BrainPy, a flexible, integrative, efficient, and extensible framework for generalpurpose brain dynamics programming
Abstract
Elucidating the intricate neural mechanisms underlying brain functions requires integrative brain dynamics modeling. To facilitate this process, it is crucial to develop a generalpurpose programming framework that allows users to freely define neural models across multiple scales, efficiently simulate, train, and analyze model dynamics, and conveniently incorporate new modeling approaches. In response to this need, we present BrainPy. BrainPy leverages the advanced justintime (JIT) compilation capabilities of JAX and XLA to provide a powerful infrastructure tailored for brain dynamics programming. It offers an integrated platform for building, simulating, training, and analyzing brain dynamics models. Models defined in BrainPy can be JIT compiled into binary instructions for various devices, including Central Processing Unit, Graphics Processing Unit, and Tensor Processing Unit, which ensures highrunning performance comparable to native C or CUDA. Additionally, BrainPy features an extensible architecture that allows for easy expansion of new infrastructure, utilities, and machinelearning approaches. This flexibility enables researchers to incorporate cuttingedge techniques and adapt the framework to their specific needs.
Editor's evaluation
The paper introduces a new, important framework for neural modelling that promises to offer efficient simulation and analysis tools for a wide range of biologicallyrealistic neural networks. It provides convincing support for the ease of use, flexibility, and performance of the framework, and features a solid comparison to existing solutions in terms of accuracy. The work is of potential interest to a wide range of computational neuroscientists and researchers working on biologically inspired machine learning applications.
https://doi.org/10.7554/eLife.86365.sa0Introduction
Brain dynamics modeling, which uses computational models to simulate and elucidate brain functions, is receiving increasing attention from researchers across different disciplines. Recently, gigantic projects in brain science have been initiated worldwide, including the BRAIN Initiative (Jorgenson et al., 2015), Human Brain Project (Amunts et al., 2016), and China Brain Project (Poo et al., 2016), which are continuously producing new data about the structures and activity patterns of neural systems. Computational modeling is a fundamental and indispensable tool for interpreting this vast amount of data. However, to date, we still lack a generalpurpose programming framework for brain dynamics modeling. By general purpose, we mean that such a programming framework can implement most brain dynamics models, integrate diverse modeling demands (e.g., simulation, training, and analysis), and accommodate new modeling approaches constantly emerging in the field while maintaining highrunning performance. Generalpurpose programming frameworks are exemplified by TensorFlow (Abadi et al., 2016) and PyTorch (Paszke et al., 2019) in the field of Deep Learning, which provides convenient interfaces for researchers to define various AI models flexibly and efficiently. These frameworks have become essential infrastructure in AI research, and play an indispensable role in this round of the AI revolution (Dean, 2022). Brain dynamics modeling also needs such a generalpurpose programming framework urgently (D’Angelo and Jirsa, 2022).
To develop a generalpurpose programming framework for brain dynamics modeling, we face several challenges.
The first challenge comes from the complexity of the brain. The brain is organized modularly, hierarchically, and across multiscales (Meunier et al., 2010), implying that the framework must support model construction at different levels (e.g., channel, neuron, network) and model composition across multiple scales (e.g., neurons to networks, networks to circuits). Current brain simulators typically focus on only one or two scales, for example, spiking networks (Gewaltig and Diesmann, 2007; Davison et al., 2008; Beyeler et al., 2015; Stimberg et al., 2019) or firing rate models (Sanz Leon et al., 2013; Cakan et al., 2021). Recently, NetPyNE (DuraBernal et al., 2019) and BMTK (Dai et al., 2020a) have adopted descriptive languages to expand the modeling scales from channels to neurons and networks, but their modeling interfaces are still limited to predefined scales.
The second challenge is the integration of different modeling needs (RamezanianPanahi et al., 2022; D’Angelo and Jirsa, 2022). To elucidate brain functions comprehensively with computational models, we need to not only simulate neural activities, but also analyze the underlying mechanisms, and sometimes, we need to train models from data or tasks, implying that a generalpurpose programming framework needs to be a platform to integrate multiple modeling demands. Current brain simulators mainly focus on simulation (Brette et al., 2007; TikidjiHamburyan et al., 2017; Blundell et al., 2018), and largely ignore training and analysis.
The third challenge is achieving highrunning performance while maintaining programming convenience (TikidjiHamburyan et al., 2017; Blundell et al., 2018), which is particularly true for brain dynamics modeling, as its unique characteristics make it difficult to run efficiently within a convenient Python interface. The current popular approach for solving this challenge is code generation based on descriptive languages (Goodman, 2010; Blundell et al., 2018). However, this approach has intrinsic limitations regarding transparency, flexibility, and extensibility (TikidjiHamburyan et al., 2017; Blundell et al., 2018) (Appendix 1).
The fourth challenge comes from the rapid development of the field. Brain dynamics modeling is relatively new and developing rapidly. New concepts, models, and mathematical approaches are constantly emerging, implying that a generalpurpose programming framework needs to be extensible to take up new advances in the field conveniently.
In this paper, we propose BrainPy (‘Brain Dynamics Programming in Python’, Figure 1) as a solution to address all the above challenges. BrainPy provides infrastructure tailored for brain dynamics programming, including mathematical operators, differential equation solvers, universal modelbuilding formats, and objectoriented JIT compilation. Such infrastructure provides the flexibility for users to define brain dynamics models freely and lays the foundation for BrainPy to build an integrative framework for brain dynamics modeling. First, BrainPy introduces a brainpy.DynamicalSystem interface to unify diverse brain dynamics models. Models at any level of resolution can be defined as DynamicalSystem classes, which further can be hierarchically composed to create higherlevel models. Second, BrainPy builds an integrated platform for studying brain dynamics models, where the same BrainPy model can be used for simulation, training (e.g., offline learning, online learning, or backpropagation training), and analysis (e.g., lowdimensional bifurcation analysis or highdimensional slow point analysis). Third, through JIT compilation and dedicated operators, BrainPy achieves impressive performance for its code execution. The same models can be deployed into different devices (such as Central Processing Unit [CPU], Graphics Processing Unit [GPU], and Tensor Processing Unit [TPU]) without additional code modification. Fourth, BrainPy is highly extensible. New extensions can be easily implemented as plugin modules. Even the lowlevel primitive operators in the kernel system can be extended in the userlevel Python interface. BrainPy is implemented in a robust continuous integration pipeline and is equipped with an automatic documentation building environment (Appendix 3). It is open sourced at https://github.com/brainpy/BrainPy. Rich tutorials and extensive examples are available at https://brainpy.readthedocs.io and https://brainpyexamples.readthedocs.io, respectively.
Method and results
Infrastructure tailored for brain dynamics programming
To support its goal of becoming a generalpurpose programming framework, BrainPy provides the infrastructure essential for brain dynamics modeling (Figure 1A). This infrastructure is a collection of interconnected utilities designed to provide foundational services that enable users to easily, flexibly, and efficiently perform various types of modeling for brain dynamics. Specifically, BrainPy implements (1) mathematical operators for conventional computation based on dense matrices and eventdriven computation based on sparse connections; (2) numerical integrators for various differential equations, the backbone of dynamical neural models; (3) a universal modelbuilding interface for constructing multiscale brain dynamics models and the associated JIT compilation for the efficient running of these models; and (4) a toolbox specialized for brain dynamics modeling.
First, BrainPy delivers rich mathematical operators as essential elements to describe diverse brain dynamics models (Appendix 4). On the one hand, brain dynamics modeling involves conventional computation based on dense matrices. In Python scientific computing ecosystem, dense matrix operators have been standardized and popularized by NumPy (Harris et al., 2020), TensorFlow (Abadi et al., 2016), and PyTorch (Paszke et al., 2019). To reduce the cost of learning a new set of computing languages, dense matrix operators in BrainPy (including multidimensional arrays, mathematical operations, linear algebra routines, Fourier transforms, and random number generations) follow the syntax of those in NumPy, TensorFlow, and PyTorch so that most Python users can directly program in BrainPy with their familiar operator syntax. On the other hand, brain dynamics modeling has specific computation properties, such as sparse connections and eventdriven computations, which are difficult to efficiently implement with conventional operators. To accommodate these needs, BrainPy provides dozens of dedicated operators tailored for brain dynamics modeling, including eventdriven operators, sparse operators, and JIT connectivity operators. Compared to traditional dense matrix operators, these operators can reduce the running time of typical brain dynamics models by several orders of magnitude (see Efficient performance of BrainPy).
Second, BrainPy offers a repertoire of numerical solvers for solving differential equations (Appendix 5). Differential equations are involved in most brain dynamics models. For ease of use, BrainPy’s numerical integration of differential equations is designed as a Python decorator. Users define differential equations as Python functions, whose numerical integration is accomplished by calling integrator functions, for example, brainpy.odeint() for ordinary differential equations (ODEs), brainpy.sdeint() for stochastic differential equations (SDEs), and brainpy.fdeint() for fractional differential equations (FDEs). These integrator functions are designed to be general, and most numerical solvers for ODEs and SDEs are provided, such as explicit Runge–Kutta methods, adaptive Runge–Kutta methods, and Exponential methods. For SDEs, BrainPy supports different stochastic integrals (Itô or Stratonovich) and different types of Wiener processes (scalar or multidimensional). As delays are ubiquitous in brain dynamics, BrainPy also supports the numerical integration of delayed ODEs, SDEs, and FDEs with various delay forms.
Third, BrainPy supports modular and composable programming and the associated objectoriented transformations (Appendix 6). To capture the fundamental characteristics of brain dynamics, which are modular, multiscaled, and hierarchical (Meunier et al., 2010), BrainPy follows the philosophy that ‘any dynamical model is just a Python class, and highlevel models can be recursively composed by lowlevel ones’ (details will be illustrated in Flexible model building in BrainPy). However, such a modular and composable interface is not directly compatible with JIT compilers such as JAX and Numba, because they are designed to work with pure functions (Appendix 2). By providing objectoriented transformations, including the JIT compilation for class objects and the automatic differentiation for class variables, models defined with the above modular and composable interface can also benefit from the powerful transformations in advanced JIT compilers.
Fourth, BrainPy offers a toolbox specialized for brain dynamics modeling. A typical modeling experiment involves multiple stages or processes, such as creating synaptic connectivity, initializing connection weights, presenting stimulus inputs, and analyzing simulated results. For the convenience of running these operations repeatedly, BrainPy presets a set of utility functions, including synaptic connection, weight initialization, input construction, and data analysis. However, this presetting does not prevent users from defining their utility functions in the toolbox.
Flexible model building in BrainPy
Brain dynamics models have the key characteristics of being modular, multiscaled, and hierarchical, and BrainPy designs a modular, composable, and flexible programming paradigm to match these features. The paradigm is realized by the DynamicalSystem interface, which has the following appealing features.
DynamicalSystem supports the definition of brain dynamics models at any organization level. Given a dynamical system, regardless of its complexity, users can implement it as a DynamicalSystem class. As an example, Figure 2A demonstrates how to define a potassium channel model with DynamicalSystem, in which the initialization function defines parameters and states, and the update function specifies how the states evolve. In this process, BrainPy toolbox can help users quickly initialize model variables, synaptic connections, weights, and delays, and BrainPy operators and integrators can support users to define model updating logic freely. In a similar fashion, other dynamical models, such as discontinuous neuron models (e.g., leaky integrateandfire model; Abbott, 1999), continuous neuron models (e.g., FitzHugh–Nagumo model; Fitzhugh, 1961), population models (e.g., Wilson–Cowan model; Wilson and Cowan, 1972), and network models (e.g., continuous attractor neural network; Wu et al., 2008), can be implemented by subclassing DynamicalSystem as standalone modules.
However, for complex dynamical models, such as Hodgkin–Huxley (HH)typed neuron models or largescale cortical networks, their model definitions can be achieved through the composition of subcomponents. All models defined with DynamicalSystem can be used as modules to form more complicated highlevel models. As an example, Figure 2B demonstrates how an HHtyped neuron model is created by combining multiple ion channel models. Such composable programming is the core of DynamicalSystem, and applies to almost all BrainPy models. For example, a synapse model consists of four components: synaptic dynamics (e.g., alpha, exponential, or dual exponential dynamics), synaptic communication (e.g., dense, sparse, or convolutional connections), synaptic output (e.g., conductance, current, or magnesium blockingbased), and synaptic plasticity (e.g., short or longterm plasticity). Composing different realizations of these components enables to create diverse kinds of synaptic models. Similarly, various network models can be implemented by combining different neuron groups and their synaptic projections.
Remarkably, DynamicalSystem supports hierarchical composable programming, such that a model composed of lowerlevel components can hierarchically serve as a new component to form higherlevel models. This property is highly useful for the construction of multiscale brain models. Figure 2 demonstrates an example of recursively composing a model from channels (Figure 2A) to neurons (Figure 2B) to networks (Figure 2C) and to systems (Figure 2D, see Appendix 9 for details of the full model). It is worth pointing out that this hierarchical composition property is not shared by other brain simulators, and BrainPy allows for flexible control of composition depth according to users’ needs. Moreover, for user convenience, BrainPy provides dozens of commonly used models, including channels, neurons, synapses, populations, and networks, as building blocks to simplify the building of largescale models.
Integrated modeling in BrainPy
BrainPy offers an integrated platform to comprehensively perform simulation, training, and analysis of brain dynamics models.
Model simulation
BrainPy designs the interface brainpy.DSRunner to simulate the dynamics of brain models. DSRunner can be used to simulate models at any level, including but not limited to channel (Figure 3A), neuron (Figure 3B), network (Figure 3C), and system (Figure 3D) levels.
Brain dynamics models often require intensive parameter searches to fit the experimental data, which is a computationally demanding task. BrainPy facilitates this process by supporting multiple parallel simulation methods. Firstly, the brainpy.running module offers convenient routines for concurrent executions based on the python multiprocessing mechanism. This method is flexible, but may introduce additional time overhead due to the model recompilation and reinitialization in each process. Secondly, most BrainPy models inherently support the automatic vectorization of jax.vmap and automatic parallelization of jax.pmap. These methods can avoid the recompilation and reinitialization of models in the same batch, and automatically parallelize the model execution on the given machines. Figure 3E illustrates the simplicity of this batch simulation approach. By using a single line of functional calls, BrainPy models can run simultaneously with different parameter settings.
Model training
The use of machinelearning methods to train neural models is becoming a new trend for studying brain functions (Masse et al., 2019; Finkelstein et al., 2021; Laje and Buonomano, 2013; Sussillo et al., 2015; Saxe et al., 2021). BrainPy provides the brainpy.DSTrainer interface to support this utility. Different subclasses of DSTrainer provide different training algorithms, which can be used to train different types of models. For instance, the trainer brainpy.BPTT implements the algorithm of backpropagation through time, which is helpful for training spiking neural networks (Figure 4A) and recurrent neural networks (Figure 4B). Similarly, brainpy.OfflineTrainer implements offline learning algorithms such as ridge regression (Lukoševičius, 2012), brainpy.OnlineTrainer implements online learning algorithms such as FORCE learning (Sussillo and Abbott, 2009), which are useful for training reservoir computing models (Figure 4C). In a typical training task, one may try different algorithms that can be used to train a model. The unified syntax for defining and training models in BrainPy enables users to train the same model using multiple algorithms (see Appendix 10). Figure 4D–F demonstrates that a reservoir network model can be trained with three different algorithms (online, offline, and backpropagation) to accomplish a classical task of chaotic time series prediction (Jaeger, 2007).
Since the training algorithms for brain dynamics models have not been standardized in the field, BrainPy provides interfaces to support the flexible customization of training algorithms. Specifically, OfflineTrainer and OnlineTrainer provide general interfaces for offline and online learning algorithms, respectively, and users can easily select the appropriate method by specifying the fit_method parameter in OfflineTrainer or OnlineTrainer. Furthermore, the BPTT interface is designed to capture the latest advances in backpropagation algorithms. For instance, it supports eligibility propagation algorithm (Bellec et al., 2020) and surrogate gradient learning (Neftci et al., 2019) for training spiking neural networks.
Model analysis
Analyzing model dynamics is as essential as model simulation and training because it helps unveil the underlying mechanism of model behaviors. Given a dynamical system, BrainPy provides the interface brainpy.DSAnalyzer for automatic dynamic analysis, and different classes of DSAnalyzer implement different analytical methods.
First, BrainPy supports phase plane and bifurcation analyses for lowdimensional dynamical systems. The phase plane is a classical and powerful technique for the analysis of dynamical systems and has been widely used in brain dynamics studies, including neuron models (e.g., Izhikevich model; Izhikevich, 2003) and population rate models (e.g., Wilson–Cowan model; Wilson and Cowan, 1972). Figure 5A shows an example where many features of phase plane analysis, including nullcline, vector field, fixed points, and their stability, for a complex ratebased decisionmaking model (Wong and Wang, 2006) are automatically evaluated by several lines of BrainPy code. Bifurcation analysis is another utility of BrainPy, which allows users to easily investigate the changing behaviors of a dynamical system when parameters are continuously varying. Figure 5B demonstrates the stability changes of the classical FitzHugh–Nagumo model (Fitzhugh, 1961) with one parameter varying can be easily inspected by the bifurcation analysis interface provided in BrainPy. Similarly, bifurcation analysis of codimension2 (with two parameters changing simultaneously; Figure 5C) can be performed with the same interface. BrainPy also supports bifurcation analysis for threedimensional fast–slow systems, for example, a bursting neuron model (Rinzel, 1985). This set of lowdimensional analyzers is performed numerically so that they are not restricted to equations with smooth functions, but are equally applicable to ones with strong and complex nonlinearity.
Second, BrainPy supports slow point computation and linearization analysis for highdimensional dynamical systems. With powerful numerical optimization methods, one can find fixed or slow points of a highdimensional nonlinear system (Sussillo and Barak, 2013). By integrating numerical methods such as gradient descent and nonlinear optimization algorithms, BrainPy provides the interface brainpy.analysis.SlowPointFinder as a fundamental tool for highdimensional analysis. Figure 5D demonstrates that the SlowPointFinder can effectively find a line of stable and unstable attractors in a CANN network (Wu et al., 2008). Furthermore, the linearized dynamics around the found fixed points can be easily inspected and visualized with SlowPointFinder interface (Figure 5E).
Efficient performance of BrainPy
Simulating dynamical models efficiently in Python is notoriously challenging (Blundell et al., 2018). To resolve this problem, BrainPy leverages the JIT compilation of JAX/XLA and exploits dedicated primitive operators to accelerate the model running.
JIT compilation
In contrast to deep neural networks (DNNs), which mainly consist of computationintensive operations (such as convolution and matrix multiplication), brain dynamics models are usually dominated by memoryintensive operations. Taking the classical leaky integrateandfire (LIF) neuron model (Abbott, 1999) as an example, its computation mainly relies on operators such as addition, multiplication, and division. As shown in Figure 6A, we measure the running times of an LIF model and a matrix multiplication with the same number of floatingpoint operations (FLOPs) on both CPU and GPU devices. The results indicate that the LIF model is significantly slower than the matrix multiplication on both devices, despite having the same theoretical complexity. This reveals the existence of large overheads when executing brain dynamics models in Python. Moreover, these overheads become dominant when simulating largescale brain networks, as they grow rapidly with the number of operators in the model.
To overcome this limitation, we employ the JIT compilation technique to dramatically reduce these overhead costs in BrainPy. The JIT compilation transforms the dynamic Python code into the static machine code during runtime, which can significantly reduce the time cost of Python interpretation. Specifically, we utilize JAX, which implements JIT compilation based on XLA (Appendix 2). The XLA JIT engine employs specialized optimizations for memoryintensive operators, for example, operator fusion, which alleviates memory access overhead by minimizing the requirement for intermediate data storage and redundant data transfers during the sequential execution of multiple unmerged operations. This renders the JIT compilation with XLA highly suitable for handling brain dynamics models. Figure 6A demonstrates that with the JIT compilation, the LIF model achieves a running speed comparable to that of the matrix multiplication operation Dot on the CPU and outperforms or matches it on the GPU (see Figure 6A, Appendix 11—figure 6A, and Appendix 11—figure 6B). To further illustrate the benefits of the JIT compilation, we apply it to a realistic brain simulation model, namely, the E/I balanced network model COBA (Vogels and Abbott, 2005). The results show that the JIT compilation boosts the running speed by 10 times on both the CPU and GPU compared to the case without JIT compilation (for CPU acceleration, see Figure 6B and Appendix 11—figure 6C; for GPU acceleration, see Figure 6C and Appendix 11—figure 6D).
Dedicated operators
Another key feature that distinguishes brain dynamics models from DNNs is that they usually have sparse connections and perform eventdriven computations. For example, neurons in a network are typically connected with each other with a probability less than 0.2 (Potjans and Diesmann, 2014), and the state of a postsynaptic neuron is updated only when a presynaptic spike event occurs. These unique features greatly impair the efficiency of brain model simulation using conventional operators, even with the help of JIT compilation. To illustrate this, Figure 7A demonstrates that when implementing a COBA network model with dense matrixbased operators, the majority of simulation time is consumed by synaptic computations on both CPU and GPU devices, and this issue becomes more pronounced as the network size increases (see ‘CPU, Dense’ and ‘GPU, Dense’ lines in Figure 7A).
In order to address this challenge, BrainPy introduces specialized primitive operators designed to accelerate eventbased computations within sparsely connected networks. These specialized operators encompass transformations among variables associated with presynaptic neurons, postsynaptic neurons, and synapses, as well as sparse computation operators, eventdriven computation operators, and JIT connectivity operators (refer to Appendix 4 for more details). By employing these specialized operators, BrainPy significantly reduces the time required for synaptic computations. As depicted in Figure 7B, the specialized eventbased operators result in a remarkable speedup of the classical COBA network model by orders of magnitude (see Appendix 11—figure 7A). Similar speed improvements are observed when utilizing GPU computations, as shown in Figure 7C and Appendix 11—figure 7B. Furthermore, an examination of the time proportion for synaptic computations indicates that the utilization of specialized operators ensures a consistent time ratio for synaptic computation, even as the network size increases (see ‘CPU, Event’ and ‘GPU, Event’ lines in Figure 7A).
Benchmarking
To conduct a formal assessment of the running efficiency of BrainPy, we conducted a comparative analysis against several widely used brain simulators, namely NEURON (Hines and Carnevale, 1997), NEST (Gewaltig and Diesmann, 2007), Brian2 (Stimberg et al., 2019), Brian2CUDA (Alevi et al., 2022), GeNN (Yavuz et al., 2016), and Brian2GeNN (Stimberg et al., 2020). Our benchmarking focused on measuring the simulation speeds of these frameworks for models with sparse and dense connectivity patterns. The tests were performed using three common computing platforms: CPU, GPU, and TPU. This comprehensive assessment provides insights into BrainPy’s efficiency relative to other mainstream simulators across different hardware configurations and network scales.
To evaluate the performance of brain simulators on sparsely connected networks, we utilized two established E/I balanced network models with LIF and HH neuron types: the COBA (Vogels and Abbott, 2005) and COBAHH (Brette et al., 2007) networks (experimental details please see Appendix 11). COBA consists of excitatory and inhibitory LIF neurons with sparse random connectivity. COBAHH uses the same network architecture but replaces the LIF neurons with biophysically detailed HH neuron models. On the CPU platform, consistent with previous benchmark experiments (Stimberg et al., 2019), we find that NEURON and NEST simulators exhibit suboptimal performance when running on a single node (see Figure 8A and Figure 8B). In contrast, BrainPy and Brian2 demonstrate comparable performance, showcasing a remarkable speed advantage of one to two orders of magnitude over NEURON and NEST. As both Brian2 and BrainPy support singleprecision floatingpoint computation (x32), we conducted an analysis of their performances in the context of x32 computation. In order to ensure accurate simulation results with x32 computation, we examined the simulation outcomes across various simulators and platforms (refer to Appendix 11). Our evaluation demonstrated that BrainPy outperforms Brian2 in terms of speedup for numerical integration using x32 arithmetic on CPU platforms. On the GPU platform, GeNN demonstrates optimal linear scaling of execution time on both COBA and COBAHH network models as the network size increases (Figure 8D and Figure 8E). In contrast, BrainPy and Brian2CUDA exhibit a slight overhead and maintain a constant running time when dealing with small network sizes. However, when it comes to network scaling, BrainPy and Brian2CUDA outperform GeNN. Particularly as the network size grows, GeNN exhibits significantly slower performance. Additionally, the utilization of singleprecision floating point in GeNN, Brian2CUDA, and BrainPy further enhances their GPU performance (excluding the COBA model in Brian2CUDA). Once again, we observed that BrainPy’s x32 mode achieves a more pronounced performance gain. Particularly, in the COBAHH model, BrainPy’s x32 computation demonstrates a substantial speedup compared to other brain simulators. BrainPy also enables model deployment on TPUs. However, since TPUs currently lack native support for sparse computations and toolchains for operator customization, we could not leverage eventdriven sparse operators to simulate the sparsely connected COBA and COBAHH networks. Instead, we used dense matrix multiplication with masking to approximate the sparse connectivity. Unfortunately, this led to significantly slower performance for the two sparsely connected models compared to the results obtained on GPUs (please refer to Appendix 11—figure 8). Moreover, the use of masked matrices resulted in a quadratic increase in memory usage. Consequently, the benchmarking experiments of COBA and COBAHH networks on TPU were limited to a scale of $4{e}^{4}$ neurons.
To evaluate the performance of brain simulators on densely connected networks, we utilized the decisionmaking network proposed by Wang, 2002. Assessing computational efficiency for dense connectivity is important for simulating models that feature dense recurrent connections (Motta et al., 2019) and facilitating the integration with DNNs which commonly employ dense connectivity between layers (Tavanaei et al., 2019). Due to the considerably slower speeds observed and the absence of a publicly available implementation of a decisionmaking network model using NEURON and NEST, we have excluded them from this benchmark test. Additionally, we did not include a comparison with GeNN because Brian2GeNN does not support the translation of the advanced Brian2 feature employed in this model. Our evaluation showcases that Brian2, Brian2CUDA, and BrainPy exhibit comparable performance on networks of small sizes. However, BrainPy demonstrated substantially better scalability on larger network sizes (see Figure 8C and Figure 8F). For these types of simulation workloads with dense connectivity, TPUs significantly outperformed CPUs and GPUs. Since TPUs primarily utilize lowprecision floating point (especially floating point with 16 bits) and are less optimized for double precision, we only tested the model with singleprecision operations. Our evaluations clearly showcase the excellent scalability of the network as the size increases (refer to the GPU and TPU comparison in Figure 8F).
Extensible architecture of BrainPy
Brain science, as well as brain dynamics modeling, is progressing rapidly. Along with the gigantic projects on brain research worldwide, new data and knowledge about brain structures and functions are constantly emerging, which impose new demands on brain dynamics modeling frequently, including, for instance, the simulation and analysis of largesize neural circuits, and the training of neural models based on recorded neural data. To be a generalpurpose brain dynamics programming framework, the architecture of the framework must be extensible to conveniently take up new advances in the field. Current brain simulators based on descriptive languages have difficulty achieving this goal, since the extension of a new component through the descriptive interface needs to be done in both high and lowlevel programming languages (Appendix 1). Through the elaborate architecture design, BrainPy enables easy extension with new infrastructure, new utility functions, and new machinelearning methods, all performed in our convenient Python interface.
First, for infrastructure (Figure 1A), BrainPy provides a convenient way of customizing a new tool by defining a new subclass. For example, a new Runge–Kutta integrator can be created by inheriting from brainpy.ode.ExplicitRKIntegrator and specifying the Butcher tableau; a new connector can be implemented by deriving from brainpy.conn.TwoEndConnector and overriding initialization function and connection building function (see Appendix 7 for details). Since models and modeling methods have not yet been standardized in the field, the abstraction and summarization of primitive operators for brain dynamics modeling are largely lacking. Although BrainPy has provided dozens of dedicated operators, it would be too soon to establish a complete operator library for brain dynamics modeling. To simplify the process of operator customization, BrainPy provides the brainpy.math.CustomOpByNumba interface that allows users to write and register an operator directly with Python syntax. Specifically, to customize a primitive operator, users need to subclass CustomOpByNumba and implement two Python functions: the abstract evaluation function eval_shape() and concrete computation function con_compute() (see Appendix 8 for more information). Notably, this approach differs from the operator customization in most DNN frameworks, in which lowlevel operators must be implemented through C++ code. We confirmed that operators customized through the BrainPy interface have comparable and even better performance than those written in C++ (please refer to Figure 9 for the results and Appendix 8 for the source code for comparison).
Second, for functional modules (Figure 1B), BrainPy enables an extension of a new module with BrainPy infrastructure, as the latter can be arbitrarily fused, chained, or combined to create new functions. For example, an analysis toolkit can be customized with BrainPy operators. Moreover, all customizations in BrainPy can benefit from the acceleration of JIT compilation, and users’ attention only needs to focus on the functionalities they require.
Third, for interactions with AI, BrainPy supports the easy extension of new machinelearning methods. Machinelearning approaches are becoming important tools for brain dynamics modeling (Saxe et al., 2021). Existing brain simulators have difficulty incorporating the latest advances in machinelearning research (Appendix 1). Built on top of JAX, BrainPy has the inherent advantage of being linked to the latest developments in machine learning. We noticed that JAX has a rich ecosystem of machine learning, including DNNs, graph neural networks, reinforcement learning, and probabilistic programming. To integrate this rich ecosystem as part of the users’ program, BrainPy is designed to be compatible with other JAX libraries. First, the objectoriented transformations in BrainPy can be applied to pure functions, thus enabling most JAX libraries with a functional programming style to be directly used as a part of the BrainPy program. Second, users can transform models in other libraries as BrainPy objects. For example, using brainpy.dnn.FromFlax, users can treat any artificial neural network model in Flax (Heek, 2020) as a BrainPy module. Alternatively, users can convert a BrainPy model into a format that is compatible with other JAX libraries. For instance, brainpy.dnn.ToFlax supports interpreting a dynamical system in BrainPy as a Flax recurrent cell, so that brain models in BrainPy can also be used in a machinelearning context.
Discussion
The field of brain dynamics modeling has long been constrained by a lack of generalpurpose programming frameworks that can support users to freely define brain dynamics models across multiple scales, comprehensively perform simulation, optimization, and analysis of the built models, and conveniently prototype new modeling methods. To address this challenge, we have developed BrainPy, a generalpurpose programming framework for brain dynamics modeling. With a combined focus on usability, performance, functionality, and extensibility, BrainPy offers a number of appealing properties, including:
Pythonic programming. In contrast to other brain simulators (Gewaltig and Diesmann, 2007; Davison et al., 2008; Beyeler et al., 2015; Stimberg et al., 2019; Hines and Carnevale, 1997; DuraBernal et al., 2019; Dai et al., 2020a; Goodman, 2010; Blundell et al., 2018; TikidjiHamburyan et al., 2017), BrainPy enables Pythonic programming. It allows users to implement and control their models directly using native Python syntax, implicating high transparency to users. This transparency is crucial for research, as standard Python debugging tools can be integrated into the implementation process of novel models, and is also appealing for education.
Integrative platform. BrainPy allows unprecedentedly integrated studying of brain dynamics models. Its multiscale modelbuilding interface facilitates the construction of datadriven models based on the structural, functional, or cellular data (Potjans and Diesmann, 2014), while its diverse model training supports enable to training brain dynamics models based on cognitive tasks that can be used to evaluate or optimize models of different brain functions (Saxe et al., 2021). BrainPy provides the first step toward an integrative framework supporting comprehensive brain modeling across different organization levels and problem dimensions (D’Angelo and Jirsa, 2022).
Intrinsic flexibility. Inspired by the success of generalpurpose programming in Deep Learning (Abadi et al., 2016; Paszke et al., 2019), BrainPy provides not only functional libraries but also infrastructure. This is essential for users to create models and modeling approaches beyond the predefined assumptions of existing libraries.
Efficient performance. One of the key strengths of BrainPy lies in its ability to compile models defined in the framework into binary instructions for various devices, including CPU, GPU, and TPU. This compilation process ensures highrunning performance comparable to native C or CUDA, enabling researchers to efficiently execute their models.
Extensible architecture. BrainPy features an extensible architecture. New primitive operators, utilities, functional modules, machinelearning approaches, etc., can be easily customized through our Python interface.
Limitations
While BrainPy’s native Pythonbased objectoriented programming paradigm confers numerous advantages compared to existing brain simulators, this novel programming approach also imposes certain limitations that must be acknowledged.
Most existing brain simulators employ a domainspecific language to define brain dynamics models. For example, Brian2 (Stimberg et al., 2019) designs an equationoriented specification that can describe a wide variety of neural models; NeuroML (Cannon et al., 2014) employs an XMLbased specification that facilitates the sharing and reuse of neuronal models; NetPyNE (DuraBernal et al., 2019) utilizes a highlevel JSONcompatible format composed of Python lists and dictionaries to support multiscale neuronal modeling; BMTK (Dai et al., 2020a) similarly employs a JSONbased language built on the SONATA file format (Dai et al., 2020b) to deliver consistent multiresolution experiences via integration with established tools like NEURON and NEST. This declarative programming approach benefits from a clear separation between the mathematical model description and its computational realization. It frees users from lowlevel implementation details, and enables intuitive specification of complex models in a concise and semantically clear manner. In contrast, the objectoriented programming used in BrainPy exposes the implementation details to users, and adds some complexity to the code. For example, users should be aware of the differences between dense and sparse connectivity schemes, online or offline training schemes, nonbatch or batch computing modes, etc.
The current objectives of BrainPy center on enabling an integrative platform for simulating, training, and analyzing largescale brain network models while retaining biologically relevant details. Incorporating excessive biological details would be extremely computationally expensive and difficult for such integration. Consequently, detailed spatial modeling with complex compartmental dynamics, as facilitated by tools like NEURON (Hines and Carnevale, 1997) and Arbor (Akar et al., 2019), exceeds BrainPy’s present scope. Moreover, in order to solve the governing partial differential equations, implicit numerical methods (e.g., Crank–Nicolson, implicit Euler) are often essential for stable multicompartment model simulation. As BrainPy does not currently support fully implicit solvers, it is ill suited to the needs and preferences of modelers focused on multicompartment dynamics in its current form. Our emphasis remains on balancing biological fidelity and computational tractability for largescale network modeling and training.
Based on the GSPMD mechanism of the XLA compiler (Xu et al., 2021), the current version of BrainPy supports various parallelism paradigms, such as data parallelism and model parallelism. Data parallelism involves dividing the training data across multiple devices, where each device independently computes and updates the model parameters using its assigned data subset. On the other hand, model parallelism entails partitioning the model across multiple devices, with each device responsible for computing a specific portion of the model computations. These parallelism paradigms are particularly applicable to brain dynamics models with dense connections or structured sparsity. However, the GSPMD parallelism mechanism is not straightforwardly applicable to sparse spiking neural networks, and requires nontrivial changes to support sparse computations. Therefore, another limitation of the current BrainPy framework is that it does not support the general parallelization of sparse spiking neural network models on multiple computing devices. Stateoftheart brain simulators now offer powerful parallelization capabilities for simulating largescale SNNs. For instance, NEST (Gewaltig and Diesmann, 2007) and NEURON (Hines and Carnevale, 1997) simulators provide convenient and efficient commands through the MPI interface to define, connect, and execute largescale networks. However, the arraybased data structure in BrainPy requires a different approach to parallelize spiking neural networks.
Future works
Although BrainPy offers substantial capabilities for brain dynamics modeling, fulfilling all demands in this domain will require large efforts for further ecosystem development.
First, supporting the efficient implementation of multicompartment neuron models is needed to enable biologically detailed modeling at the subcellular level (Poirazi and Papoutsi, 2020). Multicompartment neurons incorporate complex dendritic morphologies and spatially distributed ion channels that more precisely capture neural information processing. A substantial number of studies have demonstrated that dendritic mechanisms convey significant advantages to simplified network models of varying levels of abstraction (Bono and Clopath, 2017; Legenstein and Maass, 2011; Wu et al., 2018). Efficiently implementing such models in BrainPy could significantly advance detailed biophysical modeling and bridge the machinelearningoriented SNN models.
Second, developing parallel primitive operators and memoryefficient algorithms will be critical for ultralargescale brain simulations approaching biological realism (>billions of neurons). Massive parallelization across multiple computing devices is currently the main approach to achieve such scale. For instance, the NEST simulator uses optimized data structures and algorithms (Kunkel et al., 2011; Kunkel et al., 2014; Jordan et al., 2018) to enable largescale simulation on supercomputers and clusters. Moving forward, a priority for BrainPy will be parallelizing its arraybased data structures to simulate gigantic brain models across multiple nodes. Moreover, rather than solving largescale networks exactly, BrainPy aims to find approximating algorithms that overcome the $O({n}^{2})$ complexity, permitting very largescale modeling on much less computing devices.
Third, integrating BrainPy models with modern accelerators and neuromorphic computing systems (Schuman et al., 2017) could offer a more efficient and scalable approach for simulating largescale brain dynamics models on cuttingedge hardware accelerators. On the one hand, the implementation of sparse and eventdriven operators is necessary for TPUs. While TPUs have demonstrated promising performance and efficiency for machinelearning workloads, our experiments indicate that they are less efficient than GPUs when simulating sparse biological brain network models (see Appendix 11—figure 8). This inefficiency is primarily due to the lack of dedicated operators for sparse and eventdriven brain computations in current TPUs. In the future, we plan to explore the development of TPU kernels to enable scalable and efficient brain dynamics programming on TPU hardware accelerators. On the other hand, neuromorphic systems incorporate custom analog circuits that mimic neurobiological architectures and dynamics, resulting in significantly higher power efficiency compared to conventional digital hardware. By mapping BrainPy models onto neuromorphic platforms, simulations can be accelerated, and largescale models can be executed efficiently. However, the development of translation tools and mapping optimizations is necessary to fully harness the potential of these systems.
By addressing these limitations and enhancing BrainPy’s capabilities in these areas, we can further advance its goal of serving as a comprehensive programming framework for modeling brain dynamics. This will enable users to delve into the dynamics of brain or braininspired models that combine biological insights with machine learning. The BrainPy team encourages collaboration with the research community to expand this modeling ecosystem and facilitate a deeper understanding of brain dynamics.
Appendix 1
Review of the existing programming paradigm
In general, the existing tools for brain dynamics programming can be roughly divided into two categories: lowlevel programming and descriptive language.
The representatives of the first category include NEURON (Hines and Carnevale, 1997), NEST (Gewaltig and Diesmann, 2007), CARLsim (Beyeler et al., 2015; Chou et al., 2018), NeuronGPU (Golosio et al., 2021), Arbor (Akar et al., 2019), and others. These simulators offer a library of standard models written in C/C++ (particularly for NEST), CUDA (for CARLsim, NeuronGPU, and Arbor), or domainspecific languages (for NEURON and Arbor) to ensure efficient execution, along with a userfriendly Python interface for ease of use. Users can create neural networks in Python by utilizing the neuron and synapse models provided in the library. However, when a new model is required, users must learn to program using the lowlevel language. This significantly increases the learning cost and restricts the flexibility in defining new models (TikidjiHamburyan et al., 2017).
The second category tools include Brian (Goodman and Brette, 2008), Brian2 (Stimberg et al., 2014; Stimberg et al., 2019), ANNarchy (Vitay et al., 2015), GeNN (Yavuz et al., 2016), BMTK (Dai et al., 2020a), NetPyNE (DuraBernal et al., 2019), NeuroML (Gleeson et al., 2010), and NMODL (Krzhizhanovskaya et al., 2020), which employ a code generation approach based on descriptive languages. Descriptive simulators allow users to create new models based on convenient descriptions (such as text, Goodman and Brette, 2008; Stimberg et al., 2014; Stimberg et al., 2019; Vitay et al., 2015; JSON, Dai et al., 2020a; DuraBernal et al., 2019; XML files, Gleeson et al., 2010; or customized languages, Krzhizhanovskaya et al., 2020) and then translate the descriptions into lowlevel codes to speed up model running. In such a way, descriptive simulators enable model customization based on highlevel descriptive languages and ensure efficient running by generating lowlevel codes.
Currently, descriptive language has become a standard approach for brain simulation (Blundell et al., 2018). Simulators employing this first approach also start to provide their descriptive language interface for code generation. For instance, the NEST simulator provided its domainspecific language NESTML (Plotnikov et al., 2016) to describe stereotypical neuron and synapse models. Similarly, the NEURON simulator recently released its modern descriptive interface NetPyNE (DuraBernal et al., 2019), which employs the standard JSON format to allow users to describe neural circuit models by composing the existing available NEURON building block models. However, users still need to code based on its lowlevel programming interface to customize new models for channels, neurons, or synapses.
Descriptive languages have been highly successful for brain simulation (Blundell et al., 2018). A major benefit of these declarative approaches is the clear separation between model specification and implementation. This frees users from lowlevel programming details, enabling them to intuitively specify complex models in a concise, semantically clear way. The declarative nature of descriptive languages allows modelers to focus on computational neuroscience instead of implementation specifics. This has enabled rapid prototyping and sharing of models in the field. Overall, descriptive simulation languages have greatly improved modeler productivity thanks to their highlevel, implementationagnostic nature. However, they have intrinsic limitations on transparency, extensibility, and flexibility. One prominent feature of these descriptive languages is that they completely separate the model definition from the simulation, and therefore are not directly executable (Blundell et al., 2018). This kind of programming paradigm will cause great restrictions on usability and flexibility because it disables model debugging, error correction, and direct logic controlling. Moreover, descriptive languages are usually designed for specific kinds of models or one particular modeling approach. They are written in more than two programming languages: one is based on a lowlevel language (e.g., C++, CUDA) to implement its core functionality, and the other is based on a highlevel language (e.g., Python, Matlab) for ease of use. Once they are not tailored to users’ needs, extensions to accommodate new components must be made in both high and lowlevel languages, which is hard or nearly impossible for normal users. What is more, descriptive languages greatly reduce the expressive power of a generalpurpose programming language and make it hard to describe all aspects of a simulation experiment, including clipping variables out of bounds, input–output relations, model debugging, code optimization, dynamics analysis, and others.
In summary, significant challenges to transparency, flexibility, efficiency, and extensibility are still present in the existing programming paradigm for brain simulation. We can draw the conclusion that current software solutions cannot lead us to a generalpurpose programming framework that allows us to freely define brain dynamics models in various application domains.
Appendix 2
JIT compilation and JIT compilers
A notorious challenge in scientific computing is the tradeoff between usability and efficiency. The former seeks the fast prototyping of thoughts and ideas, whereas the latter pursues efficient code execution. For a long time in the past, it was difficult to strike a balance between the two. For example, statically typed compiled programming languages such as C or C++ are incredibly efficient in code execution, but their productivity is relatively low due to their complex and heavy syntax. In contrast, dynamically typed interpreted programming languages like Python and R are easy to learn and use, but they have slow running speeds. Nowadays, with the increasing complexity of models, the demand for both usability and efficiency has increased dramatically. Fortunately, recent advancements in justintime (JIT) compilation technology (Lattner and Adve, 2004; Lattner et al., 2020) have provided viable answers to this twolanguage problem. In particular, a new generation of computational engines based on JIT compilation (Aycock, 2003) has begun to have an impact on a variety of scientific computing disciplines.
The JIT compilation can be seen as the combination of the statically typed compilation and dynamically typed interpretation. It benefits from both the convenience of dynamic highlevel languages like Python and the efficiency of static lowlevel languages such as C++. At the start of a program execution, a JIT compiler acts like an interpreter. It runs your code step by step, and can output the intermediate results at the runtime for debugging. However, if some hot code snippets that are executed frequently, for example, certain functions or loop bodies, are detected or manually labeled, they will be submitted to the JIT compiler for compilation and storage. In this sense, it acts like a statically typed compiler. Once the compiled code snippets are entered again, the program will directly execute the compilergenerated lowlevel code without timeconsuming interpreting again. Hot code snippets can be automatically detected by the JIT compiler, or be manually labeled by users.
JIT compilation is a mature and wellestablished technology. It has been adopted in modern programming languages like JAVA, Julia, and Python. JAVA language provides JIT compilation in its JAVA virtual machine (JVM) to accelerate the execution of JAVA code (Grcevski et al., 2004). Java source code is first compiled into the platformindependent Java bytecode (.class file). Then, JVM loads the bytecode, interprets it, and executes it. To increase the running speed, JVM detects code that is frequently called through the hotspot detection and submits its bytecode to the JIT compiler to compile them into machine code. For the code with lower frequency, executing it through the JVM interpretation can save the time of the JIT compilation; while for the hot code frequently called, JIT compilation can significantly improve the running speed after the code is compiled. However, compared with Python, JAVA has poor ecosystem support for numerical computing. Its JIT is not specialized in numerical computing, but in general domains.
Julia (Bezanson et al., 2017), another dynamic highlevel programming language, is recently proposed for highperformance scientific computing. Julia features intuitive, productive, and generalpurpose syntax inspired by the success of Python, Matlab, and C++. Moreover, it achieves attractive performance through the JIT compilation based on the LLVM compiler infrastructure (Lattner and Adve, 2004). In a remarkably short time, Julia has provided excellent routines for mathematical functions, machinelearning algorithms, data processing tools, visualization utilities, and others. However, Julia is still young. Costs, such as lack of familiarity, rough edges, correctness bugs, and continual language changes, are still imposed on normal users.
Python is a wellknown and popular interactive dynamic programming language. It has a long history in numerical computing (Dubois et al., 1996; Harris et al., 2020). The ecosystem of scientific computing, including array programming (Harris et al., 2020), scientific algorithms (Virtanen et al., 2020), machine learning (Pedregosa et al., 2011), deep learning (Abadi et al., 2016; Paszke et al., 2019; Frostig et al., 2018), image processing (van der Walt et al., 2014), data analysis and statistics (McKinney, 2011), network analysis (Hagberg and Swart, 2008), visualization (Hunter, 2007), and many others, has been well established in Python. Before Julia, the JIT compilation was introduced into Python by PyPy in 2007. Later, other attempts, including Pyston, Pyjion, Psyco, JitPy, HOPE, etc., are proposed. With a long history of JIT development, Python nowadays has provided mature platforms of JIT compilation focusing on numerical computing. These numerical JIT platforms include Numba (Lam et al., 2015), JAX (Frostig et al., 2018), and XLA (Sabne, 2020). Each of them has its own characteristics.
JAX (Frostig et al., 2018) is a flourishing machinelearning library developed by Google. It aims to provide highlevel numerical functions to help users fast prototype machine learning ideas. Moreover, these numerical functions can benefit from powerful functional transformations, like automatic differentiation grad, JIT compilation jit, automatic vectorization vmap, and parallelization pmap. JAX makes heavy use of XLA (Sabne, 2020) (see the following text) for code optimization. Specifically, for ease of use, highlevel numerical functions in JAX are NumPy like. JAX provides many numerical functions in NumPy, including basic mathematical operators, linear algebra functions, and Fourier transform routines. However, some fundamental designs are significantly different from NumPy, for instance, the wellestablished syntax for inplace updating and random samplings. This is the reason why we provide another set of numerical functions consistent with NumPy. In addition to its NumPylike API, JAX provides a wonderful set of composable functional transformations. Among them, automatic differentiation in JAX supports both forward and backward modes for arbitrary numerical functions. It can take derivatives of a function with a large subset of Python syntax, including loops, conditions, recursions, and closures. Moreover, JAX utilizes XLA to JIT compile your Python code on modern devices, like Central Processing Units (CPUs), Graphics Processing Units (GPUs), and Tensor Processing Units (TPUs). It can significantly accelerate the execution speed of your code and allows you to get maximal performance without having to leave Python. JAX also provides automatic vectorization or batching. It supports transforming loops to vector operations via a single functional call vmap. What’s more, JAX delivers pmap to express singleinstruction multipledata programs. Applying pmap to a function will JIT compile and execute the code in parallel on XLA devices, like multiple GPUs or TPU cores. Similar to vmap, pmap transformation maps a function over array axes. But what is different is that the former vectorizes functions by compiling the mapped axis as primitive operations, whereas the latter replicates the function and runs each replica on its own XLA device in parallel. Automatic differentiation and compilation in JAX can be composed arbitrarily to enable rapid experimentation of novel algorithms.
XLA (Sabne, 2020) is a domainspecific linear algebra compiler developed by Google that aims to improve the execution speed, memory usage, portability, and mobile footprint reduction of machinelearning algorithms. XLA compiler provides support for JIT compilation based on LLVM (Lattner and Adve, 2004). The frontend program (e.g., JAX) which wants to take advantage of the JIT compilation of XLA should first define the computation graph as ‘HighLevel Optimizer IR’ (HLO IR). Then, XLA takes this graph defined in HLO IR and compiles it into machine instructions for different backend architectures. Currently, XLA supports JIT compilation on backend devices of x8664 CPUs, NVIDIA GPUs, and Google TPUs. XLA is designed for easy portability on new hardware. It provides an abstract interface that a new hardware device can implement to create a backend to run existing computation graphs. Instead of implementing every existing operator for new hardware, XLA provides a simple and scalable mechanism that can retarget different backends. This advantage may be valuable for neuromorphic computing (Schuman et al., 2017), because new neuromorphic hardware can be interfaced as a new backend of XLA computation.
Numba (Lam et al., 2015) is a JIT compiler for numerical functions in Python. Similar to JAX, Numba supports the JIT compilation of a subset of Python and NumPy code based on the LLVM compiler. However, different from JAX which accelerates the computation flow composed of highlevel operators, Numba pays more attention to the acceleration of loopbased functions. Numba achieves excellent optimizations on Python functions with a lot of loops. It allows users to write finegrained code with native Python control flows and meanwhile obtains the running speed approaching C. This is a huge advantage compared to JAX because JAX does not support the automatic vectorization of a forloop function.
Appendix 3
Continuous integration and documentation generation
To ensure any code changes do not introduce unintended bugs or side effects, we standardized the development process and enabled the automatic continuous integration (CI) of BrainPy with GitHub Actions. Moreover, to update the tutorial and documentation with the latest code changes, we automated the documentation building of BrainPy with Read the Docs. Appendix 3—figure 1 illustrates the whole workflow of BrainPy development. First, any code change should be proposed through GitHub Pull Request. Once a Pull Request is opened, CI pipelines are triggered to test BrainPy codes on Windows, Linux, and macOS platforms (Appendix 3—figure 1 (1)). After all test suites are passed, the code reviewer should manually inspect the significance and correctness of the proposed code changes again. If all things are fine, the reviewer can merge the code into the master branch (Appendix 3—figure 1 (2)). After merging, a new set of test cases is triggered automatically to test that the latest BrainPy codebase does not have bugs (Appendix 3—figure 1 (3)). Besides, the merging operation also triggers the automatic documentation generation through the documentation hosting platform Read the Docs (Appendix 3—figure 1 (4)), in which the latest documentation, including the code annotation, user manual, and tutorials, are automatically built with Sphinx and hosted online at https://brainpy.readthedocs.io/.
Appendix 4
Mathematical operators for brain dynamics modeling
Brain dynamics modeling involves conventional computation based on dense matrices and eventdriven computation based on sparse connections. BrainPy provides operators for these two kinds of computations. For the list of the number of currently implemented operators please see Appendix 4—table 1.
Dense matrix operators
JAX (Frostig et al., 2018) has provided most numerical functions in NumPy (Harris et al., 2020). However, there are several significant differences between JAX and NumPy. First, the array structure in JAX does not support inplace updating. Second, numerical functions that need inplace updating are missing in JAX. Third, random sampling functions are significantly different from NumPy.
The dense matrix operators in BrainPy are based on JAX’s implementations but are designed to be seamlessly consistent with NumPy. First, we provide brainpy.math.Array which is consistent with NumPy’s ndarray structure, and a series of mathematical operations for brainpy.math.Array which is similar to those for ndarray. Second, mathematical operators for brainpy.math.Array, such as indexing, slicing, sorting, rounding, arithmetic operations, linear algebraic functions, and Fourier transform routines, are all supported. Many of these operators (nearly 85%) are directly implemented through the NumPylike functions in JAX, while BrainPy provides dozens of APIs missing or inconsistent in JAX. Third, to unify random number generators, BrainPy implements most of the random sampling functions in NumPy, including its univariate distributions, multivariate distributions, standard distributions, and utility functions.
Moreover, BrainPy is working on dense operators provided in PyTorch (Paszke et al., 2019) and TensorFlow (Abadi et al., 2016) libraries. In the future, BrainPy will continue to cover dense array operators in TensorFlow and PyTorch, since these implementation syntaxes have been widely accepted in the community.
Dedicated operators
Brain dynamics models differ from deep neural network (DNN) models in the way they perform computation. Brain dynamics models typically have sparse connections (less than 20% of neurons are connected to each other) and perform eventdriven computations (synaptic currents are only transmitted when a presynaptic neuron spikes). These unique features make brain dynamics models less efficient when conventional dense array operators are used. To tackle this efficiency issue, traditional brain simulators heavily rely on eventdriven synaptic operations. Previous works have explored eventdriven synaptic operations on both CPU platforms (see Vitay et al., 2015; Plesser et al., 2007; Stimberg et al., 2019) and GPU platforms (see Fidjeland et al., 2009; Brette and Goodman, 2011; Yavuz et al., 2016; Alevi et al., 2022).
Despite the effectiveness of these simulators, one limitation is the lack of abstraction of eventdriven synaptic operations as primitive lowlevel operators. In other words, these operations are not treated as fundamental building blocks that can be easily manipulated and optimized. This absence of abstraction hampers the development of more efficient algorithms and restricts the flexibility and extensibility of the simulators. Therefore, it is crucial to bridge this gap and provide a higher level of abstraction for eventdriven synaptic operations, which we refer to as ‘eventdriven operators’. Note here in BrainPy, eventdriven operators are employed within a clockdriven simulation schema, where the simulation advances in a synchronized manner, updating all neurons and synapses at each time step. These eventdriven operators process information based on the detection of spatial spiking events. They execute computations when the presynaptic neuron fires spikes at each time step. This contrasts with an eventdriven simulation approach (Ros et al., 2006), where neuronal or synaptic state updates are triggered by temporal spiking events, rather than updating all elements at each time step. Therefore, the key distinction between our eventdriven operators and an eventdriven simulation scheme lies in their scope and application: eventdriven operators serve as fundamental building blocks that define how individual components of an SNN respond to spatial events at the current time step, while an eventdriven simulation scheme serves as a methodology for simulating the collective behavior of the entire network based on the occurrence of temporal spikes.
Moreover, by abstracting these operations into primitive lowlevel operators, BrainPy offers automatic differentiation support compatible with jax.grad. It also enables vectorization and parallelization support compatible with jax.vmap and jax.pmap. This compatibility further enhances the applicability of eventdriven operators across a wider range of contexts.
Specifically, BrainPy provides these sparse and eventdriven operators in the following modules: (1) The brainpy.math.sparse module. This module provides a set of sparse operators that can store synaptic connectivity compactly and compute synaptic currents efficiently. (2) The brainpy.math.event module. This module implements eventdriven operators that only perform computations when spikes arrive. This can lead to significant improvements in efficiency, as the state of the system does not need to be constantly updated when no spikes arrive.
In addition, efficient modeling of brain dynamics encounters scalability issues. The computational resources and device memory requirements for brain dynamics models increase quadratically with the number of neurons, as the synaptic connectivity grows almost quadratically in relation to the number of neurons. This characteristic severely restricts the size of the network that can be simulated on a single device using traditional array programming solutions.
One established approach to address this challenge is the utilization of JIT connectivity (Lytton et al., 2008; Azevedo Carvalho et al., 2020; Knight and Nowotny, 2021). This method involves regenerating the synaptic connectivity during computation by controlling the same random seed. Specifically, the brainpy.math.jitconn module provides JIT connectivity as primitive operators, specifically designed for cases where synaptic connections follow a fixed connectivity rule and do not require modifications after initialization. These operators eliminate the memory overhead required for connectivity storage, as synaptic connectivity can be generated JIT during the execution of the operators. Notably, when compared to conventional operators, they enable the execution of largescale networks that are two to three orders of magnitude larger on a single device.
Moreover, BrainPy also provides operators that are involved in transformations among presynaptic neuronal data, synaptic data, and postsynaptic neuronal data in the brainpy.math module. Specifically, this module provides operators for mapping presynaptic neuronal data to its connected synaptic dimension (pretosyn), arithmetic operators including summation, product, max, min, mean, and softmax for transforming synaptic data to postsynaptic neuronal dimension (syntopost), and arithmetic operators such as summation, product, max, min, and mean for directly computing postsynaptic data from presynaptic events (pretopost).
Appendix 5
Numerical solvers for differential equations
To meet the large demand for solving differential equations in brain dynamics modeling, BrainPy implements numerical solvers for ODEs, SDEs, fractional differential equations (FDEs), and delay differential equations (DDEs). In general, numerical integration in BrainPy defines the system evolution of $x(t)\to x(t+dt)$, where $x$ is the state, $t$ is the current time, and $dt$ is the integration step.
ODE numerical solvers
In BrainPy, the integration of an ODE system $\mathrm{d}x/\mathrm{d}t=f(x,t)$ is performed as
1 integral=brainpy.odeint(f=<function>,
2 method=<str>,
3 dt=<float>)
where method denotes the numerical method used to integrate the ODE function, and dt controls the initial or default numerical integration step. A variety of numerical integration methods for ODEs, including Runge–Kutta, adaptive Runge–Kutta, and Exponential methods, are supported in BrainPy (see Appendix 5—table 1).
SDE numerical solvers
For a general SDE system with multidimensional driving Wiener processes,
BrainPy supports its numerical integration with
1 integral = brainpy.sdeint(f=<function > ,
2 g=<function > ,
3 method =<str > ,
4 dt =<float > ,
5 wiener_type=<’scalar’ or ’vector’>,
6 intg_type=<’Ito’ or ’Stratonovich’>)
where method specifies the numerical solver, dt the default integral step, wiener_type the type of Wiener process (SCALAR_WIENER for scalar noise or VECTOR_WIENER for multidimensional driving Wiener processes), and integral_type the integral type (ITO_SDE for the Itô integral or STRA_SDE for the Stratonovich stochastic integral). See Appendix 5—table 2 for the full list of SDE solvers currently implemented in BrainPy.
FDE numerical solvers
The numerical integration of FDEs is very similar to that of ODEs, except that the initial value, memory length, and fractional order should be provided. Given the fractionalorder differential equation
where the fractional order $0<\alpha \le 1$. BrainPy supports its numerical integration with the following format of
1 brainpy.fdeint(f=<function> ,
2 alpha=<float> ,
3 num_memory=<int> ,
4 inits=<dict> ,
5 method=<str> )
BrainPy supports two types of FDE, that is, the Caputo derivative and Grünwald–Letnikov derivative. Caputo derivatives are widely used in neuroscience modeling (Kaslik and Sivasundaram, 2012). However, the numerical integration of Caputo derivatives has a high memory consumption, because it requires integration over all past activities. This implies that FDEs with the Caputo derivative definition cannot be used to simulate realistic neural systems. However, the numerical method for Grünwald–Letnikov FDEs, brainpy.fde.GLShortMemory, is highly efficient because it does not require an infinite memory length for numerical solutions. With the increasing length of short memory, the accuracy of the numerical approximation will increase. Therefore, brainpy.fde.GLShortMemory can be applied to realworld neural modeling. See Appendix 5—table 3 for the full list of FDE solvers currently implemented in BrainPy.
DDE numerical solvers
Delays occur in any type of differential equation. In realistic neural modeling, delays are often inevitable. BrainPy supports equations with variables of constant delays, like
where the time lags $\tau}_{j$ are the positive constants. It also supports systems with statedependent delays, for example,
where $f}_{k$ is the function that computes the delay length by the system state $y(t)$. For neutraltyped equations in which delays appear in derivative terms,
BrainPy also supports its numerical integration.
BrainPy, in particular, implements interfaces to define these various delay variables. brainpy.math.TimeDelay and brainpy.math.LengthDelay are provided to support statedependent variables. Both brainpy.math.TimeDelay and brainpy.math.LengthDelay are used to delay neuronal signals in BrainPy, for example, Boolean spikes, realvalued synaptic conductance, or membrane potentials.
The TimeDelay is the class representing a connection delay measured in time units. For example, one might specify a $T$ ms delay. The TimeDelay class stores history values at times $[{T}_{0}T,{T}_{0}T+\mathrm{\Delta}t,\cdots ,{T}_{0}2\mathrm{\Delta}t,{T}_{0}\mathrm{\Delta}t,{T}_{0}]$, where $T}_{0$ is the current time and $\mathrm{\Delta}t$ is the time step. Users can retrieve the history values for any $t$ in the interval $[{T}_{0}T,{T}_{0}]$. For a $t$ that exactly matches one of the stored time points, TimeDelay directly returns the stored history values; otherwise, TimeDelay uses linear interpolation to estimate values between the nearest stored data points, or rounding to return the value from the nearest data point in time.
The LengthDelay class represents a connection delay based on the number or length of running iterations. For instance, one can specify a delay of $L$ iterations. It stores historical values at previous time steps, such as $[L,L1,\cdots ,1,0]$. Unlike TimeDelay, users can only retrieve the historical values at specific discrete time steps that have been stored.
Despite the distinct usage characteristics of TimeDelay and LengthDelay, both of them employ a circular array for their delay updates. This implementation involves utilizing an array of fixed length along with a cursor that indicates the current updating position within the array (see Appendix 5—figure 1).
The classes brainpy.math.NeuTimeDelay and brainpy.math.NeuLenDelay are identical to brainpy.math.TimeDelay and brainpy.math.LengthDelay, respectively. However, they are specifically designed to model neutral delay variables.
With these delay supports, the differential equations with delayed variables are intrinsically supported in each integral function.
For delayed ODEs, users can use
1 brainpy.odeint(f=<function> ,
2 method=<str> ,
3 dt=<float> ,
4 state_delays=<dict> ,
5 neutral_delays=<dict>)
Similarly, the numerical integration of delayed SDEs should utilize
1 brainpy.sdeint(f=<function> ,
2 g=<function> ,
3 method=<str> ,
4 dt=<float> ,
5 state_delays=<dict>)
For delayed FDEs, one can use
1 brainpy.fdeint(f=<function> ,
2 method=<str> ,
3 dt=<float> ,
4 num_memory=<int> ,
5 inits=<dict>,
6 state_delays=<dict>)
Note that we currently do not support neutral delays for delayed SDEs and FDEs. However, users can easily customize their supports for equations with neutral delays.
Appendix 6
Objectoriented JIT compilation and automatic differentiation
Under minimal constraints and assumptions, BrainPy enables the JIT compilation for class objects. These assumptions include the following:
The class for JIT must be a subclass of brainpy.BrainPyObject.
Dynamically changed variables in the class must be labeled as brainpy.math.Variable. Otherwise, they will be compiled as constants and cannot be updated during the program execution.
To take advantage of the JIT compilation, we can directly apply brainpy.math.jit() onto the instantiated class objects, or functions of a class object.
brainpy.math.grad() takes a function/object ($f:{\mathbb{R}}^{n}\to \mathbb{R}$, which returns a scalar value) as the input and returns a new function ($\mathrm{\partial}f(x)\to {\mathbb{R}}^{n}$) which computes the gradient of the original function/object.
1 grad_f=brainpy.math.grad(f, grad_vars=<variables to take gradients>)
brainpy.math.vector_grad() takes vectorvalued gradients for a function/object ($f:{\mathbb{R}}^{n}\to {\mathbb{R}}^{m}$). It returns a new function ($\mathrm{\partial}f(x):{\mathbb{R}}^{m}\to {\mathbb{R}}^{n}$) which evaluates the vectorJacobian products.
1 grad_f=brainpy.math.vector_grad(f, grad_vars<variables to take gradients>)
Another way to take gradients of a vectoroutput value is using brainpy.math.jacobian(). It aims to automatically compute the Jacobian matrices $\mathrm{\partial}f(x)\in {\mathbb{R}}^{m\times n}$ by the given function/object $f:{\mathbb{R}}^{n}\to {\mathbb{R}}^{m}$ at the given point of $x\in {\mathbb{R}}^{n}$.
1 grad_f=brainpy.math.jacobian(f, grad_vars<variables to take gradients>)
Appendix 7
Extension of BrainPy infrastructure
BrainPy features extensible architecture. New extensions can be easily made by using BrainPy infrastructure. Even new tools at the infrastructure level can be customized by using BrainPy operators.
At the toolbox level, BrainPy provides a mechanism in which the extension of a new tool can be made by adding a new subclass. For instance, a new synaptic connection method can be extended by subclassing brainpy.connect.TwoEndConnector:
1 class NewConnector(bp.conn.TwoEndConnector):
2 def __init__(self):
3 # initializing connector
4
5 def build_csr(self):
6 # build the CSR data structure
7
8 def build_coo(self):
9 # build the COO data structure
As another example, customizing a new weight initialization method can be added by inheriting from brainpy.initialize.Initializer base class:
1 class NewInitializer(bp.init.Initializer):
2 def __init__(self):
3 # initializing connector
4
5 def __call__(self, shape, dtype =None):
6 # building weights
At the model building level, BrainPy enables to flexibly customize the user’s own dynamical systems by simply subclassing brainpy.DynamicalSystem base class.
At the numerical integrator level, BrainPy provides an easy way to write new integrator methods. For example, adding a new Runge–Kutta integrator can be done by subclassing brainpy.ode.ExplicitRKIntegrator and providing the corresponding Butcher tableau:
1 class NewExplicitRK(bp.ode.ExplicitRKIntegrator):
2 A = [] # The A matrix in the Butcher tableau.
3 B = [] # The B vector in the Butcher tableau.
4 C = [] # The C vector in the Butcher tableau.
In a similar way, a customized adaptive Runge–Kutta integrator can be extended by subclassing brainpy.ode.AdaptiveRKIntegrator with the specification of the corresponding Butcher tableau:
1 class NewAdaptiveRK(bp.ode.ExplicitRKIntegrator):
2 A = [] # The A matrix in the Butcher tableau.
3 B1 = [] # The B1 vector in the Butcher tableau.
4 B2 = [] # The B2 vector in the Butcher tableau.
5 C = [] # The C vector in the Butcher tableau.
At the operator level, BrainPy is trying to provide a way to write finegranularity lowlevel operators in the same Python interface by adopting the same JIT compilation technology (please refer to Appendix 8).
Appendix 8
Extension of lowlevel operators in BrainPy
By bridging Numba (Lam et al., 2015), JAX (Frostig et al., 2018), and XLA (Sabne, 2020), BrainPy enables the customization of primitive operators through the native Python syntax. Exposing a custom operator to JAX requires registering an XLA ‘custom call’, and providing its C callback for Python. Based on the following two properties of Numba, we are aware of the possibility of using Numba as a convenient method for writing lowlevel kernels that support JAX’s JIT compilation. First, unlike JAX, which only supports the JIT compilation of highlevel functions, Numba is a JIT compiler that allows users to write a function with lowlevel finegrained operations, for instance, looping over an array, or conditional branching over array values. This implies that numba.jit() can be used as a means to write lowlevel kernel functions. The second property of Numba is that it provides a mechanism to create a compiled function that is callable from the foreign C code, such as XLA. Specifically, numba.cfunc() can be used to create a C callback for Numba’s JIT function to interface with XLA. Therefore, by integrating Numba with JAX and XLA, BrainPy provides an interface where users write primitive operators directly with Python syntax. Note that Numba supports various native Python features and a large subset of NumPy functions. Therefore, there is a large flexibility in coding lowlevel primitives with Numba.
Below, we illustrate how to write a primitive operator in BrainPy. Particularly, to customize a primitive operator we need to provide two functions. The first is an abstract evaluation function that tells JAX what shapes and types of outputs are produced according to the input shapes and types:
1 def abstract_eval(*ins):
2 return outs
in which ins specifies the information of input shapes and types, outs denotes the array information of shapes and types of outputs. The other function is the concrete computation function, in which the output data is calculated according to the input data:
1 def concrete_comp(outs, ins):
2 # calculate outputs according to inputs
where outs and ins are output and input data owned by XLA, respectively. Note this function should not return anything. All computations must be made in place. Finally, by using
1 # "name" is the operator name
2 # "concrete_comp" is the concrete computation function
3 # "abstract_eval" is the abstract evaluation function
4 op =brainpy.math.CustomOpByNumba(abstract_eval, concrete_comp, name)
we register a primitive operator op. This operator op can be used anywhere the user wants. The Numbabased approach for operator customization demonstrates comparable performance to the native C++based XLA operator registration. To illustrate this, we conducted a performance comparison of the COBA network model (Vogels and Abbott, 2005) using both an eventdriven operator implementation based on Numba and C++.
This eventdriven operator implements the matrix–vector multiplication $\mathbf{y}=\mathbf{v}\cdot \mathbf{M}$ for synaptic computation, where $\mathbf{v}$ is the presynaptic spikes, $\mathbf{M}$ the synaptic connection matrix, and $\mathbf{y}$ the postsynaptic current. Specifically, it performs matrix–vector multiplication in a sparse and efficient way by exploiting the event property of the input vector $\mathbf{v}$. Particularly, we performs eventdriven matrix–vector multiplication only for the nonzero elements of the vector, which are called events. This can reduce the number of operations and memory accesses, and improve the running performance of matrix–vector multiplication.
Based on our Pythonlevel registration syntax, this operator can be implemented as:
1 from jax.core import ShapedArray
2 import brainpy.math as bm
3
4 # the abstract evaluation function
5 def abs_eval(events, indices, indptr, *, weight, post_num):
6 return [ShapedArray((post_num,), bm.float32), ]
7
8 # the concrete function implementing the eventdriven computation
9 def con_compute(outs, ins):
10 post_val, =outs
11 post_val.fill(0)
12 events, indices, indptr, weight, _=ins
13 weight=weight[()]
14 for i in range(events.size):
15 if events[i]:
16 for j in range(indptr[i], indptr[i+1]):
17 index =indices[j]
18 post_val[index]+=weight
19
20 # operator registration
21 event_sum =bm.CustomOpByNumba(eval_shape =abs_eval, cpu_func =con_compute)
Listing 1: The eventdriven operator implemented with our Python syntax for the computation of $\mathbf{y}=\mathbf{v}\cdot \mathbf{M}$.
This operator can also be implemented with the pure C++ syntax:
1 #include <cstdint>
2 #include <cstring>
3 #include <cmath>
4
5 template <typename F, typename I>
6 void cpu_csr_event_sum_homo(void *out, const void **in) {
7 const std::uint32_t pre_size = *reinterpret_cast<const std::uint32_t *>(in[0]);
8 const std::uint32_t post_size = *reinterpret_cast<const std::uint32_t *>(in(1));
9 const bool *events=reinterpret_cast<const bool *>(in(2));
10 const I *indices=reinterpret_cast <const I *>(in(3));
11 const I *indptr=reinterpret_cast <const I *>(in(4));
12 const F weight=reinterpret_cast<const F *>(in(5))[0];
13 F *result=reinterpret_cast<F *>(out);
14
15 // algorithm
16 memset(&result[0], 0, sizeof(F) * post_size);
17 for (std::uint32_t i=0; i<pre_size; ++i) {
18 if (events[i]){
19 for (I j=indptr[i]; j<indptr[i+1]; ++j) {
20 result[indices[j]]+=weight;
21 }
22 }
23 }
24 }
Listing 2: The eventdriven operator utilizes C++ for the computation of $\mathbf{y}=\mathbf{v}\cdot \mathbf{M}$. Here, we present the main code snippet that implements the eventdriven matrix–vector multiplication. Please note that we have omitted the code for Python binding, compilation, registration, and other related aspects. For detailed instructions and a comprehensive tutorial on XLA operator customization, we encourage users to refer to the appropriate resource.
The speed comparison between the two approaches has been depicted in Figure 9. Although the approach shows promising results on CPU hardware, it is not directly compatible with other computing platforms like GPUs. This restricts the applicability and scalability of the proposed method, as GPUs are increasingly used to accelerate brain dynamics models. To overcome this limitation, currently, we are working on alternative approach that can be used in both CPU and GPU devices, allowing for broader utilization of available hardware resources and unlocking new possibilities for customizing any complex brain dynamics operators.
Appendix 9
Multiscale spiking neural network for the visual system modeling
We build a spiking network model examined in Figure 2 and Figure 3 for modeling the visual system (V1, V2, V4, TEO, and TEpd). Simulations are performed using a network of Hodgkin–Huxley neurons, with the local circuit and longrange connectivity structure derived from Markov et al., 2014. Each of the five areas consists of 2000 neurons, with 1600 excitatory and 400 inhibitory neurons.
For each neuron, the membrane potential dynamics is modified from Traub and Miles, 1991 and is described by the following equations:
where $V$ is the membrane potential, $G(t)$ stands for synaptic interactions, $C}_{m$ is the membrane capacitance per unit area, $E}_{K}=90\phantom{\rule{thinmathspace}{0ex}}\mathrm{m}\mathrm{V$ and $E}_{Na}=50\phantom{\rule{thinmathspace}{0ex}}\text{mV$ are the potassium and sodium reversal potentials, respectively, $E}_{l}=60\phantom{\rule{thinmathspace}{0ex}}\text{mV$ is the leak reversal potential, $\overline{g}}_{K}=30\phantom{\rule{thinmathspace}{0ex}}{\text{mS/cm}}^{2$ and $\overline{g}}_{Na}=100\phantom{\rule{thinmathspace}{0ex}}{\text{mS/cm}}^{2$ are the potassium and sodium conductance per unit area, respectively, and $\overline{g}}_{l}=0.05\phantom{\rule{thinmathspace}{0ex}}{\text{mS/cm}}^{2$ is the leak conductance per unit area.
Each neuron is composed of two active ion channels, including the potassium and sodium channels. Because the potassium and sodium channels are voltage sensitive, according to the biological experiments, $m$, $n$, and $h$ are used to simulate the activation of the channels.
Specifically, $n$ measures the activation of potassium channels, and $m$ and $h$ measures the activation and inactivation of sodium channels, respectively. $\alpha}_{x$ and $\beta}_{x$ are rate constants for the ion channel $x$ and depend exclusively on the membrane potential. The voltagedependent expressions of the rate constants were modified from the model described by Traub and Miles, 1991:
where $V}_{T$ = −63 mV adjusts the threshold.
For the synapse, we use conductancebased synaptic interactions. Particularly, $G(t)$ is given by:
where $V}_{i$ is the membrane potential of neuron $i$. The synaptic conductance from neuron $j$ to neuron $i$ is represented by ${g}_{ji}(t)$, while $E}_{j$ signifies the reversal potential of that synapse. For excitatory synapses, $E}_{j$ was set to 0 mV, whereas for inhibitory synapses, it was −80 mV. The dynamics of the synaptic conductance is given by:
where $t}_{j}^{k$ is the spiking time of the presynaptic spike. Whenever a spike occurred in neuron $j$, the synaptic conductance $g}_{ji$ experienced an immediate increase by a fixed amount $g}_{\mathrm{m}\mathrm{a}\mathrm{x}$. Subsequently, the conductance $g}_{ji$ decayed exponentially with a time constant of ${\tau}_{\mathrm{d}\mathrm{e}\mathrm{c}\mathrm{a}\mathrm{y}}=5$ ms for excitation and ${\tau}_{\mathrm{d}\mathrm{e}\mathrm{c}\mathrm{a}\mathrm{y}}=10$ ms for inhibition.
The connection density is set according to the experimental connectivity data (Markov et al., 2014). The interareal connectivity is measured as a weight index (see Appendix 9—table 1), called the extrinsic fraction of labeled neurons (Markov et al., 2014). The intraarea connectivity is set according to the setting in a standard E/I balanced network (Brette et al., 2007).
Moreover, we introduce distancedependent interareal synaptic delays by assuming a conduction velocity of 3.5 m/s (Swadlow, 1990) and using a distance matrix based on experimentally measured wiring distances across areas (Markov et al., 2014).
Appendix 10
Training reservoir computing model with multiple algorithms
Reservoir computing is a type of recurrent neural network that is often used for processing temporal data. Unlike traditional recurrent neural networks, reservoir computing fixes the weights of the recurrent layer (known as the ‘reservoir’) and only trains the weights of the output layer. This makes training much more efficient.
A reservoir computing model can be trained using various algorithms, such as online learning, offline learning, and backpropagation learning, to optimize its performance. Online learning refers to the process of updating the model in real time as new data becomes available. This algorithm allows the model to adapt and adjust its predictions continuously. Offline learning, on the other hand, involves training the model using a fixed dataset, where the entire dataset is used to update the model’s parameters. This method is particularly useful when a large amount of data is available upfront. Lastly, backpropagation learning utilizes a technique called backpropagation to train the model by computing the gradients of the model’s parameters and adjusting them accordingly.
The unified building and training interface of BrainPy enables the training of the same reservoir model with multiple training algorithms. By employing BrainPy, we can compare the performance of different training algorithms and determine which approach yields the best results for the reservoir computing model.
The following lists the details of such training.
Reservoir model
The dynamics of the reservoir model used here are given by:
where $\mathbf{x}(t)$ is the reservoir state, $\mathbf{y}(t)$ the readout value, $\mathbf{W}}_{in$ and $\mathbf{W}}_{rec$ are input and recurrent connection matrices, respectively, $\mathbf{W}}_{out$ the readout weight matrix which can be trained by either offline learning or online learning algorithms, $\alpha \in (0,1]$ the leaky rate, $\mathbf{u}(t)$ the input at time step $t$, and $f$ the nonlinear activation function.
In BrainPy, the reservoir model can be easily instantiated as the following code:
1 reservoir =brainpy.dyn.Reservoir(input_shape, output_shape, leaky_rate)
Inferring Lorenz strange attractor
The reservoir model is utilized for inference tasks in this work. To generate training and testing data, we numerically integrate a simplified model of a weather system originally developed by Lorenz, 1963. This model comprises three coupled nonlinear differential equations:
The state $X(t)=[x(t),y(t),z(t){]}^{T}$ represents a vector of Rayleigh–Bénard convection observables. The system exhibits deterministic chaos, displaying sensitivity to initial conditions and forming a strange attractor in the phase space trajectory (Figure 4D).
In this task, we train a reservoir model to predict the $T$stepahead value of all Lorenz variables, $x$, $y$, and $z$. During training, we provide the model with all three variables. During testing, we only provide the model with $x$, $y$, and $z$ at $T$stepahead, and it must infer $x,y$, and $z$ after $T$ steps. Here, we choose $T=5$.
In this task, the input size was set to 3, the recurrent layer of the reservoir model contained 100 units, and the output size was 3, as used in Figure 4DF.
Training with ridge regression
The training objective of reservoir models is to find the optimal $\mathbf{W}}_{out$ that minimizes the square error between $\mathbf{y}(t)$ and ${\mathbf{y}}^{target}(t)$. The common way to learn the linear output weight $\mathbf{W}}_{out$ is using the ridge regression algorithm. The ridge regression, also known as regression with Tikhonov regularization, is given by:
where $\beta$ is a regularization coefficient, $I$ is the identity matrix, and $X$ is the concatenated hidden states of all samples.
In BrainPy, the reservoir model trained with ridge regression can be implemented as:
1 model =ESN(num_in, num_rec, num_out)
2 trainer =bp.RidgeTrainer(model)
3 trainer.fit([X, Y])
4 outputs =trainer.predict(X)
Training with FORCE learning
Ridge regression is an offline learning method, meaning that it needs all of the data to be present before it can learn the model parameters. This can be a problem when training reservoir models with a lot of data, because the memory requirements can be too high for some devices. FORCE learning (Sussillo and Abbott, 2009), on the other hand, is an online learning algorithm. This means that it can learn the model parameters one sample of data at a time. This makes it a much more efficient way to train reservoir models with large datasets. Therefore, FORCE learning is a good choice for training reservoir models when the amount of data is large or the memory resources are limited.
The FORCE learning is done using the recursive least squares (RLS) algorithm. It is a supervised errordriven learning rule, that is the weight changes depending on the error made by each neuron: the difference between the output of a neuron ${\mathbf{y}}_{i}(t)$ and a desired value ${\mathbf{y}}_{i}^{\mathrm{t}\mathrm{a}\mathrm{r}\mathrm{g}\mathrm{e}\mathrm{t}}(t)$.
Contrary to the delta learning rule which modifies weights proportionally to the error and to the direct input to a synapse ($\mathrm{\Delta}{w}_{ij}=\eta \cdot {e}_{i}\cdot {\mathbf{x}}_{j}$), the RLS learning uses a running estimate of the inverse correlation matrix of the inputs to each neuron:
Each neuron $i$ therefore stores a square matrix $P}^{i$, whose size depends on the number of weights arriving at the neuron. Readout neurons receive synapses from all $N$ recurrent neurons, so the $P$ matrix is $N\ast N$.
The inverse correlation matrix $P$ is updated at each time step with the following rule:
Each matrix $P}^{i$ is initialized to the diagonal matrix and scaled by a factor $1/\delta$, where $\delta$ is 1 in the current implementation and can be used to modify implicitly the learning rate (Sussillo and Abbott, 2009).
In BrainPy, the reservoir model trained with FORCE learning can be implemented as:
1 model =ESN(num_in, num_rec, num_out)
2 trainer =bp.ForceTrainer(model, alpha =0.1)
3 trainer.fit([X, Y])
4 trainer.fit([X, Y])
5 outputs =trainer.predict(X)
Training with backpropagation algorithm
The readout layer in the reservoir model is just a singlelayer Perceptron. To train its weights, we can use the backpropagation algorithm. Backpropagation is a method used in artificial neural networks to calculate a gradient that is needed in the calculation of the weights to be used in the network. The loss function used here is the mean square error between the reservoir output and the target output:
The updated weight between neuron $i$ and $j$ is calculated by:
In BrainPy, the reservoir model trained with backpropagation algorithms can be implemented as:
1 reservoir = bp.dyn.Reservoir(num_in, num_rec)
2 readout = bp.dnn.Dense(num_rec, num_out, mode =bm.training_mode)
3 trainer = bp.BPFF(target =readout,
4 loss_fun =bp.losses.mean_squared_error,
5 optimizer =bp.optim.Adam(1e3))
6 # batch_data: the data generated by "reservoir"
7 trainer.fit(batch_data, num_epoch =100)
Evaluation metrics
The performance of a reservoir computing model is usually measured with the mean squared error, that is, the average squared difference between the predicted and actual values:
where $N}_{y$ is the number of training samples and $T$ is the number of time steps.
Appendix 11
Experimental details for benchmark comparisons
In this section, we provide a comprehensive overview of the experimental benchmark details used in Figure 6, Figure 7, and Figure 8. The purpose is to present a complete picture of the experimental setup and methodology employed in our study. The details encompass the following aspects: hardware specifications, software versions, algorithm hyperparameters, and performance measurements.
By providing these experimental benchmark details, we aim to ensure transparency and reproducibility, allowing readers and researchers to understand and replicate our experiments accurately.
Hardware specifications
We conducted a series of experiments on various computing devices, namely the CPU, GPU, and TPU, in order to validate and compare the simulation speeds of several widely utilized brain simulators. The brain simulators under investigation included Brian2 (Stimberg et al., 2019), NEURON (Hines and Carnevale, 1997), NEST (Gewaltig and Diesmann, 2007), GeNN (Yavuz et al., 2016), and Brian2CUDA (Alevi et al., 2022).
Particularly, the computing devices we used here are:
CPU: The CPU used was the Intel Xeon W2255 processor. This is a 10core, 20thread CPU based on Intel’s Cascade Lake microarchitecture. It has a base clock frequency of 3.7 GHz and a max turbo boost up to 4.5 GHz. The Xeon W2255 utilizes the LGA2066 socket and supports up to 512 GB of ECCregistered DDR42933 RAM across 6 channels. It has 24.75 MB of L3 cache. As a servergrade CPU with a high core count, the Xeon W2255 is well suited for heavily parallelized simulations.
GPU: The GPU used was an NVIDIA RTX A6000. This is a highend Ampere architecture GPU aimed at professional visualization, AI, and compute workloads. The RTX A6000 has 10,752 CUDA cores, 336 tensor cores, and 84 RT cores. It comes equipped with 48 GB of GDDR6 memory clocked at 16 Gbps, providing up to 1 TB/s of memory bandwidth. The RTX A6000 has a maximum power consumption of 300 W and requires auxiliary power connectors. It uses a PCIe 4.0x16 interface. With its large number of CUDA cores and abundant memory, the RTX A6000 is well suited for massively parallel simulations and neural network training.
TPU: The TPU simulations leveraged the Kaggle free TPU v38 cloud instance. This provides access to one of Google’s TPU v3 chips via their cloud platform. Specifically, the v38 instance gives 8 TPU v3 cores, each providing 128 GB/s of bandwidth to highperformance HBM memory. The TPU v3 is optimized for both training and inferencing of DNNs, providing up to 420 TFLOPS of mixed precision computing. By utilizing Google’s cloud TPUs, researchers can run models with minimal coding changes while leveraging Google’s optimized deep learning frameworks.
Software versions
We carried out benchmark experiments using Python 3.10.12 running on Ubuntu 20.04.6 LTS. For any experiments utilizing a GPU, we used version 11.6 of the NVIDIA CUDA Toolkit to take advantage of the parallel processing capabilities of the GPU hardware. Other dependent software versions are: NumPy 1.24.3, Numba 0.57.1, jax 0.4.16, and jaxlib 0.4.16.
The comparison brain simulators for benchmarking are:
NEURON at version 8.2.0
NEST at version 3.6
Brian2 at version 2.5.4
GeNN at version 4.8.1
Brian2GeNN at version of 1.7.0: Brian2GeNN is a bridge between Brian2 and GeNN that allows Brian2 users to run their simulations on GPUs using GeNN.
Brian2CUDA at version of 1.0a3: Brian2CUDA is a native CUDA implementation of Brian2 that allows Brian2 users to run their simulations on GPUs without the need for a bridge.
Performance measurements
By testing against these simulators on benchmark tasks, we aimed to thoroughly evaluate the performance in terms of simulation speed and accuracy across different model sizes and paradigms.
When evaluating simulation speed, we focused solely on measuring the execution time of the simulation itself, excluding any time spent on compilation, initialization, or other preparatory steps. This allowed us to make a direct comparison of the raw simulation performance between our simulator and others. We simulated networks of varying sizes. This range of model scales allowed us to determine how well our simulator performs as network size and complexity increase. The final experimental results can be obtained in Figure 6, Figure 7, and Figure 8.
Accuracy evaluations
To evaluate the accuracy, we configured all simulators to use identical model parameters for a fair comparison.
First, we verified that all simulators generated consistent average firing rates for a given network model (see Appendix 11—figure 1 and Appendix 11—figure 2).
Second, we qualitatively compared the overall network activity patterns produced by each simulator to ensure they exhibited the same dynamics. While exact spiketospike reproducibility was not guaranteed between different simulator implementations, we confirmed that our simulator produced activity consistent with the reference simulators for both firing rates and networklevel dynamics (see Appendix 11—figure 3 and Appendix 11—figure 4).
Third, we recognize that the precision of numerical computation plays a crucial role in accurately simulating biologically detailed neural networks, such as the COBAHH network model used in our benchmarks. To assess the numerical integration accuracy of each neuron in the COBAHH network model, we conducted a 5s simulation and examined the presence of NaN membrane potentials at the end of the simulation. The occurrence of NaN membrane potentials indicates that the corresponding neurons are no longer active and signifies a loss of simulation accuracy. This analysis was performed on the GPU backend of Brian2GeNN, Brian2CUDA, and BrainPy. The results of this analysis can be found in Appendix 11—figure 5. We specifically focused on the analysis results of singleprecision floatingpoint simulations, as we did not encounter any NaN results when simulating with double precision. Our observations reveal that the singleprecision computation with XLA in BrainPy exhibits a higher proportion of NaN results compared to Brian2CUDA and GeNN. Notably, GeNN demonstrated very few occurrences of NaN membrane potentials after simulation, which may be attributed to the special handling of NaN within the GeNN computation.
To address the issue of a larger number of NaN membrane potentials leading to reduced neuronal spiking and communication spikes, we took steps to resolve this problem in BrainPy. Our aim was to ensure a fair comparison when benchmarking the simulation speed against other brain simulators. Specifically, the occurrence of NaN membrane potentials was attributed to the use of the $x/(\mathrm{exp}(x)1)$ operation during the integration of the Hodgkin–Huxley neuron model with lowprecision floatingpoint calculations. In order to mitigate the catastrophic loss of precision when $x$ is close to zero, we replaced this operation with the relative error exponential function, represented by $1/\mathrm{e}\mathrm{x}\mathrm{p}\mathrm{r}\mathrm{e}\mathrm{l}(x)$. This modification ensures that the numerical calculations do not result in NaN values even during significantly long simulations. As a result of this fix, we did not encounter any instances of NaN membrane potentials, even after conducting extensive and prolonged simulations. We believe that these revised operations contribute to a more equitable benchmarking process, eliminating any potential bias caused by the presence of NaN values. The speed benchmarking can be obtained in Figure 8.
Experimental settings
In the below, we describe the experimental setting details used in Figure 6, Figure 7, and Figure 8.
Figure 6
In the experiments depicted in Figure 6A, we exercise precise control over the equivalent theoretical FLOPs (floatingpoint operations) performed by the LIF (Leaky IntegrateandFire) neurons and the matrix–vector multiplication $\mathbf{M}\mathbf{v}$ ($\mathbf{W}\in {\mathbb{R}}^{m\times m}$ and $\mathbf{v}\in {\mathbb{R}}^{m}$). In each trial, subsequent to determining the size $m$, we modify the number of neurons in the LIF simulation, ensuring that they collectively execute the same theoretical FLOPs. To simplify the computation of the total FLOPS, we adopt the Euler method with a single time step to solve the differential equations within the LIF neuron model.
On the other hand, for the COBA network (Vogels and Abbott, 2005) experiments showcased in Figure 6B and Figure 6C, the dynamical equations were resolved using the Exponential Euler method with a step size of 0.1ms. The synaptic computation was performed through dense matrix multiplication. Given the presynaptic spikes represented by the vector $\mathbf{v}$, the postsynaptic conductance ($\mathbf{g}}_{post$) is computed using the equation ${\mathbf{g}}_{post}={g}_{max}\ast \mathbf{v}\cdot M$, where $g}_{max$ denotes the maximum synaptic conductance, and $M$ represents the connection matrix. We assess the simulation time of the network using the aforementioned dense operation under two conditions: with JIT compilation and without JIT compilation.
.
Figure 7
The COBA network model (Vogels and Abbott, 2005) is simulated using the Exponential Euler numerical integration method to approximate solutions to the differential equations governing network dynamics. A fixed simulation time step of 0.1 ms is utilized for numerical simulations.
Accurately isolating the computational time spent on simulating synaptic connections in the COBA network is challenging, as the synapses are computed in an eventdriven manner based on spiking activity. Since the number of spikes generated in the network varies across simulations, this causes variability in synapse simulation time measurements. To separately quantify time spent on neuron versus synapse computations, we first profile the neuron simulation time in isolation. This is measured by simulating only the neuronal dynamics without any synaptic connections for a 500ms duration. Next, we profile the endtoend run time of the full COBA network simulation including both neurons and dynamic synapses for the same 500ms duration. Finally, the computational time attributed specifically to simulating synapses can be directly estimated by subtracting the isolated neuron simulation time from the full network simulation time. This approach separates and quantifies the contributions of simulating neuronal and synaptic computations to the overall run time of COBA network simulations.
For the model without dedicated OP, we employ dense matrix multiplication to perform the synaptic computation, same as the operation used in Figure 6. On the other hand, For the model with dedicated OP, we utilize our eventdriven operator called brainpy.math.event.csrmv for handling the synaptic computation. This specialized operator is designed specifically to efficiently handle such computations in an eventdriven manner.
All simulations were performed using a single thread, excluding the acceleration effect of multithreading concurrence.
Figure 8
Same as Figure 7, the COBA network model (Vogels and Abbott, 2005), the COBAHH network model (Brette et al., 2007), and the decisionmaking network model (Wang, 2002) are simulated using the Exponential Euler numerical integration method with a fixed simulation time step of 0.1ms.
The simulations were conducted across a diverse range of computing devices (including CPUs, GPUs, and TPUs), encompassing various hardware configurations, and were executed using networks of different sizes. To ensure statistical robustness, each trial was repeated 10 times, thereby totaling 10 simulations for each experimental setup. These simulations were carried out for a duration of 5 s. Finally, to provide a representative measure, we reported the average time taken across these 10 simulations.
On the CPU device, we simulate the model using a single thread across different simulators. On Brian2, we open 12 threads for parallel simulation. However, we did not report the simulation speed results of Brian2 runs on the COBA network model, since singlethreaded Brian2 runs were faster than using multithreaded compartments in this case.
Other supplements
We evaluate the speedup of eventdriven operators over traditional dense matrix operators on both CPU and GPU devices. Evaluation results are listed in Appendix 11—figure 7. Both CPU and GPU devices demonstrate a significant speed advantage of several orders of magnitude when utilizing eventdriven operators, in comparison to dense ones. Notably, as the number of neurons increases, eventdriven operators showcase an even greater speedup on both platforms.
We also conducted COBA and COBAHH experiments on TPU devices. The experimental results are shown in Appendix 11—figure 8. Although TPUs can perform double precision operations, they are not as efficient at it as they are at lower precisions such as float16 or bfloat16. Therefore, we here only tested models with singleprecision operations.
Data availability
BrainPy is distributed via the pypi package index (https://pypi.org/project/brainpy/) and is publicly released on GitHub (https://github.com/brainpy/BrainPy/; Wang et al., 2024) under the license of GNU General Public License v3.0. Its documentation is hosted on the free documentation hosting platform Read the Docs (https://brainpy.readthedocs.io/). Rich examples and illustrations of BrainPy are publicly available at the website of https://brainpyexamples.readthedocs.io/. The source codes of these examples are available at https://github.com/brainpy/examples/ (Wang, 2023). All the codes to reproduce the results in the paper can be found at the following GitHub repository: https://github.com/brainpy/brainpyelifereproducibility/ (copy archived at Wang, 2024).
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Article and author information
Author details
Funding
Ministry of Science & Technology, People Republic of China (2021ZD0200204)
 Si Wu
PekingTsinghua Center for Life Sciences
 Si Wu
The funders had no role in study design, data collection, and interpretation, or the decision to submit the work for publication.
Acknowledgements
This work was supported by Science and Technology Innovation 2030Brain Science and Braininspired Intelligence Project (No. 2021ZD0200204) and Beijing Academy of Artificial Intelligence. We would like to express our sincere gratitude to Marcel Stimberg for his valuable insights and assistance with benchmarking brain simulators, which greatly contributed to this paper. We would like to acknowledge Xiaohan Lin, Yifeng Gong, Hongyaoxing Gu, Linfei Lu, Xiaolong Zou, Zhiyu Zhao, Yingqian Jiang, Xinyu Liu, and all other members of the Wu laboratory for their helpful discussions. We thank all GitHub users who contributed codes to BrainPy.
Copyright
© 2023, Wang et al.
This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.
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