Related papers: Modular control of Boolean network models
Novel imaging and neurostimulation techniques open doors for advancements in closed-loop control of activity in biological neural networks. This would allow for applications in the investigation of activity propagation, and for diagnosis…
Cells are regulated by networks of controllers having many targets, and targets affected by many controllers, but these "many-to-many" combinatorial control systems are poorly understood. Here we analyze distinct cellular networks…
Training a Neural Network (NN) with lots of parameters or intricate architectures creates undesired phenomena that complicate the optimization process. To address this issue we propose a first modular approach to NN design, wherein the NN…
Layered neural networks have greatly improved the performance of various applications including image processing, speech recognition, natural language processing, and bioinformatics. However, it is still difficult to discover or interpret…
In this paper, we develop a modular design method of decentralized controllers for linear dynamical network systems, where multiple subcontroller designers aim at individually regulating their local control performance with accessibility…
This paper presents a novel framework for the modeling of biological networks. It makes use of recent tools analyzing the robust satisfaction of properties of (hybrid) dynamical systems. The main challenge of this approach as applied to…
Models of biochemical networks are frequently high-dimensional and complex. Reduction methods that preserve important dynamical properties are therefore essential in their study. Interactions between the nodes in such networks are…
Identifying features of molecular regulatory networks is an important problem in systems biology. It has been shown that the combinatorial logic of such networks can be captured in many cases by special functions called nested canalyzing in…
The determination and classification of fixed points of large Boolean networks is addressed in terms of constraint satisfaction problem. We develop a general simplification scheme that, removing all those variables and functions belonging…
Boolean networks are powerful frameworks for capturing the logic of gene-regulatory circuits, yet their combinatorial explosion hampers exhaustive analyses. Here, we present a systematic reduction of a 31-node Boolean model that describes…
Complex systems are successfully reduced to interacting elements via the network concept. Transport plays a key role in the survival of networks. For example the specialized signaling cascades of cellular networks filter noise and…
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
The study of cellular signalling pathways and their deregulation in disease states, such as cancer, is a large and extremely complex task. Indeed, these systems involve many parts and processes but are studied piecewise and their…
Numerous real-world systems can be naturally modeled as multilayer networks, enabling an efficient way to characterize those complex systems. Much evidence in the context of system biology indicated that the collections between different…
Biological networks are one of the most studied object in computational biology. Several methods have been developed for studying qualitative properties of biological networks. Last decade had seen the improvement of molecular techniques…
Objective. Precise control of neural systems is essential to experimental investigations of how the brain controls behavior and holds the potential for therapeutic manipulations to correct aberrant network states. Model predictive control,…
Boolean networks have long been used as models of molecular networks and play an increasingly important role in systems biology. This paper describes a software package, Polynome, offered as a web service, that helps users construct Boolean…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
This paper investigates questions related to the modularity in discrete models of biological interaction networks. We develop a theoretical framework based on the analysis of their asymptotic dynamics. More precisely, we exhibit formal…
Boolean networks are special types of finite state time-discrete dynamical systems. A Boolean network can be described by a function from an n-dimensional vector space over the field of two elements to itself. A fundamental problem in…