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

On the possible Computational Power of the Human Mind

The aim of this paper is to address the question: Can an artificial neural network (ANN) model be used as a possible characterization of the power of the human mind? We will discuss what might be the relationship between such a model and its natural counterpart. A possible characterization of the different power capabilities of the mind is suggested in terms of the information contained (in its computational complexity) or achievable by it. Such characterization takes advantage of recent results based on natural neural networks (NNN) and the computational power of arbitrary artificial neural networks (ANN). The possible acceptance of neural networks as the model of the human mind's operation makes the aforementioned quite relevant.Comment: Complexity, Science and Society Conference, 2005, University of Liverpool, UK. 23 page

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

A Vernacular for Coherent Logic

We propose a simple, yet expressive proof representation from which proofs for different proof assistants can easily be generated. The representation uses only a few inference rules and is based on a frag- ment of first-order logic called coherent logic. Coherent logic has been recognized by a number of researchers as a suitable logic for many ev- eryday mathematical developments. The proposed proof representation is accompanied by a corresponding XML format and by a suite of XSL transformations for generating formal proofs for Isabelle/Isar and Coq, as well as proofs expressed in a natural language form (formatted in LATEX or in HTML). Also, our automated theorem prover for coherent logic exports proofs in the proposed XML format. All tools are publicly available, along with a set of sample theorems.Comment: CICM 2014 - Conferences on Intelligent Computer Mathematics (2014

Algebraic Approach to Timed Petri Nets

One aspect often needed when modelling systems of any kind is time-based analysis, especially for real-time or in general time-critical systems. Algebraic place/transition (P/T) nets do not inherently provide a way to model the passing of time or to restrict the firing behaviour with regards to passing time. In this paper, we present an extension of algebraic P/T nets by adding time durations to transitions and timestamps to tokens. We define categories for different timed net classes and functorial relations between them. Our first result is the definition of morphisms preserving firing behaviour for all timed net classes. As second result, we define structuring techniques for timed P/T nets in a way that our category fulfills the properties of M-adhesive systems, a general categorical framework for structuring and transforming high-level algebraic structures. We demonstrate our approach by applying it to model a real-time communication network