Automated unique input output sequence generation for conformance testing of FSMs

This paper describes a method for automatically generating unique input output (UIO) sequences for FSM conformance testing. UIOs are used in conformance testing to verify the end state of a transition sequence. UIO sequence generation is represented as a search problem and genetic algorithms are used to search this space. Empirical evidence indicates that the proposed method yields considerably better (up to 62% better) results compared with random UIO sequence generation

Tools for efficient analysis of concurrent software systems

The ever increasing use of distributed computing as a method of providing added computing power and reliability has sparked interest in methods to model and analyze concurrent hardware/ software systems. Efficient automated analysis tools are needed to aid designers of such systems. The Distributed Systems Project at UCI has been developing a suite of tools (dubbed the P-NUT system) which supports efficient analysis of models of concurrent software. This paper presents the principles which guide the development of P-NUT tools and discusses the development of one of the tools: the Reachability Graph Builder (RGB). The P-NUT approach to tool development has resulted in the production of a highly efficient tool for constructing reachability graphs. The careful design of data structures and associated algorithms has significantly enlarged the class of models which can be analyzed

A Stable Marriage Requires Communication

The Gale-Shapley algorithm for the Stable Marriage Problem is known to take $\Theta(n^2)$ steps to find a stable marriage in the worst case, but only $\Theta(n \log n)$ steps in the average case (with $n$ women and $n$ men). In 1976, Knuth asked whether the worst-case running time can be improved in a model of computation that does not require sequential access to the whole input. A partial negative answer was given by Ng and Hirschberg, who showed that $\Theta(n^2)$ queries are required in a model that allows certain natural random-access queries to the participants' preferences. A significantly more general - albeit slightly weaker - lower bound follows from Segal's general analysis of communication complexity, namely that $\Omega(n^2)$ Boolean queries are required in order to find a stable marriage, regardless of the set of allowed Boolean queries. Using a reduction to the communication complexity of the disjointness problem, we give a far simpler, yet significantly more powerful argument showing that $\Omega(n^2)$ Boolean queries of any type are indeed required for finding a stable - or even an approximately stable - marriage. Notably, unlike Segal's lower bound, our lower bound generalizes also to (A) randomized algorithms, (B) allowing arbitrary separate preprocessing of the women's preferences profile and of the men's preferences profile, (C) several variants of the basic problem, such as whether a given pair is married in every/some stable marriage, and (D) determining whether a proposed marriage is stable or far from stable. In order to analyze "approximately stable" marriages, we introduce the notion of "distance to stability" and provide an efficient algorithm for its computation

Impact of sample preservation and manipulation on insect gut microbiome profiling : a test case with fruit flies (Diptera, Tephritidae)

High-throughput sequencing (HTS) techniques are of great value for the investigation of microbial communities, and have been extensively used to study the gut microbiome. While most studies focus on the human gut, many others have investigated insects. However, because of the rapid spread of HTS techniques, a lot of variation exists in the protocols for sample preparation. In the present study, we investigated the impact of two widely adopted sample-processing procedures preceding library preparation, i.e., preservation of insect tissue in 70% ethanol (EtOH) and sample dissection. We used the fruit fly Ceratitis capitata (Diptera: Tephritidae) as a model organism and set up two experiments, one comparing the effects of sample manipulation and preservation across life stages and the other across fruit samples from different sources. The results of this study showed no major effects of dissection on the outcome of HTS. However, EtOH preservation did have effects on the recovered gut microbiome, the main effect being a significant reduction of the dominant genus, Providencia, in EtOH-preserved samples. Less abundant bacterial groups were also affected resulting in altered microbial profiles obtained from samples preserved in 70% EtOH. These results have important implications for the planning of future studies and when comparing studies that used different sample preparation protocols

Using genetic algorithms to generate test sequences for complex timed systems

The generation of test data for state based specifications is a computationally expensive process. This problem is magnified if we consider that time con- straints have to be taken into account to govern the transitions of the studied system. The main goal of this paper is to introduce a complete methodology, sup- ported by tools, that addresses this issue by represent- ing the test data generation problem as an optimisa- tion problem. We use heuristics to generate test cases. In order to assess the suitability of our approach we consider two different case studies: a communication protocol and the scientific application BIPS3D. We give details concerning how the test case generation problem can be presented as a search problem and automated. Genetic algorithms (GAs) and random search are used to generate test data and evaluate the approach. GAs outperform random search and seem to scale well as the problem size increases. It is worth to mention that we use a very simple fitness function that can be eas- ily adapted to be used with other evolutionary search techniques

Towards Efficient Verification of Population Protocols

Population protocols are a well established model of computation by anonymous, identical finite state agents. A protocol is well-specified if from every initial configuration, all fair executions reach a common consensus. The central verification question for population protocols is the well-specification problem: deciding if a given protocol is well-specified. Esparza et al. have recently shown that this problem is decidable, but with very high complexity: it is at least as hard as the Petri net reachability problem, which is EXPSPACE-hard, and for which only algorithms of non-primitive recursive complexity are currently known. In this paper we introduce the class WS3 of well-specified strongly-silent protocols and we prove that it is suitable for automatic verification. More precisely, we show that WS3 has the same computational power as general well-specified protocols, and captures standard protocols from the literature. Moreover, we show that the membership problem for WS3 reduces to solving boolean combinations of linear constraints over N. This allowed us to develop the first software able to automatically prove well-specification for all of the infinitely many possible inputs.Comment: 29 pages, 1 figur