable guarantees
Computing systems are becoming ever more complex, increasingly often incorporating deep learning components. Since deep learning is unstable with respect to adversarial perturbations, there is a need for rigorous software development methodologies that encompass machine learning. This paper describes progress with developing automated verification techniques for deep neural networks to ensure safety and robustness of their decisions with respect to input perturbations. This includes novel algorithms based on feature-guided search, games, global optimisation and Bayesian methods