Enhanced Operational Semantics in Systems Biology

We are faced with a great challenge: the cross-fertilization between the fields of formal methods for concurrency, in the computer science domain, and systems biology in the biological realm

Is lazy abstraction a decision procedure for broadcast protocols?

Lazy abstraction builds up an abstract reachability tree by locally refining abstractions in order to eliminate spurious counterexamples in smaller and smaller subtrees. The method has proven useful to verify systems code. It is still open how good the method is as a decision procedure, i.e., whether the method terminates for already known decidable verification problems. In this paper, we answer the question positively for broadcast protocols and other infinite-state models in the class of so-called well-structured systems. This extends an existing result on systems with a finite bisimulation quotient

Tracing Ghost Cavities with Low Frequency Radio Observations

We present X-ray and multi-frequency radio observations of the central radio sources in several X-ray cavity systems. We show that targeted radio observations are key to determining if the lobes are being actively fed by the central AGN. Low frequency observations provide a unique way to study both the lifecycle of the central radio source as well as its energy input into the ICM over several outburst episodes.Comment: 6 pages, 4 figures, To appear in the Proceedings of "Heating vs. Cooling in Galaxies and Clusters of Galaxies", eds. H. Boehringer, P. Schuecker, G. W. Pratt & A. Finoguenov (ESO Astrophysics Symposia, Springer-Verlag), Garching (Germany), August 200

River Invertebrate Classification Tool

Background to research The Regulatory Agencies in the UK (the Environment Agency; Scottish Environment Protection Agency; and the Environment & Heritage Service) currently use RIVPACS III+ software to classify the ecological quality of rivers. However, because RIVPACS III+ pre-dates the WFD, there has been a requirement to ensure that the RIVPACS reference sites are fully WFD compliant, to add new biotic indices to the RIVPACS models, and to improve the robustness of the RIVPACS software to fully meet the needs of the Agencies in their delivery of WFD monitoring. These issues have been addressed in this project and have led to the development of new RIVPACS IV predictive models that will be programmed into a new River Invertebrate Classification Tool being built by SEPA. This new system will be based on a modern software programming language, be compatible with the agencies’ computer systems and include the ability to predict new biological indices, produce biological status assessments based on these new indices and be able to estimate the errors involved in using these new indices. Because access to the new system will be essential for the UK Agencies to be able to implementation the WFD, the new tool will be readily and freely available to anyone who might seek to use it. Objectives of research • The overall objective of the project was to produce a new set of RIVPACS predictive models for use within a new River Invertebrate Classification Tool that will be used to classify the ecological status of rivers for Water Framework Directive compliance monitoring • The new RIVPACS models constructed with this project required considerably enhanced functionality compared to RIVPACS III+ to properly address the monitoring requirements of the UK Agencies in their implementation of the Water Framework Directive. Key findings and recommendations This project has produced new RIVPACS IV models with considerably enhanced functionality compared to RIVPACS III+. These models incorporate: • A full revision of the taxonomic framework of RIVPACS to bring the taxonomy up-to-date and enable compatiability across the revised Miatland, Furse code and National Biodiversity Network taxon coding systems used across the UK Agencies and beyond • Predictions that fully satisfy the WFD definition of ‘reference condition’ by adjusting predictions for certain stream types and by removal of sites that were not in reference condition when sampled • Allocation of actual abundance values to family level records in the RIVPACS reference data set. Lack of actual abundance data, especially at family level, has affected all versions of RIVPACS and has constrained the types of biotic indices that RIVPACS can predict • Extension to the suite of biotic indices so that the new system can predict a wider range of reference state “expected” index values. This enables full WFD quality reporting capabilities as well as providing the system with the general functionality to predict a much wider range of indices e.g. intercalibration indices (e.g. ICMi), stress-specific indices, and ecological and functional trait indices • Extension of the uncertainty/errors module to estimate and assess uncertainty in (i) assignment to status class and (ii) comparison of samples for temporal change in quality and status. This needs to be done for a wider range of biotic indices (including those incorporating abundance data) These new RIVPACS IV models can be used by the UK Agencies across Great Britain and Northern Ireland in their WFD compliance monitoring. All of the algorithms, variables and data necessary to build these models have been provided to SEPA for programming into a new River Invertebrate Classification Tool that will be disseminated made free of charge to all interested user

Algorithms for Game Metrics

Simulation and bisimulation metrics for stochastic systems provide a quantitative generalization of the classical simulation and bisimulation relations. These metrics capture the similarity of states with respect to quantitative specifications written in the quantitative {\mu}-calculus and related probabilistic logics. We first show that the metrics provide a bound for the difference in long-run average and discounted average behavior across states, indicating that the metrics can be used both in system verification, and in performance evaluation. For turn-based games and MDPs, we provide a polynomial-time algorithm for the computation of the one-step metric distance between states. The algorithm is based on linear programming; it improves on the previous known exponential-time algorithm based on a reduction to the theory of reals. We then present PSPACE algorithms for both the decision problem and the problem of approximating the metric distance between two states, matching the best known algorithms for Markov chains. For the bisimulation kernel of the metric our algorithm works in time O(n^4) for both turn-based games and MDPs; improving the previously best known O(n^9\cdot log(n)) time algorithm for MDPs. For a concurrent game G, we show that computing the exact distance between states is at least as hard as computing the value of concurrent reachability games and the square-root-sum problem in computational geometry. We show that checking whether the metric distance is bounded by a rational r, can be done via a reduction to the theory of real closed fields, involving a formula with three quantifier alternations, yielding O(|G|^O(|G|^5)) time complexity, improving the previously known reduction, which yielded O(|G|^O(|G|^7)) time complexity. These algorithms can be iterated to approximate the metrics using binary search.Comment: 27 pages. Full version of the paper accepted at FSTTCS 200

Subsumer-First: Steering Symbolic Reachability Analysis

Abstract. Symbolic reachability analysis provides a basis for the veri-fication of software systems by offering algorithmic support for the ex-ploration of the program state space when searching for proofs or coun-terexamples. The choice of exploration strategy employed by the anal-ysis has direct impact on its success, whereas the ability to find short counterexamples quickly and—as a complementary task—to efficiently perform the exhaustive state space traversal are of utmost importance for the majority of verification efforts. Existing exploration strategies can optimize only one of these objectives which leads to a sub-optimal reach-ability analysis, e.g., breadth-first search may sacrifice the exploration ef-ficiency and chaotic iteration can miss minimal counterexamples. In this paper we present subsumer-first, a new approach for steering symbolic reachability analysis that targets both minimal counterexample discovery and efficiency of exhaustive exploration. Our approach leverages the re-sult of fixpoint checks performed during symbolic reachability analysis to bias the exploration strategy towards its objectives, and does not require any additional computation. We demonstrate how the subsumer-first ap-proach can be applied to improve efficiency of software verification tools based on predicate abstraction. Our experimental evaluation indicates the practical usefulness of the approach: we observe significant efficiency improvements (median value 40%) on difficult verification benchmarks from the transportation domain.

Climate change impacts on living marine resources in the Eastern Tropical Pacific

Postprin

Synchronous counting and computational algorithm design

Consider a complete communication network on n nodes, each of which is a state machine with s states. In synchronous 2-counting, the nodes receive a common clock pulse and they have to agree on which pulses are “odd” and which are “even”. We require that the solution is self-stabilising (reaching the correct operation from any initial state) and it tolerates f Byzantine failures (nodes that send arbitrary misinformation). Prior algorithms are expensive to implement in hardware: they require a source of random bits or a large number of states s. We use computational techniques to construct very compact deterministic algorithms for the first non-trivial case of f = 1. While no algorithm exists for n < 4, we show that as few as 3 states are sufficient for all values n ≥ 4. We prove that the problem cannot be solved with only 2 states for n = 4, but there is a 2-state solution for all values n ≥ 6.Peer reviewe

Numerical analysis of the radio-frequency single-electron transistor operation

We have analyzed numerically the response and noise-limited charge sensitivity of a radio-frequency single-electron transistor (RF-SET) in a non-superconducting state using the orthodox theory. In particular, we have studied the performance dependence on the quality factor Q of the tank circuit for Q both below and above the value corresponding to the impedance matching between the coaxial cable and SET.Comment: 14 page