GeNN: a code generation framework for accelerated brain simulations

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/

Fast Simulations of Highly-Connected Spiking Cortical Models Using GPUs

Over the past decade there has been a growing interest in the development of parallel hardware systems for simulating large-scale networks of spiking neurons. Compared to other highly-parallel systems, GPU-accelerated solutions have the advantage of a relatively low cost and a great versatility, thanks also to the possibility of using the CUDA-C/C++ programming languages. NeuronGPU is a GPU library for large-scale simulations of spiking neural network models, written in the C++ and CUDA-C++ programming languages, based on a novel spike-delivery algorithm. This library includes simple LIF (leaky-integrate-and-fire) neuron models as well as several multisynapse AdEx (adaptive-exponential-integrate-and-fire) neuron models with current or conductance based synapses, different types of spike generators, tools for recording spikes, state variables and parameters, and it supports user-definable models. The numerical solution of the differential equations of the dynamics of the AdEx models is performed through a parallel implementation, written in CUDA-C++, of the fifth-order Runge-Kutta method with adaptive step-size control. In this work we evaluate the performance of this library on the simulation of a cortical microcircuit model, based on LIF neurons and current-based synapses, and on balanced networks of excitatory and inhibitory neurons, using AdEx or Izhikevich neuron models and conductance-based or current-based synapses. On these models, we will show that the proposed library achieves state-of-the-art performance in terms of simulation time per second of biological activity. In particular, using a single NVIDIA GeForce RTX 2080 Ti GPU board, the full-scale cortical-microcircuit model, which includes about 77,000 neurons and 3 · 108 connections, can be simulated at a speed very close to real time, while the simulation time of a balanced network of 1,000,000 AdEx neurons with 1,000 connections per neuron was about 70 s per second of biological activity

Bio-Inspired Stereo Vision Calibration for Dynamic Vision Sensors

Many advances have been made in the eld of computer vision. Several recent research trends have focused on mimicking human vision by using a stereo vision system. In multi-camera systems, a calibration process is usually implemented to improve the results accuracy. However, these systems generate a large amount of data to be processed; therefore, a powerful computer is required and, in many cases, this cannot be done in real time. Neuromorphic Engineering attempts to create bio-inspired systems that mimic the information processing that takes place in the human brain. This information is encoded using pulses (or spikes) and the generated systems are much simpler (in computational operations and resources), which allows them to perform similar tasks with much lower power consumption, thus these processes can be developed over specialized hardware with real-time processing. In this work, a bio-inspired stereovision system is presented, where a calibration mechanism for this system is implemented and evaluated using several tests. The result is a novel calibration technique for a neuromorphic stereo vision system, implemented over specialized hardware (FPGA - Field-Programmable Gate Array), which allows obtaining reduced latencies on hardware implementation for stand-alone systems, and working in real time.Ministerio de Economía y Competitividad TEC2016-77785-PMinisterio de Economía y Competitividad TIN2016-80644-

Computational Modeling of Biological Neural Networks on GPUs: Strategies and Performance

Simulating biological neural networks is an important task for computational neuroscientists attempting to model and analyze brain activity and function. As these networks become larger and more complex, the computational power required grows significantly, often requiring the use of supercomputers or compute clusters. An emerging low-cost, highly accessible alternative to many of these resources is the Graphics Processing Unit (GPU) - specialized massively-parallel graphics hardware that has seen increasing use as a general purpose computational accelerator thanks largely due to NVIDIA\u27s CUDA programming interface. We evaluated the relative benefits and limitations of GPU-based tools for large-scale neural network simulation and analysis, first by developing an agent-inspired spiking neural network simulator then by adapting a neural signal decoding algorithm. Under certain network configurations, the simulator was able to outperform an equivalent MPI-based parallel implementation run on a dedicated compute cluster, while the decoding algorithm implementation consistently outperformed its serial counterpart. Additionally, the GPU-based simulator was able to readily visualize network spiking activity in real-time due to the close integration with standard computer graphics APIs. The GPU was shown to provide significant performance benefits under certain circumstances while lagging behind in others. Given the complex nature of these research tasks, a hybrid strategy that combines GPU- and CPU-based approaches provides greater performance than either separately

SpiNNaker - A Spiking Neural Network Architecture

20 years in conception and 15 in construction, the SpiNNaker project has delivered the world’s largest neuromorphic computing platform incorporating over a million ARM mobile phone processors and capable of modelling spiking neural networks of the scale of a mouse brain in biological real time. This machine, hosted at the University of Manchester in the UK, is freely available under the auspices of the EU Flagship Human Brain Project. This book tells the story of the origins of the machine, its development and its deployment, and the immense software development effort that has gone into making it openly available and accessible to researchers and students the world over. It also presents exemplar applications from ‘Talk’, a SpiNNaker-controlled robotic exhibit at the Manchester Art Gallery as part of ‘The Imitation Game’, a set of works commissioned in 2016 in honour of Alan Turing, through to a way to solve hard computing problems using stochastic neural networks. The book concludes with a look to the future, and the SpiNNaker-2 machine which is yet to come

DART: Distribution Aware Retinal Transform for Event-based Cameras

We introduce a generic visual descriptor, termed as distribution aware retinal transform (DART), that encodes the structural context using log-polar grids for event cameras. The DART descriptor is applied to four different problems, namely object classification, tracking, detection and feature matching: (1) The DART features are directly employed as local descriptors in a bag-of-features classification framework and testing is carried out on four standard event-based object datasets (N-MNIST, MNIST-DVS, CIFAR10-DVS, NCaltech-101). (2) Extending the classification system, tracking is demonstrated using two key novelties: (i) For overcoming the low-sample problem for the one-shot learning of a binary classifier, statistical bootstrapping is leveraged with online learning; (ii) To achieve tracker robustness, the scale and rotation equivariance property of the DART descriptors is exploited for the one-shot learning. (3) To solve the long-term object tracking problem, an object detector is designed using the principle of cluster majority voting. The detection scheme is then combined with the tracker to result in a high intersection-over-union score with augmented ground truth annotations on the publicly available event camera dataset. (4) Finally, the event context encoded by DART greatly simplifies the feature correspondence problem, especially for spatio-temporal slices far apart in time, which has not been explicitly tackled in the event-based vision domain.Comment: 12 pages, revision submitted to TPAMI in Nov 201

Toward Building Hybrid Biological/in silico Neural Networks for Motor Neuroprosthetic Control

WOS: 000370402900001PubMed ID: 26321943In this article, we introduce the Bioinspired Neuroprosthetic Design Environment (BNDE) as a practical platform for the development of novel brain-machine interface (BMI) controllers, which are based on spiking model neurons. We built the BNDE around a hard real-time system so that it is capable of creating simulated synapses from extra-cellularly recorded neurons to model neurons. In order to evaluate the practicality of the BNDE for neuroprosthetic control experiments, a novel, adaptive BMI controller was developed and tested using real-time closed-loop simulations. The present controller consists of two in silico medium spiny neurons, which receive simulated synaptic inputs from recorded motor cortical neurons. In the closed-loop simulations, the recordings from the cortical neurons were imitated using an external, hardware-based neural signal synthesizer. By implementing a reward-modulated spike timing-dependent plasticity rule, the controller achieved perfect target reach accuracy for a two-target reaching task in one-dimensional space. The BNDE combines the flexibility of software-based spiking neural network (SNN) simulations with powerful online data visualization tools and is a low-cost, PC-based, and all-in-one solution for developing neurally inspired BMI controllers. We believe that the BNDE is the first implementation, which is capable of creating hybrid biological/in silico neural networks for motor neuroprosthetic control and utilizes multiple CPU cores for computationally intensive real-time SNN simulations.Bogazici University BAP Grants [10XD3]; Bogazici University Life Sciences and Technologies Research Center [09K120520]This research was supported by Bogazici University BAP Grants #10XD3 and Bogazici University Life Sciences and Technologies Research Center #09K120520