Homotopy Bisimilarity for Higher-Dimensional Automata

We introduce a new category of higher-dimensional automata in which the morphisms are functional homotopy simulations, i.e. functional simulations up to concurrency of independent events. For this, we use unfoldings of higher-dimensional automata into higher-dimensional trees. Using a notion of open maps in this category, we define homotopy bisimilarity. We show that homotopy bisimilarity is equivalent to a straight-forward generalization of standard bisimilarity to higher dimensions, and that it is finer than split bisimilarity and incomparable with history-preserving bisimilarity.Comment: Heavily revised version of arXiv:1209.492

Model-Checking the Higher-Dimensional Modal mu-Calculus

The higher-dimensional modal mu-calculus is an extension of the mu-calculus in which formulas are interpreted in tuples of states of a labeled transition system. Every property that can be expressed in this logic can be checked in polynomial time, and conversely every polynomial-time decidable problem that has a bisimulation-invariant encoding into labeled transition systems can also be defined in the higher-dimensional modal mu-calculus. We exemplify the latter connection by giving several examples of decision problems which reduce to model checking of the higher-dimensional modal mu-calculus for some fixed formulas. This way generic model checking algorithms for the logic can then be used via partial evaluation in order to obtain algorithms for theses problems which may benefit from improvements that are well-established in the field of program verification, namely on-the-fly and symbolic techniques. The aim of this work is to extend such techniques to other fields as well, here exemplarily done for process equivalences, automata theory, parsing, string problems, and games.Comment: In Proceedings FICS 2012, arXiv:1202.317

History-Preserving Bisimilarity for Higher-Dimensional Automata via Open Maps

We show that history-preserving bisimilarity for higher-dimensional automata has a simple characterization directly in terms of higher-dimensional transitions. This implies that it is decidable for finite higher-dimensional automata. To arrive at our characterization, we apply the open-maps framework of Joyal, Nielsen and Winskel in the category of unfoldings of precubical sets.Comment: Minor updates in accordance with reviewer comments. Submitted to MFPS 201

Automata with Nested Pebbles Capture First-Order Logic with Transitive Closure

String languages recognizable in (deterministic) log-space are characterized either by two-way (deterministic) multi-head automata, or following Immerman, by first-order logic with (deterministic) transitive closure. Here we elaborate this result, and match the number of heads to the arity of the transitive closure. More precisely, first-order logic with k-ary deterministic transitive closure has the same power as deterministic automata walking on their input with k heads, additionally using a finite set of nested pebbles. This result is valid for strings, ordered trees, and in general for families of graphs having a fixed automaton that can be used to traverse the nodes of each of the graphs in the family. Other examples of such families are grids, toruses, and rectangular mazes. For nondeterministic automata, the logic is restricted to positive occurrences of transitive closure. The special case of k=1 for trees, shows that single-head deterministic tree-walking automata with nested pebbles are characterized by first-order logic with unary deterministic transitive closure. This refines our earlier result that placed these automata between first-order and monadic second-order logic on trees.Comment: Paper for Logical Methods in Computer Science, 27 pages, 1 figur

Sculplexity: Sculptures of Complexity using 3D printing

We show how to convert models of complex systems such as 2D cellular automata into a 3D printed object. Our method takes into account the limitations inherent to 3D printing processes and materials. Our approach automates the greater part of this task, bypassing the use of CAD software and the need for manual design. As a proof of concept, a physical object representing a modified forest fire model was successfully printed. Automated conversion methods similar to the ones developed here can be used to create objects for research, for demonstration and teaching, for outreach, or simply for aesthetic pleasure. As our outputs can be touched, they may be particularly useful for those with visual disabilities.Comment: Free access to article on European Physics Letter

Combinatorial optimization problems in self-assembly

Self-assembly is the ubiquitous process by which simple objects autonomously assemble into intricate complexes. It has been suggested that intricate self-assembly processes will ultimately be used in circuit fabrication, nano-robotics, DNA computation, and amorphous computing. In this paper, we study two combinatorial optimization problems related to efficient self-assembly of shapes in the Tile Assembly Model of self-assembly proposed by Rothemund and Winfree [18]. The first is the Minimum Tile Set Problem, where the goal is to find the smallest tile system that uniquely produces a given shape. The second is the Tile Concentrations Problem, where the goal is to decide on the relative concentrations of different types of tiles so that a tile system assembles as quickly as possible. The first problem is akin to finding optimum program size, and the second to finding optimum running time for a "program" to assemble the shape.Self-assembly is the ubiquitous process by which simple objects autonomously assemble into intricate complexes. It has been suggested that intricate self-assembly processes will ultimately be used in circuit fabrication, nano-robotics, DNA computation, and amorphous computing. In this paper, we study two combinatorial optimization problems related to efficient self-assembly of shapes in the Tile Assembly Model of self-assembly proposed by Rothemund and Winfree [18]. The first is the Minimum Tile Set Problem, where the goal is to find the smallest tile system that uniquely produces a given shape. The second is the Tile Concentrations Problem, where the goal is to decide on the relative concentrations of different types of tiles so that a tile system assembles as quickly as possible. The first problem is akin to finding optimum program size, and the second to finding optimum running time for a "program" to assemble the shape. We prove that the first problem is NP-complete in general, and polynomial time solvable on trees and squares. In order to prove that the problem is in NP, we present a polynomial time algorithm to verify whether a given tile system uniquely produces a given shape. This algorithm is analogous to a program verifier for traditional computational systems, and may well be of independent interest. For the second problem, we present a polynomial time $O(\log n)$-approximation algorithm that works for a large class of tile systems that we call partial order systems

Linear-Space Data Structures for Range Mode Query in Arrays

A mode of a multiset $S$ is an element $a \in S$ of maximum multiplicity; that is, $a$ occurs at least as frequently as any other element in $S$. Given a list $A[1:n]$ of $n$ items, we consider the problem of constructing a data structure that efficiently answers range mode queries on $A$. Each query consists of an input pair of indices $(i, j)$ for which a mode of $A[i:j]$ must be returned. We present an $O(n^{2-2\epsilon})$-space static data structure that supports range mode queries in $O(n^\epsilon)$ time in the worst case, for any fixed $\epsilon \in [0,1/2]$. When $\epsilon = 1/2$, this corresponds to the first linear-space data structure to guarantee $O(\sqrt{n})$ query time. We then describe three additional linear-space data structures that provide $O(k)$, $O(m)$, and $O(|j-i|)$ query time, respectively, where $k$ denotes the number of distinct elements in $A$ and $m$ denotes the frequency of the mode of $A$. Finally, we examine generalizing our data structures to higher dimensions.Comment: 13 pages, 2 figure