11,073 research outputs found
Efficient CSL Model Checking Using Stratification
For continuous-time Markov chains, the model-checking problem with respect to
continuous-time stochastic logic (CSL) has been introduced and shown to be
decidable by Aziz, Sanwal, Singhal and Brayton in 1996. Their proof can be
turned into an approximation algorithm with worse than exponential complexity.
In 2000, Baier, Haverkort, Hermanns and Katoen presented an efficient
polynomial-time approximation algorithm for the sublogic in which only binary
until is allowed. In this paper, we propose such an efficient polynomial-time
approximation algorithm for full CSL. The key to our method is the notion of
stratified CTMCs with respect to the CSL property to be checked. On a
stratified CTMC, the probability to satisfy a CSL path formula can be
approximated by a transient analysis in polynomial time (using uniformization).
We present a measure-preserving, linear-time and -space transformation of any
CTMC into an equivalent, stratified one. This makes the present work the
centerpiece of a broadly applicable full CSL model checker. Recently, the
decision algorithm by Aziz et al. was shown to work only for stratified CTMCs.
As an additional contribution, our measure-preserving transformation can be
used to ensure the decidability for general CTMCs.Comment: 18 pages, preprint for LMCS. An extended abstract appeared in ICALP
201
CSL model checking of Deterministic and Stochastic Petri Nets
Deterministic and Stochastic Petri Nets (DSPNs) are a widely used high-level formalism for modeling discrete-event systems where events may occur either without consuming time, after a deterministic time, or after an exponentially distributed time. The underlying process dened by DSPNs, under certain restrictions, corresponds to a class of Markov Regenerative Stochastic Processes (MRGP). In this paper, we investigate the use of CSL (Continuous Stochastic Logic) to express probabilistic properties, such a time-bounded until and time-bounded next, at the DSPN level. The verication of such properties requires the solution of the steady-state and transient probabilities of the underlying MRGP. We also address a number of semantic issues regarding the application of CSL on MRGP and provide numerical model checking algorithms for this logic. A prototype model checker, based on SPNica, is also described
A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data
Background: A better understanding of the mechanisms involved in gas-phase fragmentation of peptides is essential for the development of more reliable algorithms for high-throughput protein identification using mass spectrometry (MS). Current methodologies depend predominantly on the use of derived m/z values of fragment ions, and, the knowledge provided by the intensity
information present in MS/MS spectra has not been fully exploited. Indeed spectrum intensity information is very rarely utilized in the algorithms currently in use for high-throughput protein identification.
Results: In this work, a Bayesian neural network approach is employed to analyze ion intensity information present in 13878 different MS/MS spectra. The influence of a library of 35 features on peptide fragmentation is examined under different proton mobility conditions. Useful rules
involved in peptide fragmentation are found and subsets of features which have significant influence on fragmentation pathway of peptides are characterised. An intensity model is built based on the selected features and the model can make an accurate prediction of the intensity patterns for given MS/MS spectra. The predictions include not only the mean values of spectra intensity but also the
variances that can be used to tolerate noises and system biases within experimental MS/MS spectra.
Conclusion: The intensity patterns of fragmentation spectra are informative and can be used to analyze the influence of various characteristics of fragmented peptides on their fragmentation pathway. The features with significant influence can be used in turn to predict spectra intensities. Such information can help develop more reliable algorithms for peptide and protein identification
A Declarative Framework for Specifying and Enforcing Purpose-aware Policies
Purpose is crucial for privacy protection as it makes users confident that
their personal data are processed as intended. Available proposals for the
specification and enforcement of purpose-aware policies are unsatisfactory for
their ambiguous semantics of purposes and/or lack of support to the run-time
enforcement of policies.
In this paper, we propose a declarative framework based on a first-order
temporal logic that allows us to give a precise semantics to purpose-aware
policies and to reuse algorithms for the design of a run-time monitor enforcing
purpose-aware policies. We also show the complexity of the generation and use
of the monitor which, to the best of our knowledge, is the first such a result
in literature on purpose-aware policies.Comment: Extended version of the paper accepted at the 11th International
Workshop on Security and Trust Management (STM 2015
DISTANCE: a framework for software measure construction.
In this paper we present a framework for software measurement that is specifically suited to satisfy the measurement needs of empirical software engineering research. The framework offers an approach to measurement that builds upon the easily imagined, detected and visualised concepts of similarity and dissimilarity between software entities. These concepts are used both to model the software attributes of interest and to define the corresponding software measures. Central to the framework is a process model that embeds constructive procedures for attribute modelling and measure construction into a goal-oriented approach to empirical software engineering studies. The underlying measurement theoretic principles of our approach ensure the construct validity of the resulting measures. The approach was tested on a popular suite of object-oriented design measures. We further show that our measure construction method compares favourably to related work.Software;
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Augmenting the Calvin-Benson-Bassham cycle by a synthetic malyl-CoA-glycerate carbon fixation pathway.
The Calvin-Benson-Bassham (CBB) cycle is presumably evolved for optimal synthesis of C3 sugars, but not for the production of C2 metabolite acetyl-CoA. The carbon loss in producing acetyl-CoA from decarboxylation of C3 sugar limits the maximum carbon yield of photosynthesis. Here we design a synthetic malyl-CoA-glycerate (MCG) pathway to augment the CBB cycle for efficient acetyl-CoA synthesis. This pathway converts a C3 metabolite to two acetyl-CoA by fixation of one additional CO2 equivalent, or assimilates glyoxylate, a photorespiration intermediate, to produce acetyl-CoA without net carbon loss. We first functionally demonstrate the design of the MCG pathway in vitro and in Escherichia coli. We then implement the pathway in a photosynthetic organism Synechococcus elongates PCC7942, and show that it increases the intracellular acetyl-CoA pool and enhances bicarbonate assimilation by roughly 2-fold. This work provides a strategy to improve carbon fixation efficiency in photosynthetic organisms
Automated Certification of Authorisation Policy Resistance
Attribute-based Access Control (ABAC) extends traditional Access Control by
considering an access request as a set of pairs attribute name-value, making it
particularly useful in the context of open and distributed systems, where
security relevant information can be collected from different sources. However,
ABAC enables attribute hiding attacks, allowing an attacker to gain some access
by withholding information. In this paper, we first introduce the notion of
policy resistance to attribute hiding attacks. We then propose the tool ATRAP
(Automatic Term Rewriting for Authorisation Policies), based on the recent
formal ABAC language PTaCL, which first automatically searches for resistance
counter-examples using Maude, and then automatically searches for an Isabelle
proof of resistance. We illustrate our approach with two simple examples of
policies and propose an evaluation of ATRAP performances.Comment: 20 pages, 4 figures, version including proofs of the paper that will
be presented at ESORICS 201
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