A System-on-Chip Based Hybrid Neuromorphic Compute Node Architecture for Reproducible Hyper-Real-Time Simulations of Spiking Neural Networks.

Despite the great strides neuroscience has made in recent decades, the underlying principles of brain function remain largely unknown. Advancing the field strongly depends on the ability to study large-scale neural networks and perform complex simulations. In this context, simulations in hyper-real-time are of high interest, as they would enable both comprehensive parameter scans and the study of slow processes, such as learning and long-term memory. Not even the fastest supercomputer available today is able to meet the challenge of accurate and reproducible simulation with hyper-real acceleration. The development of novel neuromorphic computer architectures holds out promise, but the high costs and long development cycles for application-specific hardware solutions makes it difficult to keep pace with the rapid developments in neuroscience. However, advances in System-on-Chip (SoC) device technology and tools are now providing interesting new design possibilities for application-specific implementations. Here, we present a novel hybrid software-hardware architecture approach for a neuromorphic compute node intended to work in a multi-node cluster configuration. The node design builds on the Xilinx Zynq-7000 SoC device architecture that combines a powerful programmable logic gate array (FPGA) and a dual-core ARM Cortex-A9 processor extension on a single chip. Our proposed architecture makes use of both and takes advantage of their tight coupling. We show that available SoC device technology can be used to build smaller neuromorphic computing clusters that enable hyper-real-time simulation of networks consisting of tens of thousands of neurons, and are thus capable of meeting the high demands for modeling and simulation in neuroscience.

Simulating the Cortical Microcircuit Significantly Faster Than Real Time on the IBM INC-3000 Neural Supercomputer.

This article employs the new IBM INC-3000 prototype FPGA-based neural supercomputer to implement a widely used model of the cortical microcircuit. With approximately 80,000 neurons and 300 Million synapses this model has become a benchmark network for comparing simulation architectures with regard to performance. To the best of our knowledge, the achieved speed-up factor is 2.4 times larger than the highest speed-up factor reported in the literature and four times larger than biological real time demonstrating the potential of FPGA systems for neural modeling. The work was performed at Jülich Research Centre in Germany and the INC-3000 was built at the IBM Almaden Research Center in San Jose, CA, United States. For the simulation of the microcircuit only the programmable logic part of the FPGA nodes are used. All arithmetic is implemented with single-floating point precision. The original microcircuit network with linear LIF neurons and current-based exponential-decay-, alpha-function- as well as beta-function-shaped synapses was simulated using exact exponential integration as ODE solver method. In order to demonstrate the flexibility of the approach, additionally networks with non-linear neuron models (AdEx, Izhikevich) and conductance-based synapses were simulated, applying Runge-Kutta and Parker-Sochacki solver methods. In all cases, the simulation-time speed-up factor did not decrease by more than a very few percent. It finally turns out that the speed-up factor is essentially limited by the latency of the INC-3000 communication system.

Rigorous Neural Network Simulations: A Model Substantiation Methodology for Increasing the Correctness of Simulation Results in the Absence of Experimental Validation Data.

The reproduction and replication of scientific results is an indispensable aspect of good scientific practice, enabling previous studies to be built upon and increasing our level of confidence in them. However, reproducibility and replicability are not sufficient: an incorrect result will be accurately reproduced if the same incorrect methods are used. For the field of simulations of complex neural networks, the causes of incorrect results vary from insufficient model implementations and data analysis methods, deficiencies in workmanship (e.g., simulation planning, setup, and execution) to errors induced by hardware constraints (e.g., limitations in numerical precision). In order to build credibility, methods such as verification and validation have been developed, but they are not yet well-established in the field of neural network modeling and simulation, partly due to ambiguity concerning the terminology. In this manuscript, we propose a terminology for model verification and validation in the field of neural network modeling and simulation. We outline a rigorous workflow derived from model verification and validation methodologies for increasing model credibility when it is not possible to validate against experimental data. We compare a published minimal spiking network model capable of exhibiting the development of polychronous groups, to its reproduction on the SpiNNaker neuromorphic system, where we consider the dynamics of several selected network states. As a result, by following a formalized process, we show that numerical accuracy is critically important, and even small deviations in the dynamics of individual neurons are expressed in the dynamics at network level.

Code Generation in Computational Neuroscience: A Review of Tools and Techniques.

Advances in experimental techniques and computational power allowing researchers to gather anatomical and electrophysiological data at unprecedented levels of detail have fostered the development of increasingly complex models in computational neuroscience. Large-scale, biophysically detailed cell models pose a particular set of computational challenges, and this has led to the development of a number of domain-specific simulators. At the other level of detail, the ever growing variety of point neuron models increases the implementation barrier even for those based on the relatively simple integrate-and-fire neuron model. Independently of the model complexity, all modeling methods crucially depend on an efficient and accurate transformation of mathematical model descriptions into efficiently executable code. Neuroscientists usually publish model descriptions in terms of the mathematical equations underlying them. However, actually simulating them requires they be translated into code. This can cause problems because errors may be introduced if this process is carried out by hand, and code written by neuroscientists may not be very computationally efficient. Furthermore, the translated code might be generated for different hardware platforms, operating system variants or even written in different languages and thus cannot easily be combined or even compared. Two main approaches to addressing this issues have been followed. The first is to limit users to a fixed set of optimized models, which limits flexibility. The second is to allow model definitions in a high level interpreted language, although this may limit performance. Recently, a third approach has become increasingly popular: using code generation to automatically translate high level descriptions into efficient low level code to combine the best of previous approaches. This approach also greatly enriches efforts to standardize simulator-independent model description languages. In the past few years, a number of code generation pipelines have been developed in the computational neuroscience community, which differ considerably in aim, scope and functionality. This article provides an overview of existing pipelines currently used within the community and contrasts their capabilities and the technologies and concepts behind them.

Reproducible Neural Network Simulations: Statistical Methods for Model Validation on the Level of Network Activity Data.

Computational neuroscience relies on simulations of neural network models to bridge the gap between the theory of neural networks and the experimentally observed activity dynamics in the brain. The rigorous validation of simulation results against reference data is thus an indispensable part of any simulation workflow. Moreover, the availability of different simulation environments and levels of model description require also validation of model implementations against each other to evaluate their equivalence. Despite rapid advances in the formalized description of models, data, and analysis workflows, there is no accepted consensus regarding the terminology and practical implementation of validation workflows in the context of neural simulations. This situation prevents the generic, unbiased comparison between published models, which is a key element of enhancing reproducibility of computational research in neuroscience. In this study, we argue for the establishment of standardized statistical test metrics that enable the quantitative validation of network models on the level of the population dynamics. Despite the importance of validating the elementary components of a simulation, such as single cell dynamics, building networks from validated building blocks does not entail the validity of the simulation on the network scale. Therefore, we introduce a corresponding set of validation tests and present an example workflow that practically demonstrates the iterative model validation of a spiking neural network model against its reproduction on the SpiNNaker neuromorphic hardware system. We formally implement the workflow using a generic Python library that we introduce for validation tests on neural network activity data. Together with the companion study (Trensch et al., 2018), the work presents a consistent definition, formalization, and implementation of the verification and validation process for neural network simulations.