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

The Mental Database

This article uses database, evolution and physics considerations to suggest how the mind stores and processes its data. Its innovations in its approach lie in:- A) The comparison between the capabilities of the mind to those of a modern relational database while conserving phenomenality. The strong functional similarity of the two systems leads to the conclusion that the mind may be profitably described as being a mental database. The need for material/mental bridging and addressing indexes is discussed. B) The consideration of what neural correlates of consciousness (NCC) between sensorimotor data and instrumented observation one can hope to obtain using current biophysics. It is deduced that what is seen using the various brain scanning methods reflects only that part of current activity transactions (e.g. visualizing) which update and interrogate the mind, but not the contents of the integrated mental database which constitutes the mind itself. This approach yields reasons why there is much neural activity in an area to which a conscious function is ascribed (e.g. the amygdala is associated with fear), yet there is no visible part of its activity which can be clearly identified as phenomenal. The concept is then situated in a Penrosian expanded physical environment, requiring evolutionary continuity, modularity and phenomenality.Several novel Darwinian advantages arising from the approach are described

Machine learning-guided directed evolution for protein engineering

Machine learning (ML)-guided directed evolution is a new paradigm for biological design that enables optimization of complex functions. ML methods use data to predict how sequence maps to function without requiring a detailed model of the underlying physics or biological pathways. To demonstrate ML-guided directed evolution, we introduce the steps required to build ML sequence-function models and use them to guide engineering, making recommendations at each stage. This review covers basic concepts relevant to using ML for protein engineering as well as the current literature and applications of this new engineering paradigm. ML methods accelerate directed evolution by learning from information contained in all measured variants and using that information to select sequences that are likely to be improved. We then provide two case studies that demonstrate the ML-guided directed evolution process. We also look to future opportunities where ML will enable discovery of new protein functions and uncover the relationship between protein sequence and function.Comment: Made significant revisions to focus on aspects most relevant to applying machine learning to speed up directed evolutio