Temporal constrained objects for modelling neuronal dynamics

Background Several new programming languages and technologies have emerged in the past few decades in order to ease the task of modelling complex systems. Modelling the dynamics of complex systems requires various levels of abstractions and reductive measures in representing the underlying behaviour. This also often requires making a trade-off between how realistic a model should be in order to address the scientific questions of interest and the computational tractability of the model. Methods In this paper, we propose a novel programming paradigm, called temporal constrained objects, which facilitates a principled approach to modelling complex dynamical systems. Temporal constrained objects are an extension of constrained objects with a focus on the analysis and prediction of the dynamic behaviour of a system. The structural aspects of a neuronal system are represented using objects, as in object-oriented languages, while the dynamic behaviour of neurons and synapses are modelled using declarative temporal constraints. Computation in this paradigm is a process of constraint satisfaction within a time-based simulation. Results We identified the feasibility and practicality in automatically mapping different kinds of neuron and synapse models to the constraints of temporal constrained objects. Simple neuronal networks were modelled by composing circuit components, implicitly satisfying the internal constraints of each component and interface constraints of the composition. Simulations show that temporal constrained objects provide significant conciseness in the formulation of these models. The underlying computational engine employed here automatically finds the solutions to the problems stated, reducing the code for modelling and simulation control. All examples reported in this paper have been programmed and successfully tested using the prototype language called TCOB. The code along with the programming environment are available at http://github.com/compneuro/TCOB_Neuron. Discussion Temporal constrained objects provide powerful capabilities for modelling the structural and dynamic aspects of neural systems. Capabilities of the constraint programming paradigm, such as declarative specification, the ability to express partial information and non-directionality, and capabilities of the object-oriented paradigm especially aggregation and inheritance, make this paradigm the right candidate for complex systems and computational modelling studies. With the advent of multi-core parallel computer architectures and techniques or parallel constraint-solving, the paradigm of temporal constrained objects lends itself to highly efficient execution which is necessary for modelling and simulation of large brain circuits

Neurobiological mechanisms for language, symbols and concepts: Clues from brain-constrained deep neural networks

Neural networks are successfully used to imitate and model cognitive processes. However, to provide clues about the neurobiological mechanisms enabling human cognition, these models need to mimic the structure and function of real brains. Brain-constrained networks differ from classic neural networks by implementing brain similarities at different scales, ranging from the micro- and mesoscopic levels of neuronal function, local neuronal links and circuit interaction to large-scale anatomical structure and between-area connectivity. This review shows how brain-constrained neural networks can be applied to study in silico the formation of mechanisms for symbol and concept processing and to work towards neurobiological explanations of specifically human cognitive abilities. These include verbal working memory and learning of large vocabularies of symbols, semantic binding carried by specific areas of cortex, attention focusing and modulation driven by symbol type, and the acquisition of concrete and abstract concepts partly influenced by symbols. Neuronal assembly activity in the networks is analyzed to deliver putative mechanistic correlates of higher cognitive processes and to develop candidate explanations founded in established neurobiological principles

Evolutionary robotics and neuroscience

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Simulation of networks of spiking neurons: A review of tools and strategies

We review different aspects of the simulation of spiking neural networks. We start by reviewing the different types of simulation strategies and algorithms that are currently implemented. We next review the precision of those simulation strategies, in particular in cases where plasticity depends on the exact timing of the spikes. We overview different simulators and simulation environments presently available (restricted to those freely available, open source and documented). For each simulation tool, its advantages and pitfalls are reviewed, with an aim to allow the reader to identify which simulator is appropriate for a given task. Finally, we provide a series of benchmark simulations of different types of networks of spiking neurons, including Hodgkin-Huxley type, integrate-and-fire models, interacting with current-based or conductance-based synapses, using clock-driven or event-driven integration strategies. The same set of models are implemented on the different simulators, and the codes are made available. The ultimate goal of this review is to provide a resource to facilitate identifying the appropriate integration strategy and simulation tool to use for a given modeling problem related to spiking neural networks.Comment: 49 pages, 24 figures, 1 table; review article, Journal of Computational Neuroscience, in press (2007

Reading aloud boosts connectivity through the putamen

Functional neuroimaging and lesion studies have frequently reported thalamic and putamen activation during reading and speech production. However, it is currently unknown how activity in these structures interacts with that in other reading and speech production areas. This study investigates how reading aloud modulates the neuronal interactions between visual recognition and articulatory areas, when both the putamen and thalamus are explicitly included. Using dynamic causal modeling in skilled readers who were reading regularly spelled English words, we compared 27 possible pathways that might connect the ventral anterior occipito-temporal sulcus (aOT) to articulatory areas in the precentral cortex (PrC). We focused on whether the neuronal interactions within these pathways were increased by reading relative to picture naming and other visual and articulatory control conditions. The results provide strong evidence that reading boosts the aOT–PrC pathway via the putamen but not the thalamus. However, the putamen pathway was not exclusive because there was also evidence for another reading pathway that did not involve either the putamen or the thalamus. We conclude that the putamen plays a special role in reading but this is likely to vary with individual reading preferences and strategies

Modelling the Developing Mind: From Structure to Change

This paper presents a theory of cognitive change. The theory assumes that the fundamental causes of cognitive change reside in the architecture of mind. Thus, the architecture of mind as specified by the theory is described first. It is assumed that the mind is a three-level universe involving (1) a processing system that constrains processing potentials, (2) a set of specialized capacity systems that guide understanding of different reality and knowledge domains, and (3) a hypecognitive system that monitors and controls the functioning of all other systems. The paper then specifies the types of change that may occur in cognitive development (changes within the levels of mind, changes in the relations between structures across levels, changes in the efficiency of a structure) and a series of general (e.g., metarepresentation) and more specific mechanisms (e.g., bridging, interweaving, and fusion) that bring the changes about. It is argued that different types of change require different mechanisms. Finally, a general model of the nature of cognitive development is offered. The relations between the theory proposed in the paper and other theories and research in cognitive development and cognitive neuroscience is discussed throughout the paper

Perspectives on Multi-Level Dynamics

As Physics did in previous centuries, there is currently a common dream of extracting generic laws of nature in economics, sociology, neuroscience, by focalising the description of phenomena to a minimal set of variables and parameters, linked together by causal equations of evolution whose structure may reveal hidden principles. This requires a huge reduction of dimensionality (number of degrees of freedom) and a change in the level of description. Beyond the mere necessity of developing accurate techniques affording this reduction, there is the question of the correspondence between the initial system and the reduced one. In this paper, we offer a perspective towards a common framework for discussing and understanding multi-level systems exhibiting structures at various spatial and temporal levels. We propose a common foundation and illustrate it with examples from different fields. We also point out the difficulties in constructing such a general setting and its limitations