Parallel Composition Research Articles

Stubborn Sets, Frozen Actions, and Fair Testing

Many partial order methods use some special condition for ensuring that the analysis is not terminated prematurely. In the case of stubborn set methods for safety properties, implementation of the condition is usually based on recognizing the terminal strong components of the reduced state space and, if necessary, expanding the stubborn sets used in their roots. In an earlier study it was pointed out that if the system may execute a cycle consisting of only invisible actions and that cycle is concurrent with the rest of the system in a non-obvious way, then the method may be fooled to construct all states of the full parallel composition. This problem is solved in this study by a method that “freezes” the actions in the cycle. The new method also preserves fair testing equivalence, making it usable for the verification of many progress properties.

Automatic QoS-aware web services composition based on set-cover problem

By definition, web-services composition works on developing merely optimum coordination among a number of available web-services to provide a new composed web-service intended to satisfy some users requirements for which a single web service is not (good) enough. In this article, the formulation of the automatic web-services composition is proposed as several set-cover problems and an approximation algorithm has been exploited to solve them. In proposed method, the web-service composition has been carried out within two main phases, the top-down expansion of the composition tree, and the production of composed service by bottom-up traversal of composition tree. In the first phase, the production of a composition tree (similar to the production of tree in problemsolving by searching) is proposed by starting from the output or post-conditions of the requested service towards its input or pre-conditions. Each node or state of the tree is a set of inputs and/or outputs or conditions, and services as tree edges illustrate the transition from one node to another. In the second phase, finding the path from the leaves of the produced composition tree to the root is considered equal to reaching the output of requested service, and this path specifies the involved services and the composition plan. The requested service input set determines the available leaves of the composition tree. To achieve each non-leaf node of the tree, a set-cover problem is produced and solved using a greedy approximation algorithm. If the production and solving of the set-cover problems continues hierarchically until it reaches the root node, the composition plan and cost of the required composition service will be specified. The main focus of this research is the joint sequential and parallel composition with the aim of producing near-optimal and QoS-aware composed services.

On algebraic abstractions for concurrent separation logics

Concurrent separation logic is distinguished by transfer of state ownership upon parallel composition and framing. The algebraic structure that underpins ownership transfer is that of partial commutative monoids (PCMs). Extant research considers ownership transfer primarily from the logical perspective while comparatively less attention is drawn to the algebraic considerations. This paper provides an algebraic formalization of ownership transfer in concurrent separation logic by means of structure-preserving partial functions (i.e., morphisms) between PCMs, and an associated notion of separating relations. Morphisms of structures are a standard concept in algebra and category theory, but haven't seen ubiquitous use in separation logic before. Separating relations. are binary relations that generalize disjointness and characterize the inputs on which morphisms preserve structure. The two abstractions facilitate verification by enabling concise ways of writing specs, by providing abstract views of threads' states that are preserved under ownership transfer, and by enabling user-level construction of new PCMs out of existing ones.

Probabilistic Process Algebra and Strategic Interleaving

We first present a probabilistic version of ACP that rests on the principle that probabilistic choices are always resolved before choices involved in alternative composition and parallel composition are resolved and then extend this probabilistic version of ACP with a form of interleaving in which parallel processes are interleaved according to what is known as a process-scheduling policy in the field of operating systems. We use the term strategic interleaving for this more constrained form of interleaving. The extension covers probabilistic process-scheduling policies.

Classicality without local discriminability: Decoupling entanglement and complementarity

An operational probabilistic theory where all systems are classical, and all pure states of composite systems are entangled, is constructed. The theory is endowed with a rule for composing an arbitrary number of systems, and with a nontrivial set of transformations. Hence, we demonstrate that the presence of entanglement is independent of the existence of incompatible measurements. We then study a variety of phenomena occurring in the theory -- some of them contradicting both Classical and Quantum Theories -- including: cloning, entanglement swapping, dense coding, additivity of classical capacities, non-monogamous entanglement, hypersignaling. We also prove the existence, in the theory, of a universal processor. The theory is causal and satisfies the no-restriction hypothesis. At the same time, it violates a number of information-theoretic principles enjoyed by Quantum Theory, most notably: local discriminability, purity of parallel composition of states, and purification. Moreover, we introduce an exhaustive procedure to construct generic operational probabilistic theories, and a sufficient set of conditions to verify their consistency. In addition, we prove a characterisation theorem for the parallel composition rules of arbitrary theories, and specialise it to the case of bilocal-tomographic theories. We conclude pointing out some open problems. In particular, on the basis of the fact that every separable state of the theory is a statistical mixture of entangled states, we formulate a no-go conjecture for the existence of a local-realistic ontological model.

Regularity of the vanishing ideal over a parallel composition of paths

Let G be a graph obtained by taking r≥2 paths and identifying all first vertices and identifying all last vertices. We compute the Castelnuovo–Mumford regularity of the quotient S∕I(X), where S is the polynomial ring on the edges of G and I(X) is the vanishing ideal of the projective toric subset parameterized by G. This invariant is known for several special families of graphs such as trees, cycles, complete graphs and complete bipartite graphs. For bipartite graphs, it is also known that the computation of the regularity can be reduced to the 2-connected case. Thus, we focused on the first case of a bipartite graph where the regularity was unknown. We also prove new inequalities relating the Castelnuovo–Mumford regularity of S∕I(X) with the combinatorial structure of G, for a general graph.

The convolution product is for exponential kernels transforms. Composition is suggested for other transforms

The convolution product is associated with exponential kernel transforms such as the Fourier and Laplace transforms. It's feasibility is due the important property of the simple addition operation for the arguments of the exponential kernels product. This is behind the simple form of the convolution product. No procedure that is remotely close to this exists for the transforms with non-exponential kernels such as that of the Bessel (Hankel) transform. In 1972, we used ‘generalized convolution’. Now, we suggest using a ‘Convolution Parallel (CP) Composition’ instead. This is supported through examples with a variety of integral transforms as well as testimonials from experts in the field including Ruell Churchill and Ian Sneddon. Computations with the CP - Composition are analytically complicated. Thus, there is a need for returning to the numerical integration according to the definition of the Inverse Transform of Two Transforms Product (ITTTP). In 1964, D. Haimo citing Hirschman used a different symbol, associated with the Hankel transform, than the minus sign of the convolution, without giving it a new name. Recently, other authors used the author's original ‘generalized translation and convolution.’

Penerapan Semitic Rhetorical Analysis (SRA) Pada Surah Al-Qiyamah

Nicolai Sinai has criticized the method of Qur’anic structural analysis offered by Michel Cuypers due to his arbitrary mode of cutting verses and neglecting rhyme of the Qur’an. This paper, then, attempts to apply the method, which is called as Semitic Rhetorical Analysis (SRA), into surah al-Qiyamah by concerning the waqf of the verses. The purpose of this study is to determine whether the structure of surah al-Qiyamah is coherent and consistent to the pattern of text composition in Semitic Rhetoric analysis. This paper argues that there are parallel, concentric, or mirror symmetrical composition patterns at various levels of text based on Semitic Rhetoric principles. The structure of the surah, then, shows its coherence and thus, opposes to the notion of the existing of some irrelevant verses in this surah.

On the sandpile group of Eulerian series-parallel graphs

A sandpile configuration is a representation of the current layout of theoretical sand on a graph in which every vertex is assigned a nonnegative integer value. The Abelian sandpile group is a finite group composed of the recurrent sandpile configurations of a graph. We investigate the sandpile group of graphs constructed using the composition rules of series-parallel graphs, and determine the sandpile groups of parallel compositions of path-graphs.

Prediction of m5C Modifications in RNA Sequences by Combining Multiple Sequence Features

5-Methylcytosine (m5C) is a well-known post-transcriptional modification that plays significant roles in biological processes, such as RNA metabolism, tRNA recognition, and stress responses. Traditional high-throughput techniques on identification of m5C sites are usually time consuming and expensive. In addition, the number of RNA sequences shows explosive growth in the post-genomic era. Thus, machine-learning-based methods are urgently requested to quickly predict RNA m5C modifications with high accuracy. Here, we propose a noval support-vector-machine (SVM)-based tool, called iRNA-m5C_SVM, by combining multiple sequence features to identify m5C sites in Arabidopsis thaliana. Eight kinds of popular feature-extraction methods were first investigated systematically. Then, four well-performing features were incorporated to construct a comprehensive model, including position-specific propensity (PSP) (PSNP, PSDP, and PSTP, associated with frequencies of nucleotides, dinucleotides, and trinucleotides, respectively), nucleotide composition (nucleic acid, di-nucleotide, and tri-nucleotide compositions; NAC, DNC, and TNC, respectively), electron-ion interaction pseudopotentials of trinucleotide (PseEIIPs), and general parallel correlation pseudo-dinucleotide composition (PC-PseDNC-general). Evaluated accuracies over 10-fold cross-validation and independent tests achieved 73.06% and 80.15%, respectively, which showed the best predictive performances in A. thaliana among existing models. It is believed that the proposed model in this work can be a promising alternative for further research on m5C modification sites in plant.

Compositional model checking with divergence preserving branching bisimilarity is lively

• Divergence-preserving branching Bisim, is a congruence for LTS network composition. • We present a method to safely decompose an LTS network in components. • We discuss parallel composition with alphabet synchronisation. • We prove that alphabet synchronisation is not required for DPBB to be a congruence. • We demonstrate the effectiveness of compositionally constructing state spaces. Compositional model checking approaches attempt to limit state space explosion by iteratively combining the behaviour of the components in a concurrent system and reducing the result modulo an appropriate equivalence relation. In this article, we consider Labelled Transition Systems (LTSs), in which transitions are labelled by actions, to describe component behaviour, and LTS networks to combine the behaviour of all components in a system. For an equivalence relation to be useful for the compositional model checking of LTS networks, it should be a congruence for the parallel composition operator that is used to combine component behaviour. Such an operator may define synchronisations between the actions of component transitions. An equivalence relation preserving both safety and liveness properties is divergence-preserving branching bisimilarity (DPBB). It has long been generally assumed that DPBB is a congruence for parallel composition. Fokkink, Van Glabbeek and Luttik recently proposed a congruence format that implies that this is the case. In parallel, we were the first to prove, by means of the Coq proof assistant, that DPBB is a congruence for the parallel composition of two LTS networks with synchronisation on transition labels. In the current article, we also consider an instance of our parallel composition operator that is both associative and commutative, which are two essential properties for the compositional construction of state spaces. Furthermore, we show that DPBB is a congruence for LTS networks in which many LTSs are composed in parallel at once with support for multi-party synchronisation. Additionally, we discuss how to safely decompose an existing LTS network into components such that their recomposition is equivalent to the original LTS network. Finally, to demonstrate the effectiveness of compositional model checking with intermediate DPBB reductions, we discuss the results we obtained after having conducted a number of experiments.

A linear-time branching-time perspective on interface automata

Over the past two decades, de Alfaro and Henzinger’s interface automata (IA) have become a popular formal framework for the component-based specification of concurrent systems. IA’s parallel composition assumes that a component may wait on inputs but never on outputs, implying that an output must be consumed immediately or a communication error occurs. By now, the literature contains a number of semantics for IA: linear-time semantics based on traces observing communication errors, quiescence and/or divergence, as well as branching-time semantics based on alternating simulation. This article surveys these semantics from Rob van Glabbeek’s linear-time branching-time perspective, which does not consider settings with communication errors. We shed light onto the subtleties implied by IA’s pruning of all behaviour that might lead a component to autonomously enter an error state, and investigate when exactly de Alfaro and Henzinger’s restriction of input-determinism is needed. In addition, we introduce several new semantics for IA, in particular the linear-time ready semantics and the branching-time ready simulation.

Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework.

Promoters are short consensus sequences of DNA, which are responsible for transcription activation or the repression of all genes. There are many types of promoters in bacteria with important roles in initiating gene transcription. Therefore, solving promoter-identification problems has important implications for improving the understanding of their functions. To this end, computational methods targeting promoter classification have been established; however, their performance remains unsatisfactory. In this study, we present a novel stacked-ensemble approach (termed SELECTOR) for identifying both promoters and their respective classification. SELECTOR combined the composition of k-spaced nucleic acid pairs, parallel correlation pseudo-dinucleotide composition, position-specific trinucleotide propensity based on single-strand, and DNA strand features and using five popular tree-based ensemble learning algorithms to build a stacked model. Both 5-fold cross-validation tests using benchmark datasets and independent tests using the newly collected independent test dataset showed that SELECTOR outperformed state-of-the-art methods in both general and specific types of promoter prediction in Escherichia coli. Furthermore, this novel framework provides essential interpretations that aid understanding of model success by leveraging the powerful Shapley Additive exPlanation algorithm, thereby highlighting the most important features relevant for predicting both general and specific types of promoters and overcoming the limitations of existing 'Black-box' approaches that are unable to reveal causal relationships from large amounts of initially encoded features.

2lpiRNApred: a two-layered integrated algorithm for identifying piRNAs and their functions based on LFE-GM feature selection

ABSTRACT Piwi–interacting RNAs (piRNAs) are indispensable in the transposon silencing, including in germ cell formation, germline stem cell maintenance, spermatogenesis, and oogenesis. piRNA pathways are amongst the major genome defence mechanisms, which maintain genome integrity. They also have important functions in tumorigenesis, as indicated by aberrantly expressed piRNAs being recently shown to play roles in the process of cancer development. A number of computational methods for this have recently been proposed, but they still have not yielded satisfactory predictive performance. Moreover, only one computational method that identifies whether piRNAs function in inducting target mRNA deadenylation been reported in the literature. In this study, we developed a two-layered integrated classifier algorithm, 2lpiRNApred. It identifies piRNAs in the first layer and determines whether they function in inducting target mRNA deadenylation in the second layer. A new feature selection algorithm, which was based on Luca fuzzy entropy and Gaussian membership function (LFE-GM), was proposed to reduce the dimensionality of the features. Five feature extraction strategies, namely, Kmer, General parallel correlation pseudo-dinucleotide composition, General series correlation pseudo-dinucleotide composition, Normalized Moreau–Broto autocorrelation, and Geary autocorrelation, and two types of classifier, Sparse Representation Classifier (SRC) and support vector machine with Mahalanobis distance-based radial basis function (SVMMDRBF), were used to construct a two-layered integrated classifier algorithm, 2lpiRNApred. The results indicate that 2lpiRNApred performs significantly better than six other existing prediction tools.

A Faster-Than Relation for Semi-Markov Decision Processes

When modeling concurrent or cyber-physical systems, non-functional requirements such as time are important to consider. In order to improve the timing aspects of a model, it is necessary to have some notion of what it means for a process to be faster than another, which can guide the stepwise refinement of the model. To this end we study a faster-than relation for semi-Markov decision processes and compare it to standard notions for relating systems. We consider the compositional aspects of this relation, and show that the faster-than relation is not a precongruence with respect to parallel composition, hence giving rise to so-called parallel timing anomalies. We take the first steps toward understanding this problem by identifying decidable conditions sufficient to avoid parallel timing anomalies in the absence of non-determinism.

Probabilistic verification of attack detection using logical observer

Abstract This paper focuses on the detection of cyber-attacks in a timed probabilistic setting. The plant and the possible attacks are described in terms of a labeled continuous time Markov model that includes both observable and unobservable events, and where each attack corresponds to a particular subset of states. Consequently, attack detection is reformulated as a state estimation problem. A verification methodology is described using a parallel-like composition of the Markov model and its logical observer. The construction of this parallel composition allows us to (i) concisely characterize the set of attacks that can be detected based on the sequences of observations they generate, and (ii) compute performance indicators of interest, such as the a priori probability of an undetectable attack, the average detectability, and the mean delay to detection.

Narrow peaks of full transmission in simple quantum graphs

This work deals with quantum graphs, focusing on the transmission properties they engender. We first select two simple diamond graphs, and two hexagonal graphs in which the vertices are all of degree 3, and investigate their transmission coefficients. In particular, we identified regions in which the transmission is fully suppressed. We also considered the transmission coefficients of some series and parallel arrangements of the two basic graphs, with the vertices still preserving the degree 3 condition, and then identified specific series and parallel compositions that allow for windows of no transmission. Inside some of these windows, we found very narrow peaks of full transmission, which are consequences of constructive quantum interference. Possibilities of practical use as the experimental construction of devices of current interest to control and manipulate quantum transmission are also discussed.

Congruence from the operator\u2019s point of view

A basic sanity property of a process semantics is that it constitutes a congruence with respect to standard process operators. This issue has been traditionally addressed by developing, for a specific process semantics, a syntactic format for operational semantics specifications. We suggest a novel, orthogonal approach, which focuses on a specific process operator and determines a class of congruence relations for this operator. To this end, we impose syntactic restrictions on Hennessy–Milner logic, so that a process semantics whose modal characterization satisfies those criteria is guaranteed to be a congruence with respect to the operator in question. We investigate alternative composition, action prefix, projection, encapsulation, renaming, and parallel composition with communication, in the context of both concrete and weak process semantics.

Is There Any Sequence Feature in the RNA Pseudouridine Modification Prediction Problem?

Pseudouridine (Ψ) is the most abundant RNA modification and has been found in many kinds of RNAs, including snRNA, rRNA, tRNA, mRNA, and snoRNA. Thus, Ψ sites play a significant role in basic research and drug development. Although some experimental techniques have been developed to identify Ψ sites, they are expensive and time consuming, especially in the post-genomic era with the explosive growth of known RNA sequences. Thus, highly accurate computational methods are urgently required to quickly detect the Ψ sites on uncharacterized RNA sequences. Several predictors have been proposed using multifarious features, but their evaluated performances are still unsatisfactory. In this study, we first identified Ψ sites for H. sapiens, S. cerevisiae, and M. musculus using the sequence features from the bi-profile Bayes (BPB) method based on the random forest (RF) and support vector machine (SVM) algorithms, where the performances were evaluated using 5-fold cross-validation and independent tests. It was found that the SVM-based accuracies were 3.55% and 5.09% lower than the iPseU-CUU predictor for the H_990 and S_628 datasets, respectively. Almost the same-level results were obtained for M_994 and an independent H_200 dataset, even showing a 5.0% improvement for S_200. Then, three different kinds of features, including basic Kmer, general parallel correlation pseudo-dinucleotide composition (PC-PseDNC-General), and nucleotide chemical property (NCP) and nucleotide density (ND) from the iRNA-PseU method, were combined with BPB to show their comprehensive performances, where the effective features are selected by the max-relevance-max-distance (MRMD) method. The best evaluated accuracies of the combined features for the S_628 and M_994 datasets were achieved at 70.54% and 72.45%, which were 2.39% and 0.65% higher than iPseU-CUU. For the S_200 dataset, it was also improved 8% from 69% to 77%. However, there was no obvious improvement for H. sapiens, which was evaluated as approximately 63.23% and 72.0% for the H_990 and H_200 datasets, respectively. The overall performances for Ψ identification using BPB features as well as the combined features were not obviously improved. Although some kinds of feature extraction methods based on the RNA sequence information have been applied to construct the predictors in previous studies, the corresponding accuracies are generally in the range of 60%–70%. Thus, researchers need to reconsider whether there is any sequence feature in the RNA Ψ modification prediction problem.

Towards Races in Linear Logic

Process calculi based in logic, such as $\pi$DILL and CP, provide a foundation for deadlock-free concurrent programming, but exclude non-determinism and races. HCP is a reformulation of CP which addresses a fundamental shortcoming: the fundamental operator for parallel composition from the $\pi$-calculus does not correspond to any rule of linear logic, and therefore not to any term construct in CP. We introduce non-deterministic HCP, which extends HCP with a novel account of non-determinism. Our approach draws on bounded linear logic to provide a strongly-typed account of standard process calculus expressions of non-determinism. We show that our extension is expressive enough to capture many uses of non-determinism in untyped calculi, such as non-deterministic choice, while preserving HCP's meta-theoretic properties, including deadlock freedom.