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

A Note on Efficient Computation of All Abelian Periods in a String

We derive a simple efficient algorithm for Abelian periods knowing all Abelian squares in a string. An efficient algorithm for the latter problem was given by Cummings and Smyth in 1997. By the way we show an alternative algorithm for Abelian squares. We also obtain a linear time algorithm finding all `long' Abelian periods. The aim of the paper is a (new) reduction of the problem of all Abelian periods to that of (already solved) all Abelian squares which provides new insight into both connected problems

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

Query Order and the Polynomial Hierarchy

Hemaspaandra, Hempel, and Wechsung [cs.CC/9909020] initiated the field of query order, which studies the ways in which computational power is affected by the order in which information sources are accessed. The present paper studies, for the first time, query order as it applies to the levels of the polynomial hierarchy. We prove that the levels of the polynomial hierarchy are order-oblivious. Yet, we also show that these ordered query classes form new levels in the polynomial hierarchy unless the polynomial hierarchy collapses. We prove that all leaf language classes - and thus essentially all standard complexity classes - inherit all order-obliviousness results that hold for P.Comment: 14 page