Distributed classifier based on genetically engineered bacterial cell cultures

We describe a conceptual design of a distributed classifier formed by a population of genetically engineered microbial cells. The central idea is to create a complex classifier from a population of weak or simple classifiers. We create a master population of cells with randomized synthetic biosensor circuits that have a broad range of sensitivities towards chemical signals of interest that form the input vectors subject to classification. The randomized sensitivities are achieved by constructing a library of synthetic gene circuits with randomized control sequences (e.g. ribosome-binding sites) in the front element. The training procedure consists in re-shaping of the master population in such a way that it collectively responds to the "positive" patterns of input signals by producing above-threshold output (e.g. fluorescent signal), and below-threshold output in case of the "negative" patterns. The population re-shaping is achieved by presenting sequential examples and pruning the population using either graded selection/counterselection or by fluorescence-activated cell sorting (FACS). We demonstrate the feasibility of experimental implementation of such system computationally using a realistic model of the synthetic sensing gene circuits.Comment: 31 pages, 9 figure

Nonlinear Hebbian learning as a unifying principle in receptive field formation

The development of sensory receptive fields has been modeled in the past by a variety of models including normative models such as sparse coding or independent component analysis and bottom-up models such as spike-timing dependent plasticity or the Bienenstock-Cooper-Munro model of synaptic plasticity. Here we show that the above variety of approaches can all be unified into a single common principle, namely Nonlinear Hebbian Learning. When Nonlinear Hebbian Learning is applied to natural images, receptive field shapes were strongly constrained by the input statistics and preprocessing, but exhibited only modest variation across different choices of nonlinearities in neuron models or synaptic plasticity rules. Neither overcompleteness nor sparse network activity are necessary for the development of localized receptive fields. The analysis of alternative sensory modalities such as auditory models or V2 development lead to the same conclusions. In all examples, receptive fields can be predicted a priori by reformulating an abstract model as nonlinear Hebbian learning. Thus nonlinear Hebbian learning and natural statistics can account for many aspects of receptive field formation across models and sensory modalities

Evolution and Analysis of Embodied Spiking Neural Networks Reveals Task-Specific Clusters of Effective Networks

Elucidating principles that underlie computation in neural networks is currently a major research topic of interest in neuroscience. Transfer Entropy (TE) is increasingly used as a tool to bridge the gap between network structure, function, and behavior in fMRI studies. Computational models allow us to bridge the gap even further by directly associating individual neuron activity with behavior. However, most computational models that have analyzed embodied behaviors have employed non-spiking neurons. On the other hand, computational models that employ spiking neural networks tend to be restricted to disembodied tasks. We show for the first time the artificial evolution and TE-analysis of embodied spiking neural networks to perform a cognitively-interesting behavior. Specifically, we evolved an agent controlled by an Izhikevich neural network to perform a visual categorization task. The smallest networks capable of performing the task were found by repeating evolutionary runs with different network sizes. Informational analysis of the best solution revealed task-specific TE-network clusters, suggesting that within-task homogeneity and across-task heterogeneity were key to behavioral success. Moreover, analysis of the ensemble of solutions revealed that task-specificity of TE-network clusters correlated with fitness. This provides an empirically testable hypothesis that links network structure to behavior.Comment: Camera ready version of accepted for GECCO'1

Knowing one's place: a free-energy approach to pattern regulation.

Understanding how organisms establish their form during embryogenesis and regeneration represents a major knowledge gap in biological pattern formation. It has been recently suggested that morphogenesis could be understood in terms of cellular information processing and the ability of cell groups to model shape. Here, we offer a proof of principle that self-assembly is an emergent property of cells that share a common (genetic and epigenetic) model of organismal form. This behaviour is formulated in terms of variational free-energy minimization-of the sort that has been used to explain action and perception in neuroscience. In brief, casting the minimization of thermodynamic free energy in terms of variational free energy allows one to interpret (the dynamics of) a system as inferring the causes of its inputs-and acting to resolve uncertainty about those causes. This novel perspective on the coordination of migration and differentiation of cells suggests an interpretation of genetic codes as parametrizing a generative model-predicting the signals sensed by cells in the target morphology-and epigenetic processes as the subsequent inversion of that model. This theoretical formulation may complement bottom-up strategies-that currently focus on molecular pathways-with (constructivist) top-down approaches that have proved themselves in neuroscience and cybernetics