Nengo: a Python tool for building large-scale functional brain models

ARACHNE: A neural-neuroglial network builder with remotely controlled parallel computing

Creating and running realistic models of neural networks has hitherto been a task for computing professionals rather than experimental neuroscientists. This is mainly because such networks usually engage substantial computational resources, the handling of which requires specific programing skills. Here we put forward a newly developed simulation environment ARACHNE: it enables an investigator to build and explore cellular networks of arbitrary biophysical and architectural complexity using the logic of NEURON and a simple interface on a local computer or a mobile device. The interface can control, through the internet, an optimized computational kernel installed on a remote computer cluster. ARACHNE can combine neuronal (wired) and astroglial (extracellular volume-transmission driven) network types and adopt realistic cell models from the NEURON library. The program and documentation (current version) are available at GitHub repository https://github.com/LeonidSavtchenko/Arachne under the MIT License (MIT).

A Spiking Neuron Model of Word Associations for the Remote Associates Test

Generating associations is important for cognitive tasks including language acquisition and creative problem solving. It remains an open question how the brain represents and processes associations. The Remote Associates Test (RAT) is a task, originally used in creativity research, that is heavily dependent on generating associations in a search for the solutions to individual RAT problems. In this work we present a model that solves the test. Compared to earlier modeling work on the RAT, our hybrid (i.e., non-developmental) model is implemented in a spiking neural network by means of the Neural Engineering Framework (NEF), demonstrating that it is possible for spiking neurons to be organized to store the employed representations and to manipulate them. In particular, the model shows that distributed representations can support sophisticated linguistic processing. The model was validated on human behavioral data including the typical length of response sequences and similarity relationships in produced responses. These data suggest two cognitive processes that are involved in solving the RAT: one process generates potential responses and a second process filters the responses.

Improving With Practice: A Neural Model of Mathematical Development

The ability to improve in speed and accuracy as a result of repeating some task is an important hallmark of intelligent biological systems. Although gradual behavioral improvements from practice have been modeled in spiking neural networks, few such models have attempted to explain cognitive development of a task as complex as addition. In this work, we model the progression from a counting-based strategy for addition to a recall-based strategy. The model consists of two networks working in parallel: a slower basal ganglia loop and a faster cortical network. The slow network methodically computes the count from one digit given another, corresponding to the addition of two digits, whereas the fast network gradually "memorizes" the output from the slow network. The faster network eventually learns how to add the same digits that initially drove the behavior of the slower network. Performance of this model is demonstrated by simulating a fully spiking neural network that includes basal ganglia, thalamus, and various cortical areas. Consequently, the model incorporates various neuroanatomical data, in terms of brain areas used for calculation and makes psychologically testable predictions related to frequency of rehearsal. Furthermore, the model replicates developmental progression through addition strategies in terms of reaction times and accuracy, and naturally explains observed symptoms of dyscalculia.

Deep Artificial Neural Networks and Neuromorphic Chips for Big Data Analysis: Pharmaceutical and Bioinformatics Applications

Over the past decade, Deep Artificial Neural Networks (DNNs) have become the state-of-the-art algorithms in Machine Learning (ML), speech recognition, computer vision, natural language processing and many other tasks. This was made possible by the advancement in Big Data, Deep Learning (DL) and drastically increased chip processing abilities, especially general-purpose graphical processing units (GPGPUs). All this has created a growing interest in making the most of the potential offered by DNNs in almost every field. An overview of the main architectures of DNNs, and their usefulness in Pharmacology and Bioinformatics are presented in this work. The featured applications are: drug design, virtual screening (VS), Quantitative Structure-Activity Relationship (QSAR) research, protein structure prediction and genomics (and other omics) data mining. The future need of neuromorphic hardware for DNNs is also discussed, and the two most advanced chips are reviewed: IBM TrueNorth and SpiNNaker. In addition, this review points out the importance of considering not only neurons, as DNNs and neuromorphic chips should also include glial cells, given the proven importance of astrocytes, a type of glial cell which contributes to information processing in the brain. The Deep Artificial Neuron-Astrocyte Networks (DANAN) could overcome the difficulties in architecture design, learning process and scalability of the current ML methods.

Modeling Interactions between Speech Production and Perception: Speech Error Detection at Semantic and Phonological Levels and the Inner Speech Loop

Production and comprehension of speech are closely interwoven. For example, the ability to detect an error in one's own speech, halt speech production, and finally correct the error can be explained by assuming an inner speech loop which continuously compares the word representations induced by production to those induced by perception at various cognitive levels (e.g., conceptual, word, or phonological levels). Because spontaneous speech errors are relatively rare, a picture naming and halt paradigm can be used to evoke them. In this paradigm, picture presentation (target word initiation) is followed by an auditory stop signal (distractor word) for halting speech production. The current study seeks to understand the neural mechanisms governing self-detection of speech errors by developing a biologically inspired neural model of the inner speech loop. The neural model is based on the Neural Engineering Framework (NEF) and consists of a network of about 500,000 spiking neurons. In the first experiment we induce simulated speech errors semantically and phonologically. In the second experiment, we simulate a picture naming and halt task. Target-distractor word pairs were balanced with respect to variation of phonological and semantic similarity. The results of the first experiment show that speech errors are successfully detected by a monitoring component in the inner speech loop. The results of the second experiment show that the model correctly reproduces human behavioral data on the picture naming and halt task. In particular, the halting rate in the production of target words was lower for phonologically similar words than for semantically similar or fully dissimilar distractor words. We thus conclude that the neural architecture proposed here to model the inner speech loop reflects important interactions in production and perception at phonological and semantic levels.

Serendipitous Offline Learning in a Neuromorphic Robot

We demonstrate a hybrid neuromorphic learning paradigm that learns complex sensorimotor mappings based on a small set of hard-coded reflex behaviors. A mobile robot is first controlled by a basic set of reflexive hand-designed behaviors. All sensor data is provided via a spike-based silicon retina camera (eDVS), and all control is implemented via spiking neurons simulated on neuromorphic hardware (SpiNNaker). Given this control system, the robot is capable of simple obstacle avoidance and random exploration. To train the robot to perform more complex tasks, we observe the robot and find instances where the robot accidentally performs the desired action. Data recorded from the robot during these times is then used to update the neural control system, increasing the likelihood of the robot performing that task in the future, given a similar sensor state. As an example application of this general-purpose method of training, we demonstrate the robot learning to respond to novel sensory stimuli (a mirror) by turning right if it is present at an intersection, and otherwise turning left. In general, this system can learn arbitrary relations between sensory input and motor behavior.

Optimizing Semantic Pointer Representations for Symbol-Like Processing in Spiking Neural Networks

The Semantic Pointer Architecture (SPA) is a proposal of specifying the computations and architectural elements needed to account for cognitive functions. By means of the Neural Engineering Framework (NEF) this proposal can be realized in a spiking neural network. However, in any such network each SPA transformation will accumulate noise. By increasing the accuracy of common SPA operations, the overall network performance can be increased considerably. As well, the representations in such networks present a trade-off between being able to represent all possible values and being only able to represent the most likely values, but with high accuracy. We derive a heuristic to find the near-optimal point in this trade-off. This allows us to improve the accuracy of common SPA operations by up to 25 times. Ultimately, it allows for a reduction of neuron number and a more efficient use of both traditional and neuromorphic hardware, which we demonstrate here.

Closed-Loop Neuromorphic Benchmarks

Evaluating the effectiveness and performance of neuromorphic hardware is difficult. It is even more difficult when the task of interest is a closed-loop task; that is, a task where the output from the neuromorphic hardware affects some environment, which then in turn affects the hardware's future input. However, closed-loop situations are one of the primary potential uses of neuromorphic hardware. To address this, we present a methodology for generating closed-loop benchmarks that makes use of a hybrid of real physical embodiment and a type of “minimal” simulation. Minimal simulation has been shown to lead to robust real-world performance, while still maintaining the practical advantages of simulation, such as making it easy for the same benchmark to be used by many researchers. This method is flexible enough to allow researchers to explicitly modify the benchmarks to identify specific task domains where particular hardware excels. To demonstrate the method, we present a set of novel benchmarks that focus on motor control for an arbitrary system with unknown external forces. Using these benchmarks, we show that an error-driven learning rule can consistently improve motor control performance across a randomly generated family of closed-loop simulations, even when there are up to 15 interacting joints to be controlled.

Benchmarking neuromorphic systems with Nengo

Nengo is a software package for designing and simulating large-scale neural models. Nengo is architected such that the same Nengo model can be simulated on any of several Nengo backends with few to no modifications. Backends translate a model to specific platforms, which include GPUs and neuromorphic hardware. Nengo also contains a large test suite that can be run with any backend and focuses primarily on functional performance. We propose that Nengo's large test suite can be used to benchmark neuromorphic hardware's functional performance and simulation speed in an efficient, unbiased, and future-proof manner. We implement four benchmark models and show that Nengo can collect metrics across five different backends that identify situations in which some backends perform more accurately or quickly.

ANNarchy: a code generation approach to neural simulations on parallel hardware

Many modern neural simulators focus on the simulation of networks of spiking neurons on parallel hardware. Another important framework in computational neuroscience, rate-coded neural networks, is mostly difficult or impossible to implement using these simulators. We present here the ANNarchy (Artificial Neural Networks architect) neural simulator, which allows to easily define and simulate rate-coded and spiking networks, as well as combinations of both. The interface in Python has been designed to be close to the PyNN interface, while the definition of neuron and synapse models can be specified using an equation-oriented mathematical description similar to the Brian neural simulator. This information is used to generate C++ code that will efficiently perform the simulation on the chosen parallel hardware (multi-core system or graphical processing unit). Several numerical methods are available to transform ordinary differential equations into an efficient C++code. We compare the parallel performance of the simulator to existing solutions.

A spiking neural integrator model of the adaptive control of action by the medial prefrontal cortex

Subjects performing simple reaction-time tasks can improve reaction times by learning the expected timing of action-imperative stimuli and preparing movements in advance. Success or failure on the previous trial is often an important factor for determining whether a subject will attempt to time the stimulus or wait for it to occur before initiating action. The medial prefrontal cortex (mPFC) has been implicated in enabling the top-down control of action depending on the outcome of the previous trial. Analysis of spike activity from the rat mPFC suggests that neural integration is a key mechanism for adaptive control in precisely timed tasks. We show through simulation that a spiking neural network consisting of coupled neural integrators captures the neural dynamics of the experimentally recorded mPFC. Errors lead to deviations in the normal dynamics of the system, a process that could enable learning from past mistakes. We expand on this coupled integrator network to construct a spiking neural network that performs a reaction-time task by following either a cue-response or timing strategy, and show that it performs the task with similar reaction times as experimental subjects while maintaining the same spiking dynamics as the experimentally recorded mPFC.