15877902
Tree logic with recursion and model checking algorithm
Semi-structured data plays an increasingly important role in the exchange of information between globally distributed applications, which invokes renewed interests in typed programming languages that can manipulate tree-like data structures. Tree logic, inherited from ambient logic, is introduced as the formal foundation of related programming language and type systems. In this paper, we introduce recursion into such logic system, which can describe the tree data more clearly and concisely. By making a distinction between proposition and predicate, a concise semantics interpretation for our modal logic is given. We also develop a model checking algorithm for the logic without . operator. The correctness of the algorithm is shown. Such work can be seen as the basis of the semi-structured data processing language and more flexible type system.
5876317
Framework of performance evaluation for mobile process based on mobile ambient
Formal methodology for distributed and concurrent system, especially computation system with mobility, is increasingly important both in the theory and the practice. Based on the calculus of mobile ambient (MA), a widely studied formal mechanism for mobile computation, this paper focuses on the quantitative analysis of mobile computation system and provides a framework of performance evaluation for it. In details, this paper introduces an enhanced labelled transition system as the system model, and assigns rate to each label through so-called cost function. Based on it, the labelled transition system can be mapped to continuous time Markov chains and thus performance evaluation can be carried out by standard numerical techniques and tools. In some sense the main work of this paper can be regarded as integrating behavior and performance analysis in a compositional formal framework, which provides some basis of unified formal methodology for the development of mobile system.
34739655
On the Bisimulation Congruence in chi-Calculus
In this paper, we study weak bisimulation congruences for the χ-calculus, a symmetric variant of the π-calculus. We distinguish two styles of such bisimulation definitions, i.e. “open” and “closed” bisimulation, the difference between which lies in that in open style the equivalence is closed under context in every bisimulation step whereas in closed style the equivalence is closed under context only at the very beginning. As a result, we show that both in labelled and barbed congruence, the open and closed style definitions coincide. Thus all bisimulation congruences collapse into two equivalences, that is, the well-known open congruence and open barbed congruence, which are the same in the strong case, while in the weak case their difference can be reflected by one axiom. The results of this paper close some conjectures in the literatures and shed light on the algebraic theory of a large class of mobile process calculi.
5970126
On the Complete Axiomatization for Prefix Iteration modulo Observation Congruence
Prefix iteration is a variation on the original binary version of the Kleene star operation P*Q, obtained by restricting the first argument to be an atomic action. Aceto and Ingolfsdottir provided an axiom system for observation congruence over basic CCS with prefix iteration. However hitherto the only direct completeness proof given for such a system is very long and technical. In this paper, we provide a new proof for the completeness of the axiom system in [3], which is a considerable simplification comparing to the original proof. Thus the open problem to find a direct completeness proof is closed.
8665982
Structure analysis for dynamic software architecture based on spatial logic
The requirement for modifying system structure during system execution is specified by dynamic software architectures. The system architecture style should remain one style or transform within a scope so that some constraints need to be imposed on during the system execution. Our work expands such an idea along two directions in the setting of formalism. The first direction is to model the system by a graph-based calculus stressing the structure. The other direction lies in that we tailor spatial logic to be a suitable logic as the system specification for structure. The model and specification are basis for the model checking algorithm that is to verify whether the system evolution satisfies some structure constraints. We invite a master-slave architecture style as a running example from the beginning and throughout the paper to demonstrate our approach. Such work can be seen as the basis of the structure analysis for architectures.
17432425
Structure analysis for dynamic software architecture
The open and dynamic Internet environment greatly urges software entities that are distributed on different locations to coordinate with each other to accomplish a computing task. Software architecture is applied to abstract the software entities to be components and the coordination between them to be connectors and then a model is extracted as the architecture on which the design, analysis and verification are based. Currently, the notion of dynamic software architectures that can modify their architecture and enact modifications during the system execution has become one of the most active research areas. In this paper, we focus on the dynamic evolution of system structure other than coordination mechanisms (e.g. communication protocols). It is widely recognized that some restrictions should be imposed on the system evolution to ensure that the system structure may remain one style or transform within a scope. These conditions, to a large extent, make the system execute under control as expected.
17774823
Scalable Partitioning and Exploration of Chemical Spaces Using Geometric Hashing
Virtual screening (VS) has become a preferred tool to augment high-throughput screening(1) and determine new leads in the drug discovery process. The core of a VS informatics pipeline includes several data mining algorithms that work on huge databases of chemical compounds containing millions of molecular structures and their associated data. Thus, scaling traditional applications such as classification, partitioning, and outlier detection for huge chemical data sets without a significant loss in accuracy is very important. In this paper, we introduce a data mining framework built on top of a recently developed fast approximate nearest-neighbor-finding algorithm(2) called locality-sensitive hashing (LSH) that can be used to mine huge chemical spaces in a scalable fashion using very modest computational resources. The core LSH algorithm hashes chemical descriptors so that points close to each other in the descriptor space are also close to each other in the hashed space. Using this data structure, one can perform approximate nearest-neighbor searches very quickly, in sublinear time. We validate the accuracy and performance of our framework on three real data sets of sizes ranging from 4337 to 249 071 molecules. Results indicate that the identification of nearest neighbors using the LSH algorithm is at least 2 orders of magnitude faster than the traditional k-nearest-neighbor method and is over 94% accurate for most query parameters. Furthermore, when viewed as a data-partitioning procedure, the LSH algorithm lends itself to easy parallelization of nearest-neighbor classification or regression. We also apply our framework to detect outlying (diverse) compounds in a given chemical space; this algorithm is extremely rapid in determining whether a compound is located in a sparse region of chemical space or not, and it is quite accurate when compared to results obtained using principal-component-analysis-based heuristics.
33188963
Improving the quality of classification trees via restructuring
The classification-hierarchy table developed by Chen and Poon (1996) provides a systematic approach to construct classification trees from given sets of classifications and their associated classes. The paper enhances their study by defining a metric to measure the "quality" of a classification tree, and providing an algorithm to improve this quality.
2301190
On the Informational Asymmetry between Upper and Lower Bounds for Ultrametric Evolutionary Trees
This paper addresses the informational asymmetry for constructing an ultrametric evolutionary tree from upper and lower bounds on pairwise distances between n given species. We show that the tallest ultrametric tree exists and can be constructed in O(n2) time, while the existence of the shortest ultrametric tree depends on whether the lower bounds are ultrametric. The tallest tree construction algorithm gives a very simple solution to the construction of an ultrametric tree. We also provide an efficient O(n2)-time algorithm for checking the uniqueness of an ultrametric tree, and study a query problem for testing whether an ultrametric tree satisfies both upper and lower bounds.
31957165
International Symposium on Quality Electronic Design
2822926
Sorting with Fixed-length Reversals
Abstract A popular puzzle TOP-SPIN consists of a permutation of 20 numbered disks on an oval track, with a turnstile capable of reversing a string of 4 consecutive disks. The goal is to sort the disks into identity permutation using reversals. We consider the more general case of sorting n element permutations with a turnstile of size k. The problem of computing the reversal distances is of considerable importance in reconstructing the evolutionary history of the genome. The minimum reversal sequence sorting the one genome to another corresponds to the most likely evolutionary path between them. We give a complete solution for all n and k, of the number of equivalence classes of n-permutations under k-reversal, for both permutations and circular permutations. We also prove the upper and lower bounds on the reversal distances between two permutations.