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Understanding how genetically encoded rules drive and guide complex neuronal growth processes is essential to comprehending the brain's architecture, and agent-based models (ABMs) offer a powerful simulation approach to further develop this understanding. However, accurately calibrating these models remains a challenge. Here, we present a novel application of Approximate Bayesian Computation (ABC) to address this issue. ABMs are based on parametrized stochastic rules that describe the time evolution of small components -- the so-called agents -- discretizing the system, leading to stochastic simulations that require appropriate treatment. Mathematically, the calibration defines a stochastic inverse problem. We propose to address it in a Bayesian setting using ABC. We facilitate the repeated comparison between data and simulations by quantifying the morphological information of single neurons with so-called morphometrics and resort to statistical distances to measure discrepancies between populations thereof. We conduct experiments on synthetic as well as experimental data. We find that ABC utilizing Sequential Monte Carlo sampling and the Wasserstein distance finds accurate posterior parameter distributions for representative ABMs. We further demonstrate that these ABMs capture specific features of pyramidal cells of the hippocampus (CA1). Overall, this work establishes a robust framework for calibrating agent-based neuronal growth models and opens the door for future investigations using Bayesian techniques for model building, verification, and adequacy assessment., Comment: 32 pages, 12 Figures

Agent-based modeling plays an essential role in gaining insights into biology, sociology, economics, and other fields. However, many existing agent-based simulation platforms are not suitable for large-scale studies due to the low performance of the underlying simulation engines. To overcome this limitation, we present a novel high-performance simulation engine. We identify three key challenges for which we present the following solutions. First, to maximize parallelization, we present an optimized grid to search for neighbors and parallelize the merging of thread-local results. Second, we reduce the memory access latency with a NUMA-aware agent iterator, agent sorting with a space-filling curve, and a custom heap memory allocator. Third, we present a mechanism to omit the collision force calculation under certain conditions. Our evaluation shows an order of magnitude improvement over Biocellion, three orders of magnitude speedup over Cortex3D and NetLogo, and the ability to simulate 1.72 billion agents on a single server. Supplementary Materials, including instructions to reproduce the results, are available at: https://doi.org/10.5281/zenodo.6463816, Comment: Accepted to PPoPP '23: The 28th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming

Neuromorphic systems open up opportunities to enlarge the explorative space for computational research. However, it is often challenging to unite efficiency and usability. This work presents the software aspects of this endeavor for the BrainScaleS-2 system, a hybrid accelerated neuromorphic hardware architecture based on physical modeling. We introduce key aspects of the BrainScaleS-2 Operating System: experiment workflow, API layering, software design, and platform operation. We present use cases to discuss and derive requirements for the software and showcase the implementation. The focus lies on novel system and software features such as multi-compartmental neurons, fast re-configuration for hardware-in-the-loop training, applications for the embedded processors, the non-spiking operation mode, interactive platform access, and sustainable hardware/software co-development. Finally, we discuss further developments in terms of hardware scale-up, system usability and efficiency.

We introduce the problem of proficiency modeling: Given a user's posts on a social media platform, the task is to identify the subset of posts or topics for which the user has some level of proficiency. This enables the filtering and ranking of social media posts on a given topic as per user proficiency. Unlike experts on a given topic, proficient users may not have received formal training and possess years of practical experience, but may be autodidacts, hobbyists, and people with sustained interest, enabling them to make genuine and original contributions to discourse. While predicting whether a user is an expert on a given topic imposes strong constraints on who is a true positive, proficiency modeling implies a graded scoring, relaxing these constraints. Put another way, many active social media users can be assumed to possess, or eventually acquire, some level of proficiency on topics relevant to their community. We tackle proficiency modeling in an unsupervised manner by utilizing user embeddings to model engagement with a given topic, as indicated by a user's preference for authoring related content. We investigate five alternative approaches to model proficiency, ranging from basic ones to an advanced, tailored user modeling approach, applied within two real-world benchmarks for evaluation.

Researchers in biology are faced with the tough challenge of developing high-performance computer simulations of their increasingly complex agent-based models. BioDynaMo is an open-source agent-based simulation platform that aims to alleviate researchers from the intricacies that go into the development of high-performance computing. Through a high-level interface, researchers can implement their models on top of BioDynaMo's multi-threaded core execution engine to rapidly develop simulations that effectively utilize parallel computing hardware. In biological agent-based modeling, the type of operations that are typically the most compute-intensive are those that involve agents interacting with their local neighborhood. In this work, we investigate the currently implemented method of handling neighborhood interactions of cellular agents in BioDynaMo, and ways to improve the performance to enable large-scale and complex simulations. We propose to replace the kd-tree implementation to find and iterate over the neighborhood of each agent with a uniform grid method that allows us to take advantage of the massively parallel architecture of graphics processing units (GPUs). We implement the uniform grid method in both CUDA and OpenCL to address GPUs from all major vendors and evaluate several techniques to further improve the performance. Furthermore, we analyze the performance of our implementations for models with a varying density of neighboring agents. As a result, the performance of the mechanical interactions method improved by up to two orders of magnitude in comparison to the multithreaded baseline version. The implementations are open-source and publicly available on Github., Comment: 8 pages, 12 figures

We present the BrainScaleS-2 mobile system as a compact analog inference engine based on the BrainScaleS-2 ASIC and demonstrate its capabilities at classifying a medical electrocardiogram dataset. The analog network core of the ASIC is utilized to perform the multiply-accumulate operations of a convolutional deep neural network. At a system power consumption of 5.6W, we measure a total energy consumption of 192uJ for the ASIC and achieve a classification time of 276us per electrocardiographic patient sample. Patients with atrial fibrillation are correctly identified with a detection rate of (93.7${\pm}$0.7)% at (14.0${\pm}$1.0)% false positives. The system is directly applicable to edge inference applications due to its small size, power envelope, and flexible I/O capabilities. It has enabled the BrainScaleS-2 ASIC to be operated reliably outside a specialized lab setting. In future applications, the system allows for a combination of conventional machine learning layers with online learning in spiking neural networks on a single neuromorphic platform.

The neuromorphic BrainScaleS-2 ASIC comprises mixed-signal neurons and synapse circuits as well as two versatile digital microprocessors. Primarily designed to emulate spiking neural networks, the system can also operate in a vector-matrix multiplication and accumulation mode for artificial neural networks. Analog multiplication is carried out in the synapse circuits, while the results are accumulated on the neurons' membrane capacitors. Designed as an analog, in-memory computing device, it promises high energy efficiency. Fixed-pattern noise and trial-to-trial variations, however, require the implemented networks to cope with a certain level of perturbations. Further limitations are imposed by the digital resolution of the input values (5 bit), matrix weights (6 bit) and resulting neuron activations (8 bit). In this paper, we discuss BrainScaleS-2 as an analog inference accelerator and present calibration as well as optimization strategies, highlighting the advantages of training with hardware in the loop. Among other benchmarks, we classify the MNIST handwritten digits dataset using a two-dimensional convolution and two dense layers. We reach 98.0% test accuracy, closely matching the performance of the same network evaluated in software.

We present software facilitating the usage of the BrainScaleS-2 analog neuromorphic hardware system as an inference accelerator for artificial neural networks. The accelerator hardware is transparently integrated into the PyTorch machine learning framework using its extension interface. In particular, we provide accelerator support for vector-matrix multiplications and convolutions; corresponding software-based autograd functionality is provided for hardware-in-the-loop training. Automatic partitioning of neural networks onto one or multiple accelerator chips is supported. We analyze implementation runtime overhead during training as well as inference, provide measurements for existing setups and evaluate the results in terms of the accelerator hardware design limitations. As an application of the introduced framework, we present a model that classifies activities of daily living with smartphone sensor data.

Being permanently confronted with an uncertain world, brains have faced evolutionary pressure to represent this uncertainty in order to respond appropriately. Often, this requires visiting multiple interpretations of the available information or multiple solutions to an encountered problem. This gives rise to the so-called mixing problem: since all of these "valid" states represent powerful attractors, but between themselves can be very dissimilar, switching between such states can be difficult. We propose that cortical oscillations can be effectively used to overcome this challenge. By acting as an effective temperature, background spiking activity modulates exploration. Rhythmic changes induced by cortical oscillations can then be interpreted as a form of simulated tempering. We provide a rigorous mathematical discussion of this link and study some of its phenomenological implications in computer simulations. This identifies a new computational role of cortical oscillations and connects them to various phenomena in the brain, such as sampling-based probabilistic inference, memory replay, multisensory cue combination, and place cell flickering., Comment: 34 pages, 9 figures

Motivation: Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulators do not always take full advantage of modern hardware and often have a field-specific software design. Results: We present a novel simulation platform called BioDynaMo that alleviates both of these problems. BioDynaMo features a general-purpose and high-performance simulation engine. We demonstrate that BioDynaMo can be used to simulate use cases in: neuroscience, oncology, and epidemiology. For each use case we validate our findings with experimental data or an analytical solution. Our performance results show that BioDynaMo performs up to three orders of magnitude faster than the state-of-the-art baseline. This improvement makes it feasible to simulate each use case with one billion agents on a single server, showcasing the potential BioDynaMo has for computational biology research. Availability: BioDynaMo is an open-source project under the Apache 2.0 license and is available at www.biodynamo.org. Instructions to reproduce the results are available in supplementary information. Contact: lukas.breitwieser@inf.ethz.ch, a.s.hesam@tudelft.nl, omutlu@ethz.ch, r.bauer@surrey.ac.uk Supplementary information: Available at https://doi.org/10.5281/zenodo.4501515, Comment: 8 pages, 6 figures

BrainScaleS-2 is a mixed-signal accelerated neuromorphic system targeted for research in the fields of computational neuroscience and beyond-von-Neumann computing. To augment its flexibility, the analog neural network core is accompanied by an embedded SIMD microprocessor. The BrainScaleS Operating System (BrainScaleS OS) is a software stack designed for the user-friendly operation of the BrainScaleS architectures. We present and walk through the software-architectural enhancements that were introduced for the BrainScaleS-2 architecture. Finally, using a second-version BrainScaleS-2 prototype we demonstrate its application in an example experiment based on spike-based expectation maximization.

We present first experimental results on the novel BrainScaleS-2 neuromorphic architecture based on an analog neuro-synaptic core and augmented by embedded microprocessors for complex plasticity and experiment control. The high acceleration factor of 1000 compared to biological dynamics enables the execution of computationally expensive tasks, by allowing the fast emulation of long-duration experiments or rapid iteration over many consecutive trials. The flexibility of our architecture is demonstrated in a suite of five distinct experiments, which emphasize different aspects of the BrainScaleS-2 system.

For a biological agent operating under environmental pressure, energy consumption and reaction times are of critical importance. Similarly, engineered systems are optimized for short time-to-solution and low energy-to-solution characteristics. At the level of neuronal implementation, this implies achieving the desired results with as few and as early spikes as possible. With time-to-first-spike coding both of these goals are inherently emerging features of learning. Here, we describe a rigorous derivation of a learning rule for such first-spike times in networks of leaky integrate-and-fire neurons, relying solely on input and output spike times, and show how this mechanism can implement error backpropagation in hierarchical spiking networks. Furthermore, we emulate our framework on the BrainScaleS-2 neuromorphic system and demonstrate its capability of harnessing the system's speed and energy characteristics. Finally, we examine how our approach generalizes to other neuromorphic platforms by studying how its performance is affected by typical distortive effects induced by neuromorphic substrates., Comment: 24 pages, 11 figures

An increasing body of evidence suggests that the trial-to-trial variability of spiking activity in the brain is not mere noise, but rather the reflection of a sampling-based encoding scheme for probabilistic computing. Since the precise statistical properties of neural activity are important in this context, many models assume an ad-hoc source of well-behaved, explicit noise, either on the input or on the output side of single neuron dynamics, most often assuming an independent Poisson process in either case. However, these assumptions are somewhat problematic: neighboring neurons tend to share receptive fields, rendering both their input and their output correlated; at the same time, neurons are known to behave largely deterministically, as a function of their membrane potential and conductance. We suggest that spiking neural networks may, in fact, have no need for noise to perform sampling-based Bayesian inference. We study analytically the effect of auto- and cross-correlations in functionally Bayesian spiking networks and demonstrate how their effect translates to synaptic interaction strengths, rendering them controllable through synaptic plasticity. This allows even small ensembles of interconnected deterministic spiking networks to simultaneously and co-dependently shape their output activity through learning, enabling them to perform complex Bayesian computation without any need for noise, which we demonstrate in silico, both in classical simulation and in neuromorphic emulation. These results close a gap between the abstract models and the biology of functionally Bayesian spiking networks, effectively reducing the architectural constraints imposed on physical neural substrates required to perform probabilistic computing, be they biological or artificial.

The massively parallel nature of biological information processing plays an important role for its superiority to human-engineered computing devices. In particular, it may hold the key to overcoming the von Neumann bottleneck that limits contemporary computer architectures. Physical-model neuromorphic devices seek to replicate not only this inherent parallelism, but also aspects of its microscopic dynamics in analog circuits emulating neurons and synapses. However, these machines require network models that are not only adept at solving particular tasks, but that can also cope with the inherent imperfections of analog substrates. We present a spiking network model that performs Bayesian inference through sampling on the BrainScaleS neuromorphic platform, where we use it for generative and discriminative computations on visual data. By illustrating its functionality on this platform, we implicitly demonstrate its robustness to various substrate-specific distortive effects, as well as its accelerated capability for computation. These results showcase the advantages of brain-inspired physical computation and provide important building blocks for large-scale neuromorphic applications., Comment: This preprint has been published 2019 November 14. Please cite as: Kungl A. F. et al. (2019) Accelerated Physical Emulation of Bayesian Inference in Spiking Neural Networks. Front. Neurosci. 13:1201. doi: 10.3389/fnins.2019.01201

Neural-network models of high-level brain functions such as memory recall and reasoning often rely on the presence of stochasticity. The majority of these models assumes that each neuron in the functional network is equipped with its own private source of randomness, often in the form of uncorrelated external noise. However, both in vivo and in silico, the number of noise sources is limited due to space and bandwidth constraints. Hence, neurons in large networks usually need to share noise sources. Here, we show that the resulting shared-noise correlations can significantly impair the performance of stochastic network models. We demonstrate that this problem can be overcome by using deterministic recurrent neural networks as sources of uncorrelated noise, exploiting the decorrelating effect of inhibitory feedback. Consequently, even a single recurrent network of a few hundred neurons can serve as a natural noise source for large ensembles of functional networks, each comprising thousands of units. We successfully apply the proposed framework to a diverse set of binary-unit networks with different dimensionalities and entropies, as well as to a network reproducing handwritten digits with distinct predefined frequencies. Finally, we show that the same design transfers to functional networks of spiking neurons., Comment: 22 pages, 11 figures

Spiking networks that perform probabilistic inference have been proposed both as models of cortical computation and as candidates for solving problems in machine learning. However, the evidence for spike-based computation being in any way superior to non-spiking alternatives remains scarce. We propose that short-term plasticity can provide spiking networks with distinct computational advantages compared to their classical counterparts. In this work, we use networks of leaky integrate-and-fire neurons that are trained to perform both discriminative and generative tasks in their forward and backward information processing paths, respectively. During training, the energy landscape associated with their dynamics becomes highly diverse, with deep attractor basins separated by high barriers. Classical algorithms solve this problem by employing various tempering techniques, which are both computationally demanding and require global state updates. We demonstrate how similar results can be achieved in spiking networks endowed with local short-term synaptic plasticity. Additionally, we discuss how these networks can even outperform tempering-based approaches when the training data is imbalanced. We thereby show how biologically inspired, local, spike-triggered synaptic dynamics based simply on a limited pool of synaptic resources can allow spiking networks to outperform their non-spiking relatives., Comment: corrected typo in abstract

Despite being originally inspired by the central nervous system, artificial neural networks have diverged from their biological archetypes as they have been remodeled to fit particular tasks. In this paper, we review several possibilites to reverse map these architectures to biologically more realistic spiking networks with the aim of emulating them on fast, low-power neuromorphic hardware. Since many of these devices employ analog components, which cannot be perfectly controlled, finding ways to compensate for the resulting effects represents a key challenge. Here, we discuss three different strategies to address this problem: the addition of auxiliary network components for stabilizing activity, the utilization of inherently robust architectures and a training method for hardware-emulated networks that functions without perfect knowledge of the system's dynamics and parameters. For all three scenarios, we corroborate our theoretical considerations with experimental results on accelerated analog neuromorphic platforms., Comment: accepted at ISCAS 2017

How spiking networks are able to perform probabilistic inference is an intriguing question, not only for understanding information processing in the brain, but also for transferring these computational principles to neuromorphic silicon circuits. A number of computationally powerful spiking network models have been proposed, but most of them have only been tested, under ideal conditions, in software simulations. Any implementation in an analog, physical system, be it in vivo or in silico, will generally lead to distorted dynamics due to the physical properties of the underlying substrate. In this paper, we discuss several such distortive effects that are difficult or impossible to remove by classical calibration routines or parameter training. We then argue that hierarchical networks of leaky integrate-and-fire neurons can offer the required robustness for physical implementation and demonstrate this with both software simulations and emulation on an accelerated analog neuromorphic device., Comment: accepted at IJCNN 2017

Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be executable on hybrid cloud computing systems. This paper describes challenges and lessons learnt during the early stages of the software development process, in the context of implementation issues and the international nature of the collaboration., Comment: 4th Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4), 2016

This paper is a brief update on developments in the BioDynaMo project, a new platform for computer simulations for biological research. We will discuss the new capabilities of the simulator, important new concepts simulation methodology as well as its numerous applications to the computational biology and nanoscience communities., Comment: The paper contains inaccurate content and claims that need to be verified

Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example, biological systems (such as the human brain) comprise an extremely complex organization and heterogeneous interactions across different spatial and temporal scales. In order to facilitate research on such problems, the BioDynaMo project (\url{https://biodynamo.web.cern.ch/}) aims at a general platform for computer simulations for biological research. Since the scientific investigations require extensive computer resources, this platform should be executable on hybrid cloud computing systems, allowing for the efficient use of state-of-the-art computing technology. This paper describes challenges during the early stages of the software development process. In particular, we describe issues regarding the implementation and the highly interdisciplinary as well as international nature of the collaboration. Moreover, we explain the methodologies, the approach, and the lessons learnt by the team during these first stages.

This document contains the documentation of TOBI (Tools for BCI) Interface D (TiD). TiD tries to establish a standardized interface for event transmission in neuroscience experiments. It is designed in a client-server architecture. Clients are connecting to a single server and events are delivered in a "bus-like" manner. TiD events are based on XML messages. So TiD messages can also get custom extended. A cross platform C++ library is available and provides all TiD functionality. To avoid jitter effect, hampering event processing, TiD was optimized towards performance. The documentation provides further performance tweaks to decrease TiD message processing latency and also decrease event timing jitter.

The {\pi}-plasmon dispersion in graphene was scrutinized by momentum(q)-resolved electron energy-loss spectroscopy with an improved q resolution and found to display the square root of q dispersion characteristic of the collective excitation of two-dimensional electron systems, in contrast with previous experimental and theoretical studies which reported a linear q dispersion. Our theoretical elaborations on the q-dependent spectra affirm this square root of q relation and further unveil an in-plane electronic anisotropy. The physical property of the {\pi} plasmon is thoroughly compared to that of the two-dimensional plasmon due to carriers of the Dirac fermions. A clear distinction between the {\pi} plasmon and the two-dimensional Dirac plasmon was demonstrated, clarifying the common notion on correlating the linearly-dispersed Dirac cones to the linear dispersion of the {\pi} plasmon previously reported., Comment: 20 pages, 6 figures, regular article, Physical Review B accepted 2014

Advancing the size and complexity of neural network models leads to an ever increasing demand for computational resources for their simulation. Neuromorphic devices offer a number of advantages over conventional computing architectures, such as high emulation speed or low power consumption, but this usually comes at the price of reduced configurability and precision. In this article, we investigate the consequences of several such factors that are common to neuromorphic devices, more specifically limited hardware resources, limited parameter configurability and parameter variations. Our final aim is to provide an array of methods for coping with such inevitable distortion mechanisms. As a platform for testing our proposed strategies, we use an executable system specification (ESS) of the BrainScaleS neuromorphic system, which has been designed as a universal emulation back-end for neuroscientific modeling. We address the most essential limitations of this device in detail and study their effects on three prototypical benchmark network models within a well-defined, systematic workflow. For each network model, we start by defining quantifiable functionality measures by which we then assess the effects of typical hardware-specific distortion mechanisms, both in idealized software simulations and on the ESS. For those effects that cause unacceptable deviations from the original network dynamics, we suggest generic compensation mechanisms and demonstrate their effectiveness. Both the suggested workflow and the investigated compensation mechanisms are largely back-end independent and do not require additional hardware configurability beyond the one required to emulate the benchmark networks in the first place. We hereby provide a generic methodological environment for configurable neuromorphic devices that are targeted at emulating large-scale, functional neural networks.

This document contains the documentation of TOBI (Tools for BCI) Interface A (TiA). TiA is a standardized interface to transmit raw biosignals. It is able to deal with multirate and block-oriented data transmission. Data is distinguished by different signal types (e.g., EEG, EOG, NIRS,...), whereby those signals can be acquired at the same time from different acquisition devices. TiA is built as a client-server model. Multiple clients can connect to one server. Information is exchanged via a control- and a separated data connection. Control commands and meta information are transmitted over the control connection. Raw biosignal data is delivered using the data connection in a unidirectional way. For this purpose a standardized handshaking protocol and raw data packet have been developed. Thus, an abstraction layer between hardware devices and data processing was evolved facilitating standardization.

In this paper we present a methodological framework that meets novel requirements emerging from upcoming types of accelerated and highly configurable neuromorphic hardware systems. We describe in detail a device with 45 million programmable and dynamic synapses that is currently under development, and we sketch the conceptual challenges that arise from taking this platform into operation. More specifically, we aim at the establishment of this neuromorphic system as a flexible and neuroscientifically valuable modeling tool that can be used by non-hardware-experts. We consider various functional aspects to be crucial for this purpose, and we introduce a consistent workflow with detailed descriptions of all involved modules that implement the suggested steps: The integration of the hardware interface into the simulator-independent model description language PyNN; a fully automated translation between the PyNN domain and appropriate hardware configurations; an executable specification of the future neuromorphic system that can be seamlessly integrated into this biology-to-hardware mapping process as a test bench for all software layers and possible hardware design modifications; an evaluation scheme that deploys models from a dedicated benchmark library, compares the results generated by virtual or prototype hardware devices with reference software simulations and analyzes the differences. The integration of these components into one hardware-software workflow provides an ecosystem for ongoing preparative studies that support the hardware design process and represents the basis for the maturity of the model-to-hardware mapping software. The functionality and flexibility of the latter is proven with a variety of experimental results.

The magnetic coupling between iron and alpha - MnAs in the epitaxial system Fe/MnAs/GaAs(001) has been studied at the sub-micron scale, using element selective x-ray photoemission electron microscopy. At room temperature, MnAs layers display ridges and grooves, alternating alpha (magnetic) and beta (non-magnetic) phases. The self-organised microstructure of MnAs and the stray fields that it generates govern the local alignment between the Fe and alpha - MnAs magnetization directions, which is mostly antiparallel with a marked dependence upon the magnetic domain size.

Human capital investment is central to raising wages. This chapter describes trends in human capital investment and educational attainment. It reviews the evidence of the wage returns to educational attainment and to early childhood education, K-12 education, postsecondary education, and workforce development policies and programs. Finally, this chapter synthesizes a decade of Hamilton Project policy proposals on education and human capital around a framework of access, affordability, and quality.