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What is computable with limited resources? How can we verify the correctness of computations? How to measure computational power with precision? Despite the immense scientific and engineering progress in computing, we still have only partial answers to these questions. In order to make these problems more precise, we describe an abstract algebraic definition of classical computation, generalizing traditional models to semigroups. The mathematical abstraction also allows the investigation of different computing paradigms (e.g. cellular automata, reversible computing) in the same framework. Here we summarize the main questions and recent results of the research of finite computation., Comment: 12 pages, 3 figures, will be presented at CANDAR'16 and final version published by IEEE Computer Society

We present a search algorithm for constructing embeddings and deciding isomorphisms of semigroups, working with their multiplication tables. The algorithm is used for enumerating diagram semigroups up to isomorphism and for finding minimal degree representations., Comment: 9 pages, 1 figure, 2 tables

Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. In the case of bacteria, distances can be estimated using a range of different evolutionary models, from single nucleotide polymorphisms to large-scale genome rearrangements. In the case of sequence evolution models (such as the Jukes-Cantor model and associated metric) have been used to correct pairwise distances. Similar correction methods for genome rearrangement processes are required to improve inference. Current attempts at correction fall into 3 categories: Empirical computational studies, Bayesian/MCMC approaches, and combinatorial approaches. Here we introduce a maximum likelihood estimator for the inversion distance between a pair of genomes, using the group-theoretic approach to modelling inversions introduced recently. This MLE functions as a corrected distance: in particular, we show that because of the way sequences of inversions interact with each other, it is quite possible for minimal distance and MLE distance to differently order the distances of two genomes from a third. This has obvious implications for the use of minimal distance in phylogeny reconstruction. The work also tackles the above problem allowing free rotation of the genome. Generally a frame of reference is locked, and all computation made accordingly. This work incorporates the action of the dihedral group so that distance estimates are free from any a priori frame of reference., Comment: 21 pages, 7 figures. To appear in the Journal of Theoretical Biology

We developed computer algebra tools for enumerating conjugacy classes of independent subsets and generating sets of symmetric groups up to $n=7$, and carried out an initial analysis of the obtained results., Comment: 7 pages, 5 tables, preliminary report of computational results, full paper version will be published elsewhere, v3: results recomputed for verification by new coauthor Volker Gebhardt, using MAGMA

The minimum unsatisfiability version of a constraint satisfaction problem (MinCSP) asks for an assignment where the number of unsatisfied constraints is minimum possible, or equivalently, asks for a minimum-size set of constraints whose deletion makes the instance satisfiable. For a finite set $\Gamma$ of constraints, we denote by MinCSP($\Gamma$) the restriction of the problem where each constraint is from $\Gamma$. The polynomial-time solvability and the polynomial-time approximability of MinCSP($\Gamma$) were fully characterized by Khanna et al. [Siam J. Comput. '00]. Here we study the fixed-parameter (FP-) approximability of the problem: given an instance and an integer $k$, one has to find a solution of size at most $g(k)$ in time $f(k)n^{O(1)}$ if a solution of size at most $k$ exists. We especially focus on the case of constant-factor FP-approximability. We show the following dichotomy: for each finite constraint language $\Gamma$, either we exhibit a constant-factor FP-approximation for MinCSP($\Gamma$); or we prove that MinCSP($\Gamma$) has no constant-factor FP-approximation unless FPT$=$W[1]. In particular, we show that approximating the so-called Nearest Codeword within some constant factor is W[1]-hard. Recently, Arnab et al. [ICALP '18] showed that such a W[1]-hardness of approximation implies that Even Set is W[1]-hard under randomized reductions. Combining our results, we therefore settle the parameterized complexity of Even Set, a famous open question in the field., Comment: A preliminary version of this paper has appeared in the proceedings of ESA 2016

Many models of genome rearrangement involve operations (e.g. inversions and translocations) that are self-inverse, and hence generate a group acting on the space of genomes. This gives a correspondence between genome arrangements and the elements of a group, and consequently, between evolutionary paths and walks on the Cayley graph. Many common methods for phylogeny reconstruction rely on calculating the minimal distance between two genomes; this omits much of the other information available from the Cayley graph. In this paper we begin an exploration of some of this additional information, in particular describing the phylogeny as a Steiner tree within the Cayley graph, and exploring the "interval" between two genomes. While motivated by problems in systematic biology, many of these ideas are of independent group-theoretic interest., Comment: 9 pages, 6 figures, final version will be published elsewhere

We determine many of the atoms of the algebraic lattices arising in $\mathfrak{q}$-theory of finite semigroups., Comment: 28 pages

Digraphs H for which the list homomorphism problem with template H (LHOM(H)) is in logspace (L) was characterized by Egri et al. (SODA 2014): LHOM(H) is in L if and only if H does not contain a circular N (assuming L is different from NL). Undirected graphs for which LHOM(H) is in L can be characterized in terms forbidden induced subgraphs, and also via a simple inductive construction (Egri et al., STACS 2010). As a consequence, the logspace algorithm in the undirected case is simple and easy to understand. No such forbidden subgraph or inductive characterization, and no such simple and easy-to-understand algorithm is known in the case of digraphs. In this paper, in the case of oriented trees, we refine and strengthen the results of Egri et al. (SODA 2014): we give a characterization of oriented trees T for which LHOM(T) is in L both in terms of forbidden induced subgraphs, and also via a simple inductive construction. Using this characterization, we obtain a simple and easy-to-analyze logspace algorithm for LHOM(T). We also show how these oriented trees can be recognized in time O(|V(T)|^3) (the straightforward implementation of the algorithm given in SODA 2014 runs in time O(|V(H)|^8) for oriented trees). An algebraic characterization of these trees is also provided., Comment: 30 pages, full version with algebra section included

Using a variant of Schreier's Theorem, and the theory of Green's relations, we show how to reduce the computation of an arbitrary subsemigroup of a finite regular semigroup to that of certain associated subgroups. Examples of semigroups to which these results apply include many important classes: transformation semigroups, partial permutation semigroups and inverse semigroups, partition monoids, matrix semigroups, and subsemigroups of finite regular Rees matrix and $0$-matrix semigroups over groups. For any subsemigroup of such a semigroup, it is possible to, among other things, efficiently compute its size and Green's relations, test membership, factorize elements over the generators, find the semigroup generated by the given subsemigroup and any collection of additional elements, calculate the partial order of the $\mathscr{D}$-classes, test regularity, and determine the idempotents. This is achieved by representing the given subsemigroup without exhaustively enumerating its elements. It is also possible to compute the Green's classes of an element of such a subsemigroup without determining the global structure of the semigroup., Comment: 47 pages, 12 figures (updated to include a new section "Experimental results")

We present an understandable, efficient, and streamlined proof of the Holonomy Decomposition for finite transformation semigroups and automata. This constructive proof closely follows the existing computational implementation. Its novelty lies in the strict separation of several different ideas appearing in the holonomy method. The steps of the proof and the constructions are illustrated with computed examples., Comment: 16 pages, 4 figures, final version will be published elsewhere

Diagram semigroups are interesting algebraic and combinatorial objects, several types of them originating from questions in computer science and in physics. Here we describe diagram semigroups in a general framework and extend our computational knowledge of them. The generated data set is replete with surprising observations raising many open questions for further theoretical research., Comment: 9 pages, 11 figures, final version will be published elsewhere, v2 minor corrections

We study the process of single ionization of Li in collisions with H$^+$ and O$^{8+}$ projectile ions at 6 MeV and 1.5-MeV/amu impact energies, respectively. Using the frameworks of the independent-electron model and the impact parameter picture, fully (FDCS) and doubly (DDCS) differential cross sections are evaluated in the continuum distorted-wave with eikonal initial-state approximation. Comparisons are made with the recent measurements of LaForge \textit{et al} [J. Phys. B \textbf{46} 031001 (2013)] for the DDCS and Hubele \textit{et al} [Phys. Rev. Lett. \textbf{110} 133201 (2013)] for the FDCS, respectively. For O$^{8+}$ impact inclusion of the heavy particle (NN) interaction in the calculations is crucial and effects of polarization due to the presence of the projectile ion have also to be taken into account for getting very good agreement with the measured data. Our calculation reproduces the satellite peak structure seen in the FDCS for the Li(2s) measurement, which we explain as being formed by a combination of the binary and NN interactions.

We describe how the SgpDec computer algebra package can be used for composing and decomposing permutation groups and transformation semigroups hierarchically by directly constructing substructures of wreath products, the so called cascade products., Comment: 7 pages, 4 figures, presented at the 4th International Congress on Mathematical Software, http://sgpdec.sf.net

Establishing a distance between genomes is a significant problem in computational genomics, because its solution can be used to establish evolutionary relationships including phylogeny. The "double cut and join" (DCJ) model of chromosomal rearrangement proposed by Yancopoulos et al. has received attention as it can model inversions, translocations, fusion and fission on a multichromosomal genome that may contain both linear and circular chromosomes. In this paper, we realize the DCJ operator as a group action on the space of multichromosomal genomes. We study this group action, deriving some properties of the group and finding group-theoretic analogues for the key results in the DCJ theory.

We describe general methods for enumerating subsemigroups of finite semigroups and techniques to improve the algorithmic efficiency of the calculations. As a particular application we use our algorithms to enumerate all transformation semigroups up to degree 4. Classification of these semigroups up to conjugacy, isomorphism and anti-isomorphism, by size and rank, provides a solid base for further investigations of transformation semigroups., Comment: 11 pages, 6 figures, 3 tables, v4: updated references,added T4 gap values, corrections in examples

We establish the connection between Green's ${\mathcal J}$-classes and the subduction equivalence classes defined on the image sets of an action of a semigroup. The construction of the skeleton order (on subduction equivalence classes) is shown to depend in a functorial way on transformation semigroups and surjective morphisms, and to factor through the $\leq_{\mathcal L}$-order and $\leq_{\mathcal J}$-order on the semigroup and through the inclusion order on image sets. For right regular representations, the correspondence between the ${\mathcal J}$-class order and the skeleton is one of isomorphism., Comment: 8 pages

The variation in genome arrangements among bacterial taxa is largely due to the process of inversion. Recent studies indicate that not all inversions are equally probable, suggesting, for instance, that shorter inversions are more frequent than longer, and those that move the terminus of replication are less probable than those that do not. Current methods for establishing the inversion distance between two bacterial genomes are unable to incorporate such information. In this paper we suggest a group-theoretic framework that in principle can take these constraints into account. In particular, we show that by lifting the problem from circular permutations to the affine symmetric group, the inversion distance can be found in polynomial time for a model in which inversions are restricted to acting on two regions. This requires the proof of new results in group theory, and suggests a vein of new combinatorial problems concerning permutation groups on which group theorists will be needed to collaborate with biologists. We apply the new method to inferring distances and phylogenies for published Yersinia pestis data., Comment: 19 pages, 7 figures, in Press, Journal of Mathematical Biology

Symmetric Datalog, a fragment of the logic programming language Datalog, is conjectured to capture all constraint satisfaction problems (CSP) in L. Therefore developing tools that help us understand whether or not a CSP can be defined in symmetric Datalog is an important task. It is widely known that a CSP is definable in Datalog and linear Datalog if and only if that CSP has bounded treewidth and bounded pathwidth duality, respectively. In the case of symmetric Datalog, Bulatov, Krokhin and Larose ask for such a duality (2008). We provide two such dualities, and give applications. In particular, we give a short and simple new proof of the result of Dalmau and Larose that "Maltsev + Datalog -> symmetric Datalog" (2008). In the second part of the paper, we provide some evidence for the conjecture of Dalmau (2002) that every CSP in NL is definable in linear Datalog. Our results also show that a wide class of CSPs-CSPs which do not have bounded pathwidth duality (e.g., the P-complete Horn-3Sat problem)-cannot be defined by any polynomial size family of monotone read-once nondeterministic branching programs.

In the deletion version of the list homomorphism problem, we are given graphs G and H, a list L(v) that is a subset of V(H) for each vertex v of G, and an integer k. The task is to decide whether there exists a subset W of V(G) of size at most k such that there is a homomorphism from G \ W to H respecting the lists. We show that DL-Hom(H), parameterized by k and |H|, is fixed-parameter tractable for any (P6, C6)-free bipartite graph H; already for this restricted class of graphs, the problem generalizes Vertex Cover, Odd Cycle Transversal, and Vertex Multiway Cut parameterized by the size of the cutset and the number of terminals. We conjecture that DL-Hom(H) is fixed-parameter tractable for the class of graphs H for which the list homomorphism problem (without deletions) is polynomial-time solvable; by a result of Feder, Hell and Huang (1999), a graph H belongs to this class precisely if it is a bipartite graph whose complement is a circular arc graph. We show that this conjecture is equivalent to the fixed-parameter tractability of a single fairly natural satisfiability problem, Clause Deletion Chain-SAT.

The Dichotomy Conjecture for constraint satisfaction problems (CSPs) states that every CSP is in P or is NP-complete (Feder-Vardi, 1993). It has been verified for conservative problems (also known as list homomorphism problems) by A. Bulatov (2003). We augment this result by showing that for digraph templates H, every conservative CSP, denoted LHOM(H), is solvable in logspace or is hard for NL. More precisely, we introduce a digraph structure we call a circular N, and prove the following dichotomy: if H contains no circular N then LHOM(H) admits a logspace algorithm, and otherwise LHOM(H) is hard for NL. Our algorithm operates by reducing the lists in a complex manner based on a novel decomposition of an auxiliary digraph, combined with repeated applications of Reingold's algorithm for undirected reachability (2005). We also prove an algebraic version of this dichotomy: the digraphs without a circular N are precisely those that admit a finite chain of polymorphisms satisfying the Hagemann-Mitschke identities. This confirms a conjecture of Larose and Tesson (2007) for LHOM(H). Moreover, we show that the presence of a circular N can be decided in time polynomial in the size of H.

We describe a new notation for finite transformations. This attractor-cycle notation extends the orbit-cycle notation for permutations and builds upon existing transformation notations. How the basins of attraction of a finite transformation flow into permuted orbit cycles is visible from the notation. It gives insight into the structure of transformations and reduces the length of expressions without increasing the number of types of symbols., Comment: 8 pages, 4 figures, notation itself and the title changed!, this final version is implemented in SgpDec http://gap-packages.github.io/sgpdec/

Motivated by computational efficiency in algebraic automata theory here we define the cascade product of permutation groups as an external product, as a generic extension. It is the most general hierarchical product that uses arbitrary total functions to combine a linearly ordered set of permutation groups. Algebraically speaking, cascade products are explicitly constructed substructures of the iterated wreath product. We show how direct, semidirect and wreath products can be described as cascade products and we also discuss examples of composite groups that can only be constructed exactly as generic extensions by cascade products. The cascade construction naturally generalizes to the transformation semigroup case by leaving out the details of defining inverse operations., Comment: 12 pages, 4 figures, v5: updated link to software package and minor changes

Motivated by issues arising in computer science, we investigate the loop-free paths from the identity transformation and corresponding straight words in the Cayley graph of a finite transformation semigroup with a fixed generator set. Of special interest are words that permute a given subset of the state set. Certain such words, called minimal permutators, are shown to comprise a code, and the straight ones comprise a finite code. Thus, words that permute a given subset are uniquely factorizable as products of the subset's minimal permutators, and these can be further reduced to straight minimal permutators. This leads to insight into structure of local pools of reversibility in transformation semigroups in terms of the set of words permuting a given subset. These findings can be exploited in practical calculations for hierarchical decompositions of finite automata. As an example we consider groups arising in biological systems., Comment: 12 pages, 2 figures

We completely classify the computational complexity of the list H-colouring problem for graphs (with possible loops) in combinatorial and algebraic terms: for every graph H the problem is either NP-complete, NL-complete, L-complete or is first-order definable; descriptive complexity equivalents are given as well via Datalog and its fragments. Our algebraic characterisations match important conjectures in the study of constraint satisfaction problems., Comment: 12 pages, STACS 2010

We give a general constructive proof for hierarchical coordinatizations (Lagrange Decompositions) of permutation groups. The generalization originates from the investigation of how the subgroup chains of finite permutation groups yield different coordinate systems. The study is motivated by the practical needs and the verification of an existing computational implementation. Large scale machine calculated examples are also presented., Comment: 10 pages, 1 figure