Order-Invariant MSO is Stronger than Counting MSO in the Finite

We compare the expressiveness of two extensions of monadic second-order logic (MSO) over the class of finite structures. The first, counting monadic second-order logic (CMSO), extends MSO with first-order modulo-counting quantifiers, allowing the expression of queries like ``the number of elements in the structure is even''. The second extension allows the use of an additional binary predicate, not contained in the signature of the queried structure, that must be interpreted as an arbitrary linear order on its universe, obtaining order-invariant MSO. While it is straightforward that every CMSO formula can be translated into an equivalent order-invariant MSO formula, the converse had not yet been settled. Courcelle showed that for restricted classes of structures both order-invariant MSO and CMSO are equally expressive, but conjectured that, in general, order-invariant MSO is stronger than CMSO. We affirm this conjecture by presenting a class of structures that is order-invariantly definable in MSO but not definable in CMSO.Comment: Revised version contributed to STACS 200

Reducing CMSO model checking to highly connected graphs

Given a Counting Monadic Second Order (CMSO) sentence psi, the CMSO[psi] problem is defined as follows. The input to CMSO[psi] is a graph G, and the objective is to determine whether G |= psi. Our main theorem states that for every CMSO sentence psi, if CMSO[psi] is solvable in polynomial time on "globally highly connected graphs", then CMSO[psi] is solvable in polynomial time (on general graphs). We demonstrate the utility of our theorem in the design of parameterized algorithms. Specifically we show that technical problem-specific ingredients of a powerful method for designing parameterized algorithms, recursive understanding, can be replaced by a black-box invocation of our main theorem. We also show that our theorem can be easily deployed to show fixed parameterized tractability of a wide range of problems, where the input is a graph G and the task is to find a connected induced subgraph of G such that "few" vertices in this subgraph have neighbors outside the subgraph, and additionally the subgraph has a CMSO-definable property

Community standards for open cell migration data

Cell migration research has become a high-content field. However, the quantitative information encapsulated in these complex and high-dimensional datasets is not fully exploited owing to the diversity of experimental protocols and non-standardized output formats. In addition, typically the datasets are not open for reuse. Making the data open and Findable, Accessible, Interoperable, and Reusable (FAIR) will enable meta-analysis, data integration, and data mining. Standardized data formats and controlled vocabularies are essential for building a suitable infrastructure for that purpose but are not available in the cell migration domain. We here present standardization efforts by the Cell Migration Standardisation Organisation (CMSO), an open community-driven organization to facilitate the development of standards for cell migration data. This work will foster the development of improved algorithms and tools and enable secondary analysis of public datasets, ultimately unlocking new knowledge of the complex biological process of cell migration

Order Invariance on Decomposable Structures

Order-invariant formulas access an ordering on a structure's universe, but the model relation is independent of the used ordering. Order invariance is frequently used for logic-based approaches in computer science. Order-invariant formulas capture unordered problems of complexity classes and they model the independence of the answer to a database query from low-level aspects of databases. We study the expressive power of order-invariant monadic second-order (MSO) and first-order (FO) logic on restricted classes of structures that admit certain forms of tree decompositions (not necessarily of bounded width). While order-invariant MSO is more expressive than MSO and, even, CMSO (MSO with modulo-counting predicates), we show that order-invariant MSO and CMSO are equally expressive on graphs of bounded tree width and on planar graphs. This extends an earlier result for trees due to Courcelle. Moreover, we show that all properties definable in order-invariant FO are also definable in MSO on these classes. These results are applications of a theorem that shows how to lift up definability results for order-invariant logics from the bags of a graph's tree decomposition to the graph itself.Comment: Accepted for LICS 201

Large induced subgraphs via triangulations and CMSO

We obtain an algorithmic meta-theorem for the following optimization problem. Let \phi\ be a Counting Monadic Second Order Logic (CMSO) formula and t be an integer. For a given graph G, the task is to maximize |X| subject to the following: there is a set of vertices F of G, containing X, such that the subgraph G[F] induced by F is of treewidth at most t, and structure (G[F],X) models \phi. Some special cases of this optimization problem are the following generic examples. Each of these cases contains various problems as a special subcase: 1) "Maximum induced subgraph with at most l copies of cycles of length 0 modulo m", where for fixed nonnegative integers m and l, the task is to find a maximum induced subgraph of a given graph with at most l vertex-disjoint cycles of length 0 modulo m. 2) "Minimum \Gamma-deletion", where for a fixed finite set of graphs \Gamma\ containing a planar graph, the task is to find a maximum induced subgraph of a given graph containing no graph from \Gamma\ as a minor. 3) "Independent \Pi-packing", where for a fixed finite set of connected graphs \Pi, the task is to find an induced subgraph G[F] of a given graph G with the maximum number of connected components, such that each connected component of G[F] is isomorphic to some graph from \Pi. We give an algorithm solving the optimization problem on an n-vertex graph G in time O(#pmc n^{t+4} f(t,\phi)), where #pmc is the number of all potential maximal cliques in G and f is a function depending of t and \phi\ only. We also show how a similar running time can be obtained for the weighted version of the problem. Pipelined with known bounds on the number of potential maximal cliques, we deduce that our optimization problem can be solved in time O(1.7347^n) for arbitrary graphs, and in polynomial time for graph classes with polynomial number of minimal separators

Deterministic Automata for Unordered Trees

Automata for unordered unranked trees are relevant for defining schemas and queries for data trees in Json or Xml format. While the existing notions are well-investigated concerning expressiveness, they all lack a proper notion of determinism, which makes it difficult to distinguish subclasses of automata for which problems such as inclusion, equivalence, and minimization can be solved efficiently. In this paper, we propose and investigate different notions of "horizontal determinism", starting from automata for unranked trees in which the horizontal evaluation is performed by finite state automata. We show that a restriction to confluent horizontal evaluation leads to polynomial-time emptiness and universality, but still suffers from coNP-completeness of the emptiness of binary intersections. Finally, efficient algorithms can be obtained by imposing an order of horizontal evaluation globally for all automata in the class. Depending on the choice of the order, we obtain different classes of automata, each of which has the same expressiveness as CMso.Comment: In Proceedings GandALF 2014, arXiv:1408.556

Bidimensionality and EPTAS

Bidimensionality theory is a powerful framework for the development of metaalgorithmic techniques. It was introduced by Demaine et al. as a tool to obtain sub-exponential time parameterized algorithms for problems on H-minor free graphs. Demaine and Hajiaghayi extended the theory to obtain PTASs for bidimensional problems, and subsequently improved these results to EPTASs. Fomin et. al related the theory to the existence of linear kernels for parameterized problems. In this paper we revisit bidimensionality theory from the perspective of approximation algorithms and redesign the framework for obtaining EPTASs to be more powerful, easier to apply and easier to understand. Two of the most widely used approaches to obtain PTASs on planar graphs are the Lipton-Tarjan separator based approach, and Baker's approach. Demaine and Hajiaghayi strengthened both approaches using bidimensionality and obtained EPTASs for a multitude of problems. We unify the two strenghtened approaches to combine the best of both worlds. At the heart of our framework is a decomposition lemma which states that for "most" bidimensional problems, there is a polynomial time algorithm which given an H-minor-free graph G as input and an e > 0 outputs a vertex set X of size e * OPT such that the treewidth of G n X is f(e). Here, OPT is the objective function value of the problem in question and f is a function depending only on e. This allows us to obtain EPTASs on (apex)-minor-free graphs for all problems covered by the previous framework, as well as for a wide range of packing problems, partial covering problems and problems that are neither closed under taking minors, nor contractions. To the best of our knowledge for many of these problems including cycle packing, vertex-h-packing, maximum leaf spanning tree, and partial r-dominating set no EPTASs on planar graphs were previously known