On the Sensitivity Conjecture for Read-k Formulas

Various combinatorial/algebraic parameters are used to quantify the complexity of a Boolean function. Among them, sensitivity is one of the simplest and block sensitivity is one of the most useful. Nisan (1989) and Nisan and Szegedy (1991) showed that block sensitivity and several other parameters, such as certificate complexity, decision tree depth, and degree over R, are all polynomially related to one another. The sensitivity conjecture states that there is also a polynomial relationship between sensitivity and block sensitivity, thus supplying the "missing link". Since its introduction in 1991, the sensitivity conjecture has remained a challenging open question in the study of Boolean functions. One natural approach is to prove it for special classes of functions. For instance, the conjecture is known to be true for monotone functions, symmetric functions, and functions describing graph properties. In this paper, we consider the conjecture for Boolean functions computable by read-k formulas. A read-k formula is a tree in which each variable appears at most k times among the leaves and has Boolean gates at its internal nodes. We show that the sensitivity conjecture holds for read-once formulas with gates computing symmetric functions. We next consider regular formulas with OR and AND gates. A formula is regular if it is a leveled tree with all gates at a given level having the same fan-in and computing the same function. We prove the sensitivity conjecture for constant depth regular read-k formulas for constant k

The Influence of Canalization on the Robustness of Boolean Networks

Time- and state-discrete dynamical systems are frequently used to model molecular networks. This paper provides a collection of mathematical and computational tools for the study of robustness in Boolean network models. The focus is on networks governed by $k$-canalizing functions, a recently introduced class of Boolean functions that contains the well-studied class of nested canalizing functions. The activities and sensitivity of a function quantify the impact of input changes on the function output. This paper generalizes the latter concept to $c$-sensitivity and provides formulas for the activities and $c$-sensitivity of general $k$-canalizing functions as well as canalizing functions with more precisely defined structure. A popular measure for the robustness of a network, the Derrida value, can be expressed as a weighted sum of the $c$-sensitivities of the governing canalizing functions, and can also be calculated for a stochastic extension of Boolean networks. These findings provide a computationally efficient way to obtain Derrida values of Boolean networks, deterministic or stochastic, that does not involve simulation.Comment: 16 pages, 2 figures, 3 table

Logical Reduction of Biological Networks to Their Most Determinative Components

Boolean networks have been widely used as models for gene regulatory networks, signal transduction networks, or neural networks, among many others. One of the main difficulties in analyzing the dynamics of a Boolean network and its sensitivity to perturbations or mutations is the fact that it grows exponentially with the number of nodes. Therefore, various approaches for simplifying the computations and reducing the network to a subset of relevant nodes have been proposed in the past few years. We consider a recently introduced method for reducing a Boolean network to its most determinative nodes that yield the highest information gain. The determinative power of a node is obtained by a summation of all mutual information quantities over all nodes having the chosen node as a common input, thus representing a measure of information gain obtained by the knowledge of the node under consideration. The determinative power of nodes has been considered in the literature under the assumption that the inputs are independent in which case one can use the Bahadur orthonormal basis. In this article, we relax that assumption and use a standard orthonormal basis instead. We use techniques of Hilbert space operators and harmonic analysis to generate formulas for the sensitivity to perturbations of nodes, quantified by the notions of influence, average sensitivity, and strength. Since we work on finite-dimensional spaces, our formulas and estimates can be and are formulated in plain matrix algebra terminology. We analyze the determinative power of nodes for a Boolean model of a signal transduction network of a generic fibroblast cell. We also show the similarities and differences induced by the alternative complete orthonormal basis used. Among the similarities, we mention the fact that the knowledge of the states of the most determinative nodes reduces the entropy or uncertainty of the overall network significantly. In a special case, we obtain a stronger result than in previous works, showing that a large information gain from a set of input nodes generates increased sensitivity to perturbations of those inputs

On abstraction refinement for program analyses in Datalog

A central task for a program analysis concerns how to efficiently find a program abstraction that keeps only information relevant for proving properties of interest. We present a new approach for finding such abstractions for program analyses written in Datalog. Our approach is based on counterexample-guided abstraction refinement: when a Datalog analysis run fails using an abstraction, it seeks to generalize the cause of the failure to other abstractions, and pick a new abstraction that avoids a similar failure. Our solution uses a boolean satisfiability formulation that is general, complete, and optimal: it is independent of the Datalog solver, it generalizes the failure of an abstraction to as many other abstractions as possible, and it identifies the cheapest refined abstraction to try next. We show the performance of our approach on a pointer analysis and a typestate analysis, on eight real-world Java benchmark programs