On the Monadic Second-Order Transduction Hierarchy

We compare classes of finite relational structures via monadic second-order transductions. More precisely, we study the preorder where we set C \subseteq K if, and only if, there exists a transduction {\tau} such that C\subseteq{\tau}(K). If we only consider classes of incidence structures we can completely describe the resulting hierarchy. It is linear of order type {\omega}+3. Each level can be characterised in terms of a suitable variant of tree-width. Canonical representatives of the various levels are: the class of all trees of height n, for each n \in N, of all paths, of all trees, and of all grids

The Equivalence Problem for Deterministic MSO Tree Transducers is Decidable

It is decidable for deterministic MSO definable graph-to-string or graph-to-tree transducers whether they are equivalent on a context-free set of graphs

Answering the Call: Coping with DNA Damage at the Most Inopportune Time

DNA damage incurred during the process of chromosomal replication has a particularly high possibility of resulting in mutagenesis or lethality for the cell. The SOS response of Escherichia coli appears to be well adapted for this particular situation and involves the coordinated up-regulation of genes whose products center upon the tasks of maintaining the integrity of the replication fork when it encounters DNA damage, delaying the replication process (a DNA damage checkpoint), repairing the DNA lesions or allowing replication to occur over these DNA lesions, and then restoring processive replication before the SOS response itself is turned off. Recent advances in the fields of genomics and biochemistry has given a much more comprehensive picture of the timing and coordination of events which allow cells to deal with potentially lethal or mutagenic DNA lesions at the time of chromosomal replication

Between Treewidth and Clique-width

Many hard graph problems can be solved efficiently when restricted to graphs of bounded treewidth, and more generally to graphs of bounded clique-width. But there is a price to be paid for this generality, exemplified by the four problems MaxCut, Graph Coloring, Hamiltonian Cycle and Edge Dominating Set that are all FPT parameterized by treewidth but none of which can be FPT parameterized by clique-width unless FPT = W[1], as shown by Fomin et al [7, 8]. We therefore seek a structural graph parameter that shares some of the generality of clique-width without paying this price. Based on splits, branch decompositions and the work of Vatshelle [18] on Maximum Matching-width, we consider the graph parameter sm-width which lies between treewidth and clique-width. Some graph classes of unbounded treewidth, like distance-hereditary graphs, have bounded sm-width. We show that MaxCut, Graph Coloring, Hamiltonian Cycle and Edge Dominating Set are all FPT parameterized by sm-width

Compact Labelings For Efficient First-Order Model-Checking

We consider graph properties that can be checked from labels, i.e., bit sequences, of logarithmic length attached to vertices. We prove that there exists such a labeling for checking a first-order formula with free set variables in the graphs of every class that is \emph{nicely locally cwd-decomposable}. This notion generalizes that of a \emph{nicely locally tree-decomposable} class. The graphs of such classes can be covered by graphs of bounded \emph{clique-width} with limited overlaps. We also consider such labelings for \emph{bounded} first-order formulas on graph classes of \emph{bounded expansion}. Some of these results are extended to counting queries

On the stable degree of graphs

We define the stable degree s(G) of a graph G by s(G)∈=∈ min max d (v), where the minimum is taken over all maximal independent sets U of G. For this new parameter we prove the following. Deciding whether a graph has stable degree at most k is NP-complete for every fixed k∈≥∈3; and the stable degree is hard to approximate. For asteroidal triple-free graphs and graphs of bounded asteroidal number the stable degree can be computed in polynomial time. For graphs in these classes the treewidth is bounded from below and above in terms of the stable degree

Streaming Tree Transducers

Theory of tree transducers provides a foundation for understanding expressiveness and complexity of analysis problems for specification languages for transforming hierarchically structured data such as XML documents. We introduce streaming tree transducers as an analyzable, executable, and expressive model for transforming unranked ordered trees in a single pass. Given a linear encoding of the input tree, the transducer makes a single left-to-right pass through the input, and computes the output in linear time using a finite-state control, a visibly pushdown stack, and a finite number of variables that store output chunks that can be combined using the operations of string-concatenation and tree-insertion. We prove that the expressiveness of the model coincides with transductions definable using monadic second-order logic (MSO). Existing models of tree transducers either cannot implement all MSO-definable transformations, or require regular look ahead that prohibits single-pass implementation. We show a variety of analysis problems such as type-checking and checking functional equivalence are solvable for our model.Comment: 40 page

Small Shelly Fossil Preservation and the Role of Early Diagenetic Redox in the Early Triassic

Minute fossils from a variety of different metazoan clades, collectively referred to as small shelly fossils, represent a distinctive taphonomic mode that is most commonly reported from the Cambrian Period. Lower Triassic successions of the western United States, deposited in the aftermath of the end-Permian mass extinction, provide an example of small shelly style preservation that significantly post-dates Cambrian occurrences. Glauconitized and phosphatized echinoderms and gastropods are preserved in the insoluble residues of carbonates from the Virgin Limestone Member of the Moenkopi Formation. Echinoderm plates, spines and other skeletal elements are preserved as stereomic molds; gastropods are preserved as steinkerns. All small shelly style fossils are preserved in the small size fractions of the residues (177 to 420 lm), which is consistent with the size selection of small shelly fossils in the Cambrian. Energy-dispersive X-ray spectra of individual fossils coupled with X-ray diffraction of residues confirm that the fossils are dominantly preserved by apatite and glauconite, and sometimes a combination of the two minerals. The nucleation of both of these minerals requires that pore water redox oscillated between oxic and anoxic conditions, which, in turn, implies that Lower Triassic carbonates periodically experienced oxygen depletion after deposition and during early diagenesis. Long-term oxygen depletion persisted through the Early Triassic, creating diagenetic conditions that were instrumental in the preservation of small shelly fossils in Triassic and, likely, Paleozoic examples

Parameterized Edge Hamiltonicity

We study the parameterized complexity of the classical Edge Hamiltonian Path problem and give several fixed-parameter tractability results. First, we settle an open question of Demaine et al. by showing that Edge Hamiltonian Path is FPT parameterized by vertex cover, and that it also admits a cubic kernel. We then show fixed-parameter tractability even for a generalization of the problem to arbitrary hypergraphs, parameterized by the size of a (supplied) hitting set. We also consider the problem parameterized by treewidth or clique-width. Surprisingly, we show that the problem is FPT for both of these standard parameters, in contrast to its vertex version, which is W-hard for clique-width. Our technique, which may be of independent interest, relies on a structural characterization of clique-width in terms of treewidth and complete bipartite subgraphs due to Gurski and Wanke

Recognizing hyperelliptic graphs in polynomial time

Recently, a new set of multigraph parameters was defined, called "gonalities". Gonality bears some similarity to treewidth, and is a relevant graph parameter for problems in number theory and multigraph algorithms. Multigraphs of gonality 1 are trees. We consider so-called "hyperelliptic graphs" (multigraphs of gonality 2) and provide a safe and complete sets of reduction rules for such multigraphs, showing that for three of the flavors of gonality, we can recognize hyperelliptic graphs in O(n log n+m) time, where n is the number of vertices and m the number of edges of the multigraph.Comment: 33 pages, 8 figure