How cognitive neural systems process information is largely unknown, in part because of how difficult it is to accurately follow the flow of information from sensors via neurons to actuators. Measuring the flow of information is different from measuring correlations between firing neurons, for which several measures are available, foremost among them the Shannon information, which is an undirected measure. Several information-theoretic notions of “directed information” have been used to successfully detect the flow of information in some systems, in particular in the neuroscience community. However, recent work has shown that directed information measures such as transfer entropy can sometimes inadequately estimate information flow, or even fail to identify manifest directed influences, especially if neurons contribute in a cryptographic manner to influence the effector neuron. Because it is unclear how often such cryptic influences emerge in cognitive systems, the usefulness of transfer entropy measures to reconstruct information flow is unknown. Here, we test how often cryptographic logic emerges in an evolutionary process that generates artificial neural circuits for two fundamental cognitive tasks (motion detection and sound localization). Besides counting the frequency of problematic logic gates, we also test whether transfer entropy applied to an activity time-series recorded from behaving digital brains can infer information flow, compared to a ground-truth model of direct influence constructed from connectivity and circuit logic. Our results suggest that transfer entropy will sometimes fail to infer directed information when it exists, and sometimes suggest a causal connection when there is none. However, the extent of incorrect inference strongly depends on the cognitive task considered. These results emphasize the importance of understanding the fundamental logic processes that contribute to information flow in cognitive processing, and quantifying their relevance in any given nervous system.
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