Computational Modeling of Biological Neural Networks on GPUs: Strategies and Performance

Simulating biological neural networks is an important task for computational neuroscientists attempting to model and analyze brain activity and function. As these networks become larger and more complex, the computational power required grows significantly, often requiring the use of supercomputers or compute clusters. An emerging low-cost, highly accessible alternative to many of these resources is the Graphics Processing Unit (GPU) - specialized massively-parallel graphics hardware that has seen increasing use as a general purpose computational accelerator thanks largely due to NVIDIA\u27s CUDA programming interface. We evaluated the relative benefits and limitations of GPU-based tools for large-scale neural network simulation and analysis, first by developing an agent-inspired spiking neural network simulator then by adapting a neural signal decoding algorithm. Under certain network configurations, the simulator was able to outperform an equivalent MPI-based parallel implementation run on a dedicated compute cluster, while the decoding algorithm implementation consistently outperformed its serial counterpart. Additionally, the GPU-based simulator was able to readily visualize network spiking activity in real-time due to the close integration with standard computer graphics APIs. The GPU was shown to provide significant performance benefits under certain circumstances while lagging behind in others. Given the complex nature of these research tasks, a hybrid strategy that combines GPU- and CPU-based approaches provides greater performance than either separately

A brain-machine interface for assistive robotic control

Brain-machine interfaces (BMIs) are the only currently viable means of communication for many individuals suffering from locked-in syndrome (LIS) – profound paralysis that results in severely limited or total loss of voluntary motor control. By inferring user intent from task-modulated neurological signals and then translating those intentions into actions, BMIs can enable LIS patients increased autonomy. Significant effort has been devoted to developing BMIs over the last three decades, but only recently have the combined advances in hardware, software, and methodology provided a setting to realize the translation of this research from the lab into practical, real-world applications. Non-invasive methods, such as those based on the electroencephalogram (EEG), offer the only feasible solution for practical use at the moment, but suffer from limited communication rates and susceptibility to environmental noise. Maximization of the efficacy of each decoded intention, therefore, is critical. This thesis addresses the challenge of implementing a BMI intended for practical use with a focus on an autonomous assistive robot application. First an adaptive EEG- based BMI strategy is developed that relies upon code-modulated visual evoked potentials (c-VEPs) to infer user intent. As voluntary gaze control is typically not available to LIS patients, c-VEP decoding methods under both gaze-dependent and gaze- independent scenarios are explored. Adaptive decoding strategies in both offline and online task conditions are evaluated, and a novel approach to assess ongoing online BMI performance is introduced. Next, an adaptive neural network-based system for assistive robot control is presented that employs exploratory learning to achieve the coordinated motor planning needed to navigate toward, reach for, and grasp distant objects. Exploratory learning, or “learning by doing,” is an unsupervised method in which the robot is able to build an internal model for motor planning and coordination based on real-time sensory inputs received during exploration. Finally, a software platform intended for practical BMI application use is developed and evaluated. Using online c-VEP methods, users control a simple 2D cursor control game, a basic augmentative and alternative communication tool, and an assistive robot, both manually and via high-level goal-oriented commands

A neural network-based exploratory learning and motor planning system for co-robots

Collaborative robots, or co-robots, are semi-autonomous robotic agents designed to work alongside humans in shared workspaces. To be effective, co-robots require the ability to respond and adapt to dynamic scenarios encountered in natural environments. One way to achieve this is through exploratory learning, or "learning by doing," an unsupervised method in which co-robots are able to build an internal model for motor planning and coordination based on real-time sensory inputs. In this paper, we present an adaptive neural network-based system for co-robot control that employs exploratory learning to achieve the coordinated motor planning needed to navigate toward, reach for, and grasp distant objects. To validate this system we used the 11-degrees-of-freedom RoPro Calliope mobile robot. Through motor babbling of its wheels and arm, the Calliope learned how to relate visual and proprioceptive information to achieve hand-eye-body coordination. By continually evaluating sensory inputs and externally provided goal directives, the Calliope was then able to autonomously select the appropriate wheel and joint velocities needed to perform its assigned task, such as following a moving target or retrieving an indicated object

The Unlock Project: A Python-based framework for practical brain-computer interface communication “app” development

In this paper we present a framework for reducing the development time needed for creating applications for use in non-invasive brain-computer interfaces (BCI). Our framework is primarily focused on facilitating rapid software “app” development akin to current efforts in consumer portable computing (e.g. smart phones and tablets). This is accomplished by handling intermodule communication without direct user or developer implementation, instead relying on a core subsystem for communication of standard, internal data formats. We also provide a library of hardware interfaces for common mobile EEG platforms for immediate use in BCI applications. A use-case example is described in which a user with amyotrophic lateral sclerosis participated in an electroencephalography-based BCI protocol developed using the proposed framework. We show that our software environment is capable of running in real-time with updates occurring 50–60 times per second with limited computational overhead (5 ms system lag) while providing accurate data acquisition and signal analysis

Stratus 14 : fourteenth setting of the Stratus Ocean Reference Station cruise on board RV Cabo de Hornos April 14 - 30, 2015 Valparaiso, Chile

The Ocean Reference Station at 20°S, 85°W under the stratus clouds west of northern Chile is being maintained to provide ongoing climate-quality records of surface meteorology, air-sea fluxes of heat, freshwater, and momentum, and of upper ocean temperature, salinity, and velocity variability. The Stratus Ocean Reference Station (ORS Stratus) is supported by the National Oceanic and Atmospheric Administration’s (NOAA) Climate Observation Program. It is recovered and redeployed annually, with past cruises that have come between October and January. This cruise was conducted on the Chilean research vessel Cabo de Hornos. During the 2015 cruise on the Cabo de Hornos to the ORS Stratus site, the primary activities were the recovery of the previous (Stratus 13) WHOI surface mooring, deployment of the new Stratus 14 WHOI surface mooring, in-situ calibration of the buoy meteorological sensors by comparison with instrumentation installed on the ship and CTD casts near the moorings. Surface drifters were also launched along the track.Funding was provided by the National Oceanic and Atmospheric Administration under Grant No. NA140AR432015

Neuromatch Academy: Teaching Computational Neuroscience with global accessibility

Neuromatch Academy designed and ran a fully online 3-week Computational Neuroscience summer school for 1757 students with 191 teaching assistants working in virtual inverted (or flipped) classrooms and on small group projects. Fourteen languages, active community management, and low cost allowed for an unprecedented level of inclusivity and universal accessibility.Comment: 10 pages, 3 figures. Equal contribution by the executive committee members of Neuromatch Academy: Tara van Viegen, Athena Akrami, Kate Bonnen, Eric DeWitt, Alexandre Hyafil, Helena Ledmyr, Grace W. Lindsay, Patrick Mineault, John D. Murray, Xaq Pitkow, Aina Puce, Madineh Sedigh-Sarvestani, Carsen Stringer. and equal contribution by the board of directors of Neuromatch Academy: Gunnar Blohm, Konrad Kording, Paul Schrater, Brad Wyble, Sean Escola, Megan A. K. Peter

Neuromatch Academy: a 3-week, online summer school in computational neuroscience

Neuromatch Academy (https://academy.neuromatch.io; (van Viegen et al., 2021)) was designed as an online summer school to cover the basics of computational neuroscience in three weeks. The materials cover dominant and emerging computational neuroscience tools, how they complement one another, and specifically focus on how they can help us to better understand how the brain functions. An original component of the materials is its focus on modeling choices, i.e. how do we choose the right approach, how do we build models, and how can we evaluate models to determine if they provide real (meaningful) insight. This meta-modeling component of the instructional materials asks what questions can be answered by different techniques, and how to apply them meaningfully to get insight about brain function