MONAA: A Tool for Timed Pattern Matching with Automata-Based Acceleration

We present monaa, a monitoring tool over a real-time property specified by either a timed automaton or a timed regular expression. It implements a timed pattern matching algorithm that combines 1) features suited for online monitoring, and 2) acceleration by automata-based skipping. Our experiments demonstrate monaa's performance advantage, especially in online usage.Comment: Published in: 2018 IEEE Workshop on Monitoring and Testing of Cyber-Physical Systems (MT-CPS

On the Verification of a WiMax Design Using Symbolic Simulation

In top-down multi-level design methodologies, design descriptions at higher levels of abstraction are incrementally refined to the final realizations. Simulation based techniques have traditionally been used to verify that such model refinements do not change the design functionality. Unfortunately, with computer simulations it is not possible to completely check that a design transformation is correct in a reasonable amount of time, as the number of test patterns required to do so increase exponentially with the number of system state variables. In this paper, we propose a methodology for the verification of conformance of models generated at higher levels of abstraction in the design process to the design specifications. We model the system behavior using sequence of recurrence equations. We then use symbolic simulation together with equivalence checking and property checking techniques for design verification. Using our proposed method, we have verified the equivalence of three WiMax system models at different levels of design abstraction, and the correctness of various system properties on those models. Our symbolic modeling and verification experiments show that the proposed verification methodology provides performance advantage over its numerical counterpart.Comment: In Proceedings SCSS 2012, arXiv:1307.802

Efficient exact pattern-matching in proteomic sequences

This paper proposes a novel algorithm for complete exact pattern-matching focusing the specificities of protein sequences (alphabet of 20 symbols) but, also highly efficient considering larger alphabets. The searching strategy uses large search windows allowing multiple alignments per iteration. A new filtering heuristic, named compatibility rule, contributed decisively to the efficiency improvement. The new algorithm’s performance is, on average, superior in comparison with its best-rated competitors

Métodos eficientes para a detecção de padrões exactos (pattern-matching) em sequências biológicas

Os algoritmos de detecção de padrões (pattern-matching), sejam exactos ou aproximados, são fundamentais na maioria das aplicações orientadas à análise de sequências biológicas. Nesta comunicação apresenta-se um novo algoritmo, denominado DC, desenvolvido para a especificidade do pattern-matching exacto, bem como uma análise comparativa do seu desempenho. Conclui-se que o desempenho do novo algoritmo supera, em média, o dos seus concorrentes, atribuindo-se o ganho de eficiência, sobretudo, à introdução de uma nova regra de filtragem denominada regra de compatibilidade

Designing optimal- and fast-on-average pattern matching algorithms

Given a pattern $w$ and a text $t$, the speed of a pattern matching algorithm over $t$ with regard to $w$, is the ratio of the length of $t$ to the number of text accesses performed to search $w$ into $t$. We first propose a general method for computing the limit of the expected speed of pattern matching algorithms, with regard to $w$, over iid texts. Next, we show how to determine the greatest speed which can be achieved among a large class of algorithms, altogether with an algorithm running this speed. Since the complexity of this determination make it impossible to deal with patterns of length greater than 4, we propose a polynomial heuristic. Finally, our approaches are compared with 9 pre-existing pattern matching algorithms from both a theoretical and a practical point of view, i.e. both in terms of limit expected speed on iid texts, and in terms of observed average speed on real data. In all cases, the pre-existing algorithms are outperformed

Efficient Online Timed Pattern Matching by Automata-Based Skipping

The timed pattern matching problem is an actively studied topic because of its relevance in monitoring of real-time systems. There one is given a log $w$ and a specification $\mathcal{A}$ (given by a timed word and a timed automaton in this paper), and one wishes to return the set of intervals for which the log $w$, when restricted to the interval, satisfies the specification $\mathcal{A}$. In our previous work we presented an efficient timed pattern matching algorithm: it adopts a skipping mechanism inspired by the classic Boyer--Moore (BM) string matching algorithm. In this work we tackle the problem of online timed pattern matching, towards embedded applications where it is vital to process a vast amount of incoming data in a timely manner. Specifically, we start with the Franek-Jennings-Smyth (FJS) string matching algorithm---a recent variant of the BM algorithm---and extend it to timed pattern matching. Our experiments indicate the efficiency of our FJS-type algorithm in online and offline timed pattern matching

An adaptive hybrid pattern-matching algorithm on indeterminate strings

We describe a hybrid pattern-matching algorithm that works on both regular and indeterminate strings. This algorithm is inspired by the recently proposed hybrid algorithm FJS and its indeterminate successor. However, as discussed in this paper, because of the special properties of indeterminate strings, it is not straightforward to directly migrate FJS to an indeterminate version. Our new algorithm combines two fast pattern-matching algorithms, ShiftAnd and BMS (the Sunday variant of the Boyer-Moore algorithm), and is highly adaptive to the nature of the text being processed. It avoids using the border array, therefore avoids some of the cases that are awkward for indeterminate strings. Although not always the fastest in individual test cases, our new algorithm is superior in overall performance to its two component algorithms — perhaps a general advantage of hybrid algorithms