Stratification and enumeration of Boolean functions by canalizing depth

Boolean network models have gained popularity in computational systems biology over the last dozen years. Many of these networks use canalizing Boolean functions, which has led to increased interest in the study of these functions. The canalizing depth of a function describes how many canalizing variables can be recursively picked off, until a non-canalizing function remains. In this paper, we show how every Boolean function has a unique algebraic form involving extended monomial layers and a well-defined core polynomial. This generalizes recent work on the algebraic structure of nested canalizing functions, and it yields a stratification of all Boolean functions by their canalizing depth. As a result, we obtain closed formulas for the number of n-variable Boolean functions with depth k, which simultaneously generalizes enumeration formulas for canalizing, and nested canalizing functions

The Partial Visibility Representation Extension Problem

For a graph $G$, a function $\psi$ is called a \emph{bar visibility representation} of $G$ when for each vertex $v \in V(G)$, $\psi(v)$ is a horizontal line segment (\emph{bar}) and $uv \in E(G)$ iff there is an unobstructed, vertical, $\varepsilon$-wide line of sight between $\psi(u)$ and $\psi(v)$. Graphs admitting such representations are well understood (via simple characterizations) and recognizable in linear time. For a directed graph $G$, a bar visibility representation $\psi$ of $G$, additionally, puts the bar $\psi(u)$ strictly below the bar $\psi(v)$ for each directed edge $(u,v)$ of $G$. We study a generalization of the recognition problem where a function $\psi'$ defined on a subset $V'$ of $V(G)$ is given and the question is whether there is a bar visibility representation $\psi$ of $G$ with $\psi(v) = \psi'(v)$ for every $v \in V'$. We show that for undirected graphs this problem together with closely related problems are \NP-complete, but for certain cases involving directed graphs it is solvable in polynomial time.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Some Applications of Coding Theory in Computational Complexity

Error-correcting codes and related combinatorial constructs play an important role in several recent (and old) results in computational complexity theory. In this paper we survey results on locally-testable and locally-decodable error-correcting codes, and their applications to complexity theory and to cryptography. Locally decodable codes are error-correcting codes with sub-linear time error-correcting algorithms. They are related to private information retrieval (a type of cryptographic protocol), and they are used in average-case complexity and to construct ``hard-core predicates'' for one-way permutations. Locally testable codes are error-correcting codes with sub-linear time error-detection algorithms, and they are the combinatorial core of probabilistically checkable proofs

Efficient Parallel Path Checking for Linear-Time Temporal Logic With Past and Bounds

Path checking, the special case of the model checking problem where the model under consideration is a single path, plays an important role in monitoring, testing, and verification. We prove that for linear-time temporal logic (LTL), path checking can be efficiently parallelized. In addition to the core logic, we consider the extensions of LTL with bounded-future (BLTL) and past-time (LTL+Past) operators. Even though both extensions improve the succinctness of the logic exponentially, path checking remains efficiently parallelizable: Our algorithm for LTL, LTL+Past, and BLTL+Past is in AC^1(logDCFL) \subseteq NC

Envelopes of conditional probabilities extending a strategy and a prior probability

Any strategy and prior probability together are a coherent conditional probability that can be extended, generally not in a unique way, to a full conditional probability. The corresponding class of extensions is studied and a closed form expression for its envelopes is provided. Then a topological characterization of the subclasses of extensions satisfying the further properties of full disintegrability and full strong conglomerability is given and their envelopes are studied.Comment: 2

Involutive Categories and Monoids, with a GNS-correspondence

This paper develops the basics of the theory of involutive categories and shows that such categories provide the natural setting in which to describe involutive monoids. It is shown how categories of Eilenberg-Moore algebras of involutive monads are involutive, with conjugation for modules and vector spaces as special case. The core of the so-called Gelfand-Naimark-Segal (GNS) construction is identified as a bijective correspondence between states on involutive monoids and inner products. This correspondence exists in arbritrary involutive categories

Searchable Sky Coverage of Astronomical Observations: Footprints and Exposures

Sky coverage is one of the most important pieces of information about astronomical observations. We discuss possible representations, and present algorithms to create and manipulate shapes consisting of generalized spherical polygons with arbitrary complexity and size on the celestial sphere. This shape specification integrates well with our Hierarchical Triangular Mesh indexing toolbox, whose performance and capabilities are enhanced by the advanced features presented here. Our portable implementation of the relevant spherical geometry routines comes with wrapper functions for database queries, which are currently being used within several scientific catalog archives including the Sloan Digital Sky Survey, the Galaxy Evolution Explorer and the Hubble Legacy Archive projects as well as the Footprint Service of the Virtual Observatory.Comment: 11 pages, 7 figures, submitted to PAS

On the Complexity and Performance of Parsing with Derivatives

Current algorithms for context-free parsing inflict a trade-off between ease of understanding, ease of implementation, theoretical complexity, and practical performance. No algorithm achieves all of these properties simultaneously. Might et al. (2011) introduced parsing with derivatives, which handles arbitrary context-free grammars while being both easy to understand and simple to implement. Despite much initial enthusiasm and a multitude of independent implementations, its worst-case complexity has never been proven to be better than exponential. In fact, high-level arguments claiming it is fundamentally exponential have been advanced and even accepted as part of the folklore. Performance ended up being sluggish in practice, and this sluggishness was taken as informal evidence of exponentiality. In this paper, we reexamine the performance of parsing with derivatives. We have discovered that it is not exponential but, in fact, cubic. Moreover, simple (though perhaps not obvious) modifications to the implementation by Might et al. (2011) lead to an implementation that is not only easy to understand but also highly performant in practice.Comment: 13 pages; 12 figures; implementation at http://bitbucket.org/ucombinator/parsing-with-derivatives/ ; published in PLDI '16, Proceedings of the 37th ACM SIGPLAN Conference on Programming Language Design and Implementation, June 13 - 17, 2016, Santa Barbara, CA, US