Simulation of networks of spiking neurons: A review of tools and strategies

We review different aspects of the simulation of spiking neural networks. We start by reviewing the different types of simulation strategies and algorithms that are currently implemented. We next review the precision of those simulation strategies, in particular in cases where plasticity depends on the exact timing of the spikes. We overview different simulators and simulation environments presently available (restricted to those freely available, open source and documented). For each simulation tool, its advantages and pitfalls are reviewed, with an aim to allow the reader to identify which simulator is appropriate for a given task. Finally, we provide a series of benchmark simulations of different types of networks of spiking neurons, including Hodgkin-Huxley type, integrate-and-fire models, interacting with current-based or conductance-based synapses, using clock-driven or event-driven integration strategies. The same set of models are implemented on the different simulators, and the codes are made available. The ultimate goal of this review is to provide a resource to facilitate identifying the appropriate integration strategy and simulation tool to use for a given modeling problem related to spiking neural networks.Comment: 49 pages, 24 figures, 1 table; review article, Journal of Computational Neuroscience, in press (2007

GeNN: a code generation framework for accelerated brain simulations

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

SurReal: enhancing Surgical simulation Realism using style transfer

Surgical simulation is an increasingly important element of surgical education. Using simulation can be a means to address some of the significant challenges in developing surgical skills with limited time and resources. The photo-realistic fidelity of simulations is a key feature that can improve the experience and transfer ratio of trainees. In this paper, we demonstrate how we can enhance the visual fidelity of existing surgical simulation by performing style transfer of multi-class labels from real surgical video onto synthetic content. We demonstrate our approach on simulations of cataract surgery using real data labels from an existing public dataset. Our results highlight the feasibility of the approach and also the powerful possibility to extend this technique to incorporate additional temporal constraints and to different applications

CMU DeepLens: Deep Learning For Automatic Image-based Galaxy-Galaxy Strong Lens Finding

Galaxy-scale strong gravitational lensing is not only a valuable probe of the dark matter distribution of massive galaxies, but can also provide valuable cosmological constraints, either by studying the population of strong lenses or by measuring time delays in lensed quasars. Due to the rarity of galaxy-scale strongly lensed systems, fast and reliable automated lens finding methods will be essential in the era of large surveys such as LSST, Euclid, and WFIRST. To tackle this challenge, we introduce CMU DeepLens, a new fully automated galaxy-galaxy lens finding method based on Deep Learning. This supervised machine learning approach does not require any tuning after the training step which only requires realistic image simulations of strongly lensed systems. We train and validate our model on a set of 20,000 LSST-like mock observations including a range of lensed systems of various sizes and signal-to-noise ratios (S/N). We find on our simulated data set that for a rejection rate of non-lenses of 99%, a completeness of 90% can be achieved for lenses with Einstein radii larger than 1.4" and S/N larger than 20 on individual $g$-band LSST exposures. Finally, we emphasize the importance of realistically complex simulations for training such machine learning methods by demonstrating that the performance of models of significantly different complexities cannot be distinguished on simpler simulations. We make our code publicly available at https://github.com/McWilliamsCenter/CMUDeepLens .Comment: 12 pages, 9 figures, submitted to MNRA

KInNeSS: A Modular Framework for Computational Neuroscience

Making use of very detailed neurophysiological, anatomical, and behavioral data to build biological-realistic computational models of animal behavior is often a difficult task. Until recently, many software packages have tried to resolve this mismatched granularity with different approaches. This paper presents KInNeSS, the KDE Integrated NeuroSimulation Software environment, as an alternative solution to bridge the gap between data and model behavior. This open source neural simulation software package provides an expandable framework incorporating features such as ease of use, scalabiltiy, an XML based schema, and multiple levels of granularity within a modern object oriented programming design. KInNeSS is best suited to simulate networks of hundreds to thousands of branched multu-compartmental neurons with biophysical properties such as membrane potential, voltage-gated and ligand-gated channels, the presence of gap junctions of ionic diffusion, neuromodulation channel gating, the mechanism for habituative or depressive synapses, axonal delays, and synaptic plasticity. KInNeSS outputs include compartment membrane voltage, spikes, local-field potentials, and current source densities, as well as visualization of the behavior of a simulated agent. An explanation of the modeling philosophy and plug-in development is also presented. Further developement of KInNeSS is ongoing with the ultimate goal of creating a modular framework that will help researchers across different disciplines to effecitively collaborate using a modern neural simulation platform.Center for Excellence for Learning Education, Science, and Technology (SBE-0354378); Air Force Office of Scientific Research (F49620-01-1-0397); Office of Naval Research (N00014-01-1-0624

Imitating Driver Behavior with Generative Adversarial Networks

The ability to accurately predict and simulate human driving behavior is critical for the development of intelligent transportation systems. Traditional modeling methods have employed simple parametric models and behavioral cloning. This paper adopts a method for overcoming the problem of cascading errors inherent in prior approaches, resulting in realistic behavior that is robust to trajectory perturbations. We extend Generative Adversarial Imitation Learning to the training of recurrent policies, and we demonstrate that our model outperforms rule-based controllers and maximum likelihood models in realistic highway simulations. Our model both reproduces emergent behavior of human drivers, such as lane change rate, while maintaining realistic control over long time horizons.Comment: 8 pages, 6 figure

Formal Modeling of Connectionism using Concurrency Theory, an Approach Based on Automata and Model Checking

This paper illustrates a framework for applying formal methods techniques, which are symbolic in nature, to specifying and verifying neural networks, which are sub-symbolic in nature. The paper describes a communicating automata [Bowman & Gomez, 2006] model of neural networks. We also implement the model using timed automata [Alur & Dill, 1994] and then undertake a verification of these models using the model checker Uppaal [Pettersson, 2000] in order to evaluate the performance of learning algorithms. This paper also presents discussion of a number of broad issues concerning cognitive neuroscience and the debate as to whether symbolic processing or connectionism is a suitable representation of cognitive systems. Additionally, the issue of integrating symbolic techniques, such as formal methods, with complex neural networks is discussed. We then argue that symbolic verifications may give theoretically well-founded ways to evaluate and justify neural learning systems in the field of both theoretical research and real world applications