Abstract State Machines 1988-1998: Commented ASM Bibliography

An annotated bibliography of papers which deal with or use Abstract State Machines (ASMs), as of January 1998.Comment: Also maintained as a BibTeX file at http://www.eecs.umich.edu/gasm

Reconfigurable Decorated PT Nets with Inhibitor Arcs and Transition Priorities

In this paper we deal with additional control structures for decorated PT Nets. The main contribution are inhibitor arcs and priorities. The first ensure that a marking can inhibit the firing of a transition. Inhibitor arcs force that the transition may only fire when the place is empty. an order of transitions restrict the firing, so that an transition may fire only if it has the highest priority of all enabled transitions. This concept is shown to be compatible with reconfigurable Petri nets

The Tandem Duplication Distance Is NP-Hard

In computational biology, tandem duplication is an important biological phenomenon which can occur either at the genome or at the DNA level. A tandem duplication takes a copy of a genome segment and inserts it right after the segment - this can be represented as the string operation AXB ? AXXB. Tandem exon duplications have been found in many species such as human, fly or worm, and have been largely studied in computational biology. The Tandem Duplication (TD) distance problem we investigate in this paper is defined as follows: given two strings S and T over the same alphabet, compute the smallest sequence of tandem duplications required to convert S to T. The natural question of whether the TD distance can be computed in polynomial time was posed in 2004 by Leupold et al. and had remained open, despite the fact that tandem duplications have received much attention ever since. In this paper, we prove that this problem is NP-hard, settling the 16-year old open problem. We further show that this hardness holds even if all characters of S are distinct. This is known as the exemplar TD distance, which is of special relevance in bioinformatics. One of the tools we develop for the reduction is a new problem called the Cost-Effective Subgraph, for which we obtain W[1]-hardness results that might be of independent interest. We finally show that computing the exemplar TD distance between S and T is fixed-parameter tractable. Our results open the door to many other questions, and we conclude with several open problems

ReConNet: A Tool for Modeling and Simulating with Reconfigurable Place/Transition Nets

In this contribution we present a tool for modeling and simulation with reconfigurable Petri nets. Taking the idea of algebraic graph transformations to marked Petri nets we obtain Petri nets whose net structure can be changed dynamically. The rule-based change of the net structure enables the adequate modeling of complex, dynamic structures as for example of  the scenarios of the Living Place Hamburg. The tool \reconnet \ uses decorated  place/transition nets that are extended by various annotations. Especially, they  have transition labels that may change when the transition fires. The  transformation approach is based on the well-known algebraic transformation approach, but here we use a variant, namely the cospan approach, that inverts the relation between  left- and right-hand sides and interface in the  rules

Abstract Interleaving Semantics for Reconfigurable Petri Nets

Reconfigurable Petri nets are Petri nets together with rules for the dynamic change of the nets. We employ them for the formal modeling in the context of the Living Place Hamburg, a smart home that is an urban apartment serving as  a laboratory for investigating different areas of ambient intelligence. The interaction of the resident and the smart home is modeled using informal descriptions of scenarios. These scenarios provide the resident's procedures together with the smart home's support. A case study using reconfigurable Petri nets for modeling these scenarios has required extensions of the theory and has clearly shown the need for an interleaving semantics for reconfigurable Petri nets. Scenarios are then given by nets, namely decorated place/transition nets that can be adapted to the evolving subgoals by applying rules that change the nets and hence the behavior of the smart home. Decorated place/transition nets are annotated place/transition nets with additional transition labels that may change when the transition is fired. To obtain such reconfigurable Petri nets  we prove that decorated place/transition nets  give rise to an M-adhesive HLR category. The abstract interleaving semantics we introduce is a graph with nodes that consist of an isomorphism class of the net structure and an isomorphism class of the current  marking. Arcs between these nodes represent computation steps being either a transition firing or a direct transformation

Distributed Detection of Cycles

Distributed property testing in networks has been introduced by Brakerski and Patt-Shamir (2011), with the objective of detecting the presence of large dense sub-networks in a distributed manner. Recently, Censor-Hillel et al. (2016) have shown how to detect 3-cycles in a constant number of rounds by a distributed algorithm. In a follow up work, Fraigniaud et al. (2016) have shown how to detect 4-cycles in a constant number of rounds as well. However, the techniques in these latter works were shown not to generalize to larger cycles $C_k$ with $k\geq 5$. In this paper, we completely settle the problem of cycle detection, by establishing the following result. For every $k\geq 3$, there exists a distributed property testing algorithm for $C_k$-freeness, performing in a constant number of rounds. All these results hold in the classical CONGEST model for distributed network computing. Our algorithm is 1-sided error. Its round-complexity is $O(1/\epsilon)$ where $\epsilon\in(0,1)$ is the property testing parameter measuring the gap between legal and illegal instances