Non-Definability Results for Randomised First-Order Logic

We investigate the expressive power of randomised first-order logic (BPFO) on restricted classes of structures. While BPFO is stronger than FO in general, even on structures with a built-in addition relation, we show that BPFO is not stronger than FO on structures with a unary vocabulary, nor on the class of equivalence relations. The same techniques can be applied to show that evenness of a linear order, and therefore graph connectivity, can not be defined in BPFO. Finally, we show that there is an FO[<]-definable query on word structures which can not be defined in BPFO[+1]

Successor-Invariant First-Order Logic on Graphs with Excluded Topological Subgraphs

We show that the model-checking problem for successor-invariant first-order logic is fixed-parameter tractable on graphs with excluded topological subgraphs when parameterised by both the size of the input formula and the size of the exluded topological subgraph. Furthermore, we show that model-checking for order-invariant first-order logic is tractable on coloured posets of bounded width, parameterised by both the size of the input formula and the width of the poset. Our result for successor-invariant FO extends previous results for this logic on planar graphs (Engelmann et al., LICS 2012) and graphs with excluded minors (Eickmeyer et al., LICS 2013), further narrowing the gap between what is known for FO and what is known for successor-invariant FO. The proof uses Grohe and Marx's structure theorem for graphs with excluded topological subgraphs. For order-invariant FO we show that Gajarsk\'y et al.'s recent result for FO carries over to order-invariant FO

On the optimality of the neighbor-joining algorithm

The popular neighbor-joining (NJ) algorithm used in phylogenetics is a greedy algorithm for finding the balanced minimum evolution (BME) tree associated to a dissimilarity map. From this point of view, NJ is ``optimal'' when the algorithm outputs the tree which minimizes the balanced minimum evolution criterion. We use the fact that the NJ tree topology and the BME tree topology are determined by polyhedral subdivisions of the spaces of dissimilarity maps ${\R}_{+}^{n \choose 2}$ to study the optimality of the neighbor-joining algorithm. In particular, we investigate and compare the polyhedral subdivisions for $n \leq 8$. A key requirement is the measurement of volumes of spherical polytopes in high dimension, which we obtain using a combination of Monte Carlo methods and polyhedral algorithms. We show that highly unrelated trees can be co-optimal in BME reconstruction, and that NJ regions are not convex. We obtain the $l_2$ radius for neighbor-joining for $n=5$ and we conjecture that the ability of the neighbor-joining algorithm to recover the BME tree depends on the diameter of the BME tree

On the number of types in sparse graphs

We prove that for every class of graphs $\mathcal{C}$ which is nowhere dense, as defined by Nesetril and Ossona de Mendez, and for every first order formula $\phi(\bar x,\bar y)$, whenever one draws a graph $G\in \mathcal{C}$ and a subset of its nodes $A$, the number of subsets of $A^{|\bar y|}$ which are of the form $\{\bar v\in A^{|\bar y|}\, \colon\, G\models\phi(\bar u,\bar v)\}$ for some valuation $\bar u$ of $\bar x$ in $G$ is bounded by $\mathcal{O}(|A|^{|\bar x|+\epsilon})$, for every $\epsilon>0$. This provides optimal bounds on the VC-density of first-order definable set systems in nowhere dense graph classes. We also give two new proofs of upper bounds on quantities in nowhere dense classes which are relevant for their logical treatment. Firstly, we provide a new proof of the fact that nowhere dense classes are uniformly quasi-wide, implying explicit, polynomial upper bounds on the functions relating the two notions. Secondly, we give a new combinatorial proof of the result of Adler and Adler stating that every nowhere dense class of graphs is stable. In contrast to the previous proofs of the above results, our proofs are completely finitistic and constructive, and yield explicit and computable upper bounds on quantities related to uniform quasi-wideness (margins) and stability (ladder indices)