Boolean dynamics revisited through feedback interconnections

Boolean models of physical or biological systems describe the global dynamics of the system and their attractors typically represent asymptotic behaviors. In the case of large networks composed of several modules, it may be difficult to identify all the attractors. To explore Boolean dynamics from a novel viewpoint, we will analyse the dynamics emerging from the composition of two known Boolean modules. The state transition graphs and attractors for each of the modules can be combined to construct a new asymptotic graph which will (1) provide a reliable method for attractor computation with partial information; (2) illustrate the differences in dynamical behavior induced by the updating strategy (asynchronous, synchronous, or mixed); and (3) show the inherited organization/structure of the original network’s state transition graph.publishe

Uncovering operational interactions in genetic networks using asynchronous boolean dynamics

To analyze and gain intuition on the mechanisms of complex systems of large dimensions, one strategy is to simplify the model by identifying a reduced system, in the form of a smaller set of variables and interactions that still capture specific properties of the system. For large models of biological networks, the diagram of interactions is often well represented by a Boolean model with a family of logical rules. The state space of a Boolean model is finite, and its asynchronous dynamics are fully described by a transition graph in the state space. In this context, a method will be developed for identifying the active or operational interactions responsible for a given dynamic behaviour. The first step in this procedure is the decomposition of the asynchronous transition graph into its strongly connected components, to obtain a ``reduced'' and hierarchically organized graph of transitions. The second step consists of the identification of a partial graph of interactions and a sub-family of logical rules that remain operational in a given region of the state space. This model reduction method and its usefulness are illustrated by an application to a model of programmed cell death. The method identifies two mechanisms used by the cell to respond to death-receptor stimulation and decide between the survival or apoptotic pathways

Relating bisimulations with attractors in boolean network models

When studying a biological regulatory network, it is usual to use boolean network models. In these models, boolean variables represent the behavior of each component of the biological system. Taking in account that the size of these state transition models grows exponentially along with the number of components considered, it becomes important to have tools to minimize such models. In this paper, we relate bisimulations, which are relations used in the study of automata (general state transition models) with attractors, which are an important feature of biological boolean models. Hence, we support the idea that bisimulations can be important tools in the study some main features of boolean network models.We also discuss the differences between using this approach and other well-known methodologies to study this kind of systems and we illustrate it with some examples

A Theory of Cortical Neural Processing.

This dissertation puts forth an original theory of cortical neural processing that is unique in its view of the interplay of chaotic and stable oscillatory neurodynamics and is meant to stimulate new ideas in artificial neural network modeling. Our theory is the first to suggest two new purposes for chaotic neurodynamics: (i) as a natural means of representing the uncertainty in the outcome of performed tasks, such as memory retrieval or classification, and (ii) as an automatic way of producing an economic representation of distributed information. We developed new models, to better understand how the cerebral cortex processes information, which led to our theory. Common to these models is a neuron interaction function that alternates between excitatory and inhibitory neighborhoods. Our theory allows characteristics of the input environment to influence the structural development of the cortex. We view low intensity chaotic activity as the a priori uncertain base condition of the cortex, resulting from the interaction of a multitude of stronger potential responses. Data, distinguishing one response from many others, drives bifurcations back toward the direction of less complex (stable) behavior. Stability appears as temporary bubble-like clusters within the boundaries of cortical columns and begins to propagate through frequency sensitive and non-specific neurons. But this is limited by destabilizing long-path connections. An original model of the post-natal development of ocular dominance columns in the striate cortex is presented and compared to autoradiographic images from the literature with good matching results. Finally, experiments are shown to favor computed update order over traditional approaches for better performance of the pattern completion process

Uncovering operational interactions in genetic networks using asynchronous boolean dynamics

To analyze and gain intuition on the mechanisms of complex systems of large dimensions, one strategy is to simplify the model by identifying a reduced system, in the form of a smaller set of variables and interactions that still capture specific properties of the system. For large models of biological networks, the diagram of interactions is often well represented by a Boolean model with a family of logical rules. The state space of a Boolean model is finite, and its asynchronous dynamics are fully described by a transition graph in the state space. In this context, a method will be developed for identifying the active or operational interactions responsible for a given dynamic behaviour. The first step in this procedure is the decomposition of the asynchronous transition graph into its strongly connected components, to obtain a ``reduced'' and hierarchically organized graph of transitions. The second step consists of the identification of a partial graph of interactions and a sub-family of logical rules that remain operational in a given region of the state space. This model reduction method and its usefulness are illustrated by an application to a model of programmed cell death. The method identifies two mechanisms used by the cell to respond to death-receptor stimulation and decide between the survival or apoptotic pathways