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Inspired by Solomonoffs theory of inductive inference, we propose a prior based on circuit complexity. There are several advantages to this approach. First, it relies on a complexity measure that does not depend on the choice of UTM. There…
Efficient consistency maintenance of incomplete and dynamic real-life databases is a quality label for further data analysis. In prior work, we tackled the generic problem of database updating in the presence of tuple generating constraints…
Random Boolean networks were introduced in 1969 by Kauffman as a model for gene regulation. By combining analytical arguments and efficient numerical simulations, we evaluate the properties of relevant components of critical random Boolean…
Dynamic complexity is concerned with updating the output of a problem when the input is slightly changed. We study the dynamic complexity of Dyck reachability problems in directed and undirected graphs, where updates may add or delete…
Boolean networks can be viewed as functions on the set of binary strings of a given length, described via logical rules. They were introduced as dynamic models into biology, in particular as logical models of intracellular regulatory…
We prove that the fully asynchronous dynamics of a Boolean network $f:\{0,1\}^n\to\{0,1\}^n$ without negative loop can be simulated, in a very specific way, by a monotone Boolean network with $2n$ components. We then use this result to…
Understanding control mechanisms in biological systems plays a crucial role in important applications, for instance in cell reprogramming. Boolean modeling allows the identification of possible efficient strategies, helping to reduce the…
In this paper we investigate formal verification problems for Neural Network computations. Various reachability problems will be in the focus, such as: Given symbolic specifications of allowed inputs and outputs in form of Linear…
This paper characterizes the attractor structure of synchronous and asynchronous Boolean networks induced by bi-threshold functions. Bi-threshold functions are generalizations of classical threshold functions and have separate threshold…
Automata networks are mappings of the form f : Q Z $\rightarrow$ Q Z , where Q is a finite alphabet and Z is a set of entities; they generalise Cellular Automata and Boolean networks. An update schedule dictates when each entity updates its…
Feedback loops in a dynamic network play an important role in determining the dynamics of that network. Through a computational study, in this paper we show that networks with fewer independent negative feedback loops tend to exhibit more…
The complex dynamics of gene expression in living cells can be well-approximated using Boolean networks. The average sensitivity is a natural measure of stability in these systems: values below one indicate typically stable dynamics…
We construct and investigate Boolean networks that follow a given reliable trajectory in state space, which is insensitive to fluctuations in the updating schedule, and which is also robust against noise. Robustness is quantified as the…
In arXiv:1710.08163 a generalization of Boolean circuits to arbitrary finite algebras had been introduced and applied to sketch P versus NP-complete borderline for circuits satisfiability over algebras from congruence modular varieties.…
This Thesis presents research at the boundary between Statistical Physics and Biology. First, we have devised a class of Boolean constraint satisfaction problems (CSP) whose solutions describe the feasible operational states of a chemical…
In this paper, we investigate the problem of controlling probabilistic Boolean control networks (PBCNs) to achieve reachability with maximum probability in the finite time horizon. We address three questions: 1) finding control policies…
This paper studies the fundamental problem of how to reroute $k$ unsplittable flows of a certain demand in a capacitated network from their current paths to their respective new paths, in a congestion-free manner and fast. This scheduling…
We introduce a new threshold model of social networks, in which the nodes influenced by their neighbours can adopt one out of several alternatives. We characterize social networks for which adoption of a product by the whole network is…
The problem of constructing hazard-free Boolean circuits dates back to the 1940s and is an important problem in circuit design. Our main lower-bound result unconditionally shows the existence of functions whose circuit complexity is…
We develop a general method to explore how the function performed by a biological network can constrain both its structural and dynamical network properties. This approach is orthogonal to prior studies which examine the functional…