An Open Pipeline for Generating Executable Neural Circuits from Fruit Fly Brain Data

Lev E. Givon
Despite considerable progress in mapping the fly's connectome and elucidating the patterns of information flow in its brain, the complexity of the fly brain's structure and the still-incomplete state of knowledge regarding its neural circuitry pose significant challenges beyond satisfying the computational resource requirements of current fly brain models that must be addressed to successfully reverse the information processing capabilities of the fly brain. These include the need to explicitly
more » ... need to explicitly facilitate collaborative development of brain models by combining the efforts of multiple researchers, and the need to enable programmatic generation of brain models that effectively utilize the burgeoning amount of increasingly detailed publicly available fly connectome data. This thesis presents an open pipeline for modular construction of executable models of the fruit fly brain from incomplete biological brain data that addresses both of the above requirements. This pipeline consists of two major open-source components respectively called Neurokernel and NeuroArch. Neurokernel is a framework for collaborative construction of executable connectome-based fly brain models by integration of independently developed models of different functional units in the brain into a single emulation that can be executed upon multiple Graphics Processing Units (GPUs). Neurokernel enforces a programming model that enables functional unit models that comply with its interface requirements to communicate during execution regardless of their internal design. We demonstrate the power of this programming model by using it to integrate independently developed models of the fly retina and lamina into a single vision processing system. We also show how Neurokernel's communication performance can scale over multiple GPUs, number of functional units in a brain emulation, and over the number of communication ports exposed by a functional unit model. Although the increasing amount of experimentally obtained biological data regardin [...]
doi:10.7916/d8p26z34 fatcat:jdzz7q2p7zaw5plfuyrara5hxq