Data Models in Neuroinformatics

Advancements in integrated neuroscience are often characterized with data-driven approaches for discovery; these progressions are the result of continuous efforts aimed at developing integrated frameworks for the investigation of neuronal dynamics at increasing resolution and in varying scales. Since insights from integrated neuronal models frequently rely on both experimental and computational approaches, simulations and data modeling have inimitable roles. Moreover, data sharing across the neuroscientific community has become an essential component of data-driven approaches to neuroscience as is evident from the number and scale of ongoing national and multinational projects, engaging scientists from diverse branches of knowledge. In this heterogeneous environment, the need to share neuroscientific data as well as to utilize it across different simulation environments drove the momentum for standardizing data models for neuronal morphologies, biophysical properties, and connectivity schemes. Here, I review existing data models in neuroinformatics, ranging from flat to hybrid object-hierarchical approaches, and suggest a framework with which these models can be linked to experimental data, as well as to established records from existing databases. Linking neuronal models and experimental results with data on relevant articles, genes, proteins, disease, etc., might open a new dimension for data-driven neuroscience

OpenVX-Based Python Framework for Real-time Cross-Platform Acceleration of Embedded Computer Vision Applications

Embedded real-time vision applications are being rapidly deployed in a large realm of consumer electronics, ranging from automotive safety to surveillance systems. However, the relatively limited computational power of embedded platforms is considered as a bottleneck for many vision applications, necessitating optimization. OpenVX is a standardized interface, released in late 2014, in an attempt to provide both system and kernel level optimization to vision applications. With OpenVX, Vision processing are modeled with coarse-grained data flow graphs, which can be optimized and accelerated by the platform implementer. Current full implementations of OpenVX are given in the programming language C, which does not support advanced programming paradigms such as object-oriented, imperative and functional programming, nor does it have runtime or type-checking. Here we present a python-based full Implementation of OpenVX, which eliminates much of the discrepancies between the object-oriented paradigm used by many modern applications and the native C implementations. Our open-source implementation can be used for rapid development of OpenVX applications in embedded platforms. Demonstration includes static and real-time image acquisition and processing using a Raspberry Pi and a GoPro camera. Code is given as supplementary information. Code project and linked deployable virtual machine are located on GitHub: https://github.com/NBEL-lab/PythonOpenVX

Additional file 1: of Rapid development of entity-based data models for bioinformatics with persistence object-oriented design and structured interfaces

Supplemntary information: framework's design and architecture. (DOCX 500 kb

Neuromorphic Neural Engineering Framework-Inspired Online Continuous Learning with Analog Circuitry

Neuromorphic hardware designs realize neural principles in electronics to provide high-performing, energy-efficient frameworks for machine learning. Here, we propose a neuromorphic analog design for continuous real-time learning. Our hardware design realizes the underlying principles of the neural engineering framework (NEF). NEF brings forth a theoretical framework for the representation and transformation of mathematical constructs with spiking neurons, thus providing efficient means for neuromorphic machine learning and the design of intricate dynamical systems. Our analog circuit design implements the neuromorphic prescribed error sensitivity (PES) learning rule with OZ neurons. OZ is an analog implementation of a spiking neuron, which was shown to have complete correspondence with NEF across firing rates, encoding vectors, and intercepts. We demonstrate PES-based neuromorphic representation of mathematical constructs with varying neuron configurations, the transformation of mathematical constructs, and the construction of a dynamical system with the design of an inducible leaky oscillator. We further designed a circuit emulator, allowing the evaluation of our electrical designs on a large scale. We used the circuit emulator in conjunction with a robot simulator to demonstrate adaptive learning-based control of a robotic arm with six degrees of freedom

Biologically Plausible Spiking Neural Networks for Perceptual Filling-In

Visual perception initiated with a low-level derivation of Spatio-temporal edges and advances to a higher-level perception of filled surfaces. According to the isomorphic theory, this perceptual filling-in is governed by an activation spread across the retinotopic map, driven from edges to interiors. Here we propose two biologically plausible spiking neural networks, which demonstrate perceptual filling-in by resolving the Poisson equation. Each network exhibits a distinct dynamic and architecture and could be realized and further integrated in the brain

Distributed retrieval engine for the development of cloud-deployed biological databases

Abstract The integration of cloud resources with federated data retrieval has the potential of improving the maintenance, accessibility and performance of specialized databases in the biomedical field. However, such an integrative approach requires technical expertise in cloud computing, usage of a data retrieval engine and development of a unified data-model, which can encapsulate the heterogeneity of biological data. Here, a framework for the development of cloud-based biological specialized databases is proposed. It is powered by a distributed biodata retrieval system, able to interface with different data formats, as well as provides an integrated way for data exploration. The proposed framework was implemented using Java as the development environment, and MongoDB as the database manager. Syntactic analysis was based on BSON, jsoup, Apache Commons and w3c.dom open libraries. Framework is available in: http://nbel-lab.com and is distributed under the creative common agreement

Computational modeling of color perception with biologically plausible spiking neural networks.

Biologically plausible computational modeling of visual perception has the potential to link high-level visual experiences to their underlying neurons' spiking dynamic. In this work, we propose a neuromorphic (brain-inspired) Spiking Neural Network (SNN)-driven model for the reconstruction of colorful images from retinal inputs. We compared our results to experimentally obtained V1 neuronal activity maps in a macaque monkey using voltage-sensitive dye imaging and used the model to demonstrate and critically explore color constancy, color assimilation, and ambiguous color perception. Our parametric implementation allows critical evaluation of visual phenomena in a single biologically plausible computational framework. It uses a parametrized combination of high and low pass image filtering and SNN-based filling-in Poisson processes to provide adequate color image perception while accounting for differences in individual perception

Video_1_Adaptive control of a wheelchair mounted robotic arm with neuromorphically integrated velocity readings and online-learning.MOV

Wheelchair-mounted robotic arms support people with upper extremity disabilities with various activities of daily living (ADL). However, the associated cost and the power consumption of responsive and adaptive assistive robotic arms contribute to the fact that such systems are in limited use. Neuromorphic spiking neural networks can be used for a real-time machine learning-driven control of robots, providing an energy efficient framework for adaptive control. In this work, we demonstrate a neuromorphic adaptive control of a wheelchair-mounted robotic arm deployed on Intel’s Loihi chip. Our algorithm design uses neuromorphically represented and integrated velocity readings to derive the arm’s current state. The proposed controller provides the robotic arm with adaptive signals, guiding its motion while accounting for kinematic changes in real-time. We pilot-tested the device with an able-bodied participant to evaluate its accuracy while performing ADL-related trajectories. We further demonstrated the capacity of the controller to compensate for unexpected inertia-generating payloads using online learning. Videotaped recordings of ADL tasks performed by the robot were viewed by caregivers; data summarizing their feedback on the user experience and the potential benefit of the system is reported.</p