Brian2CUDA: Flexible and Efficient Simulation of Spiking Neural Network Models on GPUs.

Graphics processing units (GPUs) are widely available and have been used with great success to accelerate scientific computing in the last decade. These advances, however, are often not available to researchers interested in simulating spiking neural networks, but lacking the technical knowledge to write the necessary low-level code. Writing low-level code is not necessary when using the popular Brian simulator, which provides a framework to generate efficient CPU code from high-level model definitions in Python. Here, we present Brian2CUDA, an open-source software that extends the Brian simulator with a GPU backend. Our implementation generates efficient code for the numerical integration of neuronal states and for the propagation of synaptic events on GPUs, making use of their massively parallel arithmetic capabilities. We benchmark the performance improvements of our software for several model types and find that it can accelerate simulations by up to three orders of magnitude compared to Brian's CPU backend. Currently, Brian2CUDA is the only package that supports Brian's full feature set on GPUs, including arbitrary neuron and synapse models, plasticity rules, and heterogeneous delays. When comparing its performance with Brian2GeNN, another GPU-based backend for the Brian simulator with fewer features, we find that Brian2CUDA gives comparable speedups, while being typically slower for small and faster for large networks. By combining the flexibility of the Brian simulator with the simulation speed of GPUs, Brian2CUDA enables researchers to efficiently simulate spiking neural networks with minimal effort and thereby makes the advancements of GPU computing available to a larger audience of neuroscientists.

Hebbian plasticity in parallel synaptic pathways: A circuit mechanism for systems memory consolidation.

Systems memory consolidation involves the transfer of memories across brain regions and the transformation of memory content. For example, declarative memories that transiently depend on the hippocampal formation are transformed into long-term memory traces in neocortical networks, and procedural memories are transformed within cortico-striatal networks. These consolidation processes are thought to rely on replay and repetition of recently acquired memories, but the cellular and network mechanisms that mediate the changes of memories are poorly understood. Here, we suggest that systems memory consolidation could arise from Hebbian plasticity in networks with parallel synaptic pathways-two ubiquitous features of neural circuits in the brain. We explore this hypothesis in the context of hippocampus-dependent memories. Using computational models and mathematical analyses, we illustrate how memories are transferred across circuits and discuss why their representations could change. The analyses suggest that Hebbian plasticity mediates consolidation by transferring a linear approximation of a previously acquired memory into a parallel pathway. Our modelling results are further in quantitative agreement with lesion studies in rodents. Moreover, a hierarchical iteration of the mechanism yields power-law forgetting-as observed in psychophysical studies in humans. The predicted circuit mechanism thus bridges spatial scales from single cells to cortical areas and time scales from milliseconds to years.