Smaller Extended Formulations for Spanning Tree Polytopes in Minor-closed Classes and Beyond

Let $G$ be a connected $n$-vertex graph in a proper minor-closed class $\mathcal G$. We prove that the extension complexity of the spanning tree polytope of $G$ is $O(n^{3/2})$. This improves on the $O(n^2)$ bounds following from the work of Wong (1980) and Martin (1991). It also extends a result of Fiorini, Huynh, Joret, and Pashkovich (2017), who obtained a $O(n^{3/2})$ bound for graphs embedded in a fixed surface. Our proof works more generally for all graph classes admitting strongly sublinear balanced separators: We prove that for every constant $\beta$ with $0<\beta<1$, if $\mathcal G$ is a graph class closed under induced subgraphs such that all $n$-vertex graphs in $\mathcal G$ have balanced separators of size $O(n^\beta)$, then the extension complexity of the spanning tree polytope of every connected $n$-vertex graph in $\mathcal{G}$ is $O(n^{1+\beta})$. We in fact give two proofs of this result, one is a direct construction of the extended formulation, the other is via communication protocols. Using the latter approach we also give a short proof of the $O(n)$ bound for planar graphs due to Williams (2002).

Oscillation of nonlinear neutral dynamic equations on time scales

The authors present necessary and sufficient conditions for the oscillation of a class of second order non-linear neutral dynamic equations with non-positive neutral coefficients by using Krasnosel’skii’s fixed point theorem on time scales. The nonlinear function may be strongly sublinear or strongly superlinear.

Text Indexing for Regular Expression Matching

Finding substrings of a text T that match a regular expression p is a fundamental problem. Despite being the subject of extensive research, no solution with a time complexity significantly better than O(|T||p|) has been found. Backurs and Indyk in FOCS 2016 established conditional lower bounds for the algorithmic problem based on the Strong Exponential Time Hypothesis that helps explain this difficulty. A natural question is whether we can improve the time complexity for matching the regular expression by preprocessing the text T? We show that conditioned on the Online Matrix–Vector Multiplication (OMv) conjecture, even with arbitrary polynomial preprocessing time, a regular expression query on a text cannot be answered in strongly sublinear time, i.e., O(|T|1−ε) for any ε>0. Furthermore, if we extend the OMv conjecture to a plausible conjecture regarding Boolean matrix multiplication with polynomial preprocessing time, which we call Online Matrix–Matrix Multiplication (OMM), we can strengthen this hardness result to there being no solution with a query time that is O(|T|3/2−ε). These results hold for alphabet sizes three or greater. We then provide data structures that answer queries in O(|T||p|τ) time where τ∈[1,|T|] is fixed at construction. These include a solution that works for all regular expressions with Expτ·|T| preprocessing time and space. For patterns containing only ‘concatenation’ and ‘or’ operators (the same type used in the hardness result), we provide (1) a deterministic solution which requires Expτ·|T|log2|T| preprocessing time and space, and (2) when |p|≤|T|z for z=2o(log|T|), a randomized solution with amortized query time which answers queries correctly with high probability, requiring Expτ·|T|2Ωlog|T| preprocessing time and space.

Information capacity of specific interactions

Specific interactions are a hallmark feature of self-assembly and signal-processing systems in both synthetic and biological settings. Specificity between components may arise from a wide variety of physical and chemical mechanisms in diverse contexts, from DNA hybridization to shape-sensitive depletion interactions. Despite this diversity, all systems that rely on interaction specificity operate under the constraint that increasing the number of distinct components inevitably increases off-target binding. Here we introduce “capacity,” the maximal information encodable using specific interactions, to compare specificity across diverse experimental systems and to compute how specificity changes with physical parameters. Using this framework, we find that “shape” coding of interactions has higher capacity than chemical (“color”) coding because the strength of off-target binding is strongly sublinear in binding-site size for shapes while being linear for colors. We also find that different specificity mechanisms, such as shape and color, can be combined in a synergistic manner, giving a capacity greater than the sum of the parts.