Automatic linearity detection

Given a function, or more generally an operator, the question "Is it linear?" seems simple to answer. In many applications of scientific computing it might be worth determining the answer to this question in an automated way; some functionality, such as operator exponentiation, is only defined for linear operators, and in other problems, time saving is available if it is known that the problem being solved is linear. Linearity detection is closely connected to sparsity detection of Hessians, so for large-scale applications, memory savings can be made if linearity information is known. However, implementing such an automated detection is not as straightforward as one might expect. This paper describes how automatic linearity detection can be implemented in combination with automatic differentiation, both for standard scientific computing software, and within the Chebfun software system. The key ingredients for the method are the observation that linear operators have constant derivatives, and the propagation of two logical vectors, $\ell$ and $c$, as computations are carried out. The values of $\ell$ and $c$ are determined by whether output variables have constant derivatives and constant values with respect to each input variable. The propagation of their values through an evaluation trace of an operator yields the desired information about the linearity of that operator

On the Complexity of Solving Quadratic Boolean Systems

A fundamental problem in computer science is to find all the common zeroes of $m$ quadratic polynomials in $n$ unknowns over $\mathbb{F}_2$. The cryptanalysis of several modern ciphers reduces to this problem. Up to now, the best complexity bound was reached by an exhaustive search in $4\log_2 n\,2^n$ operations. We give an algorithm that reduces the problem to a combination of exhaustive search and sparse linear algebra. This algorithm has several variants depending on the method used for the linear algebra step. Under precise algebraic assumptions on the input system, we show that the deterministic variant of our algorithm has complexity bounded by $O(2^{0.841n})$ when $m=n$, while a probabilistic variant of the Las Vegas type has expected complexity $O(2^{0.792n})$. Experiments on random systems show that the algebraic assumptions are satisfied with probability very close to~1. We also give a rough estimate for the actual threshold between our method and exhaustive search, which is as low as~200, and thus very relevant for cryptographic applications.Comment: 25 page

Identification of control targets in Boolean molecular network models via computational algebra

Motivation: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into another, more desirable, state through an intervention, such as a drug or other therapeutic treatment. The identification of such strategies is typically based on a mathematical model of the process to be altered through targeted control inputs. This paper focuses on processes at the molecular level that determine the state of an individual cell, involving signaling or gene regulation. The mathematical model type considered is that of Boolean networks. The potential control targets can be represented by a set of nodes and edges that can be manipulated to produce a desired effect on the system. Experimentally, node manipulation requires technology to completely repress or fully activate a particular gene product while edge manipulations only require a drug that inactivates the interaction between two gene products. Results: This paper presents a method for the identification of potential intervention targets in Boolean molecular network models using algebraic techniques. The approach exploits an algebraic representation of Boolean networks to encode the control candidates in the network wiring diagram as the solutions of a system of polynomials equations, and then uses computational algebra techniques to find such controllers. The control methods in this paper are validated through the identification of combinatorial interventions in the signaling pathways of previously reported control targets in two well studied systems, a p53-mdm2 network and a blood T cell lymphocyte granular leukemia survival signaling network.Comment: 12 pages, 4 figures, 2 table

Quantum adiabatic optimization and combinatorial landscapes

In this paper we analyze the performance of the Quantum Adiabatic Evolution algorithm on a variant of Satisfiability problem for an ensemble of random graphs parametrized by the ratio of clauses to variables, $\gamma=M/N$. We introduce a set of macroscopic parameters (landscapes) and put forward an ansatz of universality for random bit flips. We then formulate the problem of finding the smallest eigenvalue and the excitation gap as a statistical mechanics problem. We use the so-called annealing approximation with a refinement that a finite set of macroscopic variables (versus only energy) is used, and are able to show the existence of a dynamic threshold $\gamma=\gamma_d$ starting with some value of K -- the number of variables in each clause. Beyond dynamic threshold, the algorithm should take exponentially long time to find a solution. We compare the results for extended and simplified sets of landscapes and provide numerical evidence in support of our universality ansatz. We have been able to map the ensemble of random graphs onto another ensemble with fluctuations significantly reduced. This enabled us to obtain tight upper bounds on satisfiability transition and to recompute the dynamical transition using the extended set of landscapes.Comment: 41 pages, 10 figures; added a paragraph on paper's organization to the introduction, fixed reference

A Mathematical Framework for Agent Based Models of Complex Biological Networks

Agent-based modeling and simulation is a useful method to study biological phenomena in a wide range of fields, from molecular biology to ecology. Since there is currently no agreed-upon standard way to specify such models it is not always easy to use published models. Also, since model descriptions are not usually given in mathematical terms, it is difficult to bring mathematical analysis tools to bear, so that models are typically studied through simulation. In order to address this issue, Grimm et al. proposed a protocol for model specification, the so-called ODD protocol, which provides a standard way to describe models. This paper proposes an addition to the ODD protocol which allows the description of an agent-based model as a dynamical system, which provides access to computational and theoretical tools for its analysis. The mathematical framework is that of algebraic models, that is, time-discrete dynamical systems with algebraic structure. It is shown by way of several examples how this mathematical specification can help with model analysis.Comment: To appear in Bulletin of Mathematical Biolog