An Efficient generic algorithm for the generation of unlabelled cycles

In this report we combine two recent generation algorithms to obtain a new algorithm for the generation of unlabelled cycles. Sawada's algorithm lists all k-ary unlabelled cycles with fixed content, that is, the number of occurences of each symbol is fixed and given a priori. The other algorithm, by the authors, generates all multisets of objects with given total size n from any admissible unlabelled class A. By admissible we mean that the class can be specificied using atomic classes, disjoints unions, products, sequences, (multi)sets, etc. The resulting algorithm, which is the main contribution of this paper, generates all cycles of objects with given total size n from any admissible class A. Given the generic nature of the algorithm, it is suitable for inclusion in combinatorial libraries and for rapid prototyping. The new algorithm incurs constant amortized time per generated cycle, the constant only depending in the class A to which the objects in the cycle belong.Postprint (published version

Combinatorial Route to Algebra: The Art of Composition & Decomposition

We consider a general concept of composition and decomposition of objects, and discuss a few natural properties one may expect from a reasonable choice thereof. It will be demonstrated how this leads to multiplication and co- multiplication laws, thereby providing a generic scheme furnishing combinatorial classes with an algebraic structure. The paper is meant as a gentle introduction to the concepts of composition and decomposition with the emphasis on combinatorial origin of the ensuing algebraic constructions.Comment: 20 pages, 6 figure

Local description of phylogenetic group-based models

Motivated by phylogenetics, our aim is to obtain a system of equations that define a phylogenetic variety on an open set containing the biologically meaningful points. In this paper we consider phylogenetic varieties defined via group-based models. For any finite abelian group $G$, we provide an explicit construction of $codim X$ phylogenetic invariants (polynomial equations) of degree at most $|G|$ that define the variety $X$ on a Zariski open set $U$. The set $U$ contains all biologically meaningful points when $G$ is the group of the Kimura 3-parameter model. In particular, our main result confirms a conjecture by the third author and, on the set $U$, a couple of conjectures by Bernd Sturmfels and Seth Sullivant.Comment: 22 pages, 7 figure

Comparing fbeta-optimal with distance based merge functions

Merge functions informally combine information from a certain universe into a solution over that same universe. This typically results in a, preferably optimal, summarization. In previous research, merge functions over sets have been looked into extensively. A specic case concerns sets that allow elements to appear more than once, multisets. In this paper we compare two types of merge functions over multisets against each other. We examine both general properties as practical usability in a real world application

A Comparison of Well-Quasi Orders on Trees

Well-quasi orders such as homeomorphic embedding are commonly used to ensure termination of program analysis and program transformation, in particular supercompilation. We compare eight well-quasi orders on how discriminative they are and their computational complexity. The studied well-quasi orders comprise two very simple examples, two examples from literature on supercompilation and four new proposed by the author. We also discuss combining several well-quasi orders to get well-quasi orders of higher discriminative power. This adds 19 more well-quasi orders to the list.Comment: In Proceedings Festschrift for Dave Schmidt, arXiv:1309.455

A Potpourri of Reason Maintenance Methods

We present novel methods to compute changes to materialized views in logic databases like those used by rule-based reasoners. Such reasoners have to address the problem of changing axioms in the presence of materializations of derived atoms. Existing approaches have drawbacks: some require to generate and evaluate large transformed programs that are in Datalog - while the source program is in Datalog and significantly smaller; some recompute the whole extension of a predicate even if only a small part of this extension is affected by the change. The methods presented in this article overcome these drawbacks and derive additional information useful also for explanation, at the price of an adaptation of the semi-naive forward chaining