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

Ecological models at fish community and species level to support effective river restoration

RESUMEN Los peces nativos son indicadores de la salud de los ecosistemas acuáticos, y se han convertido en un elemento de calidad clave para evaluar el estado ecológico de los ríos. La comprensión de los factores que afectan a las especies nativas de peces es importante para la gestión y conservación de los ecosistemas acuáticos. El objetivo general de esta tesis es analizar las relaciones entre variables biológicas y de hábitat (incluyendo la conectividad) a través de una variedad de escalas espaciales en los ríos Mediterráneos, con el desarrollo de herramientas de modelación para apoyar la toma de decisiones en la restauración de ríos. Esta tesis se compone de cuatro artículos. El primero tiene como objetivos modelar la relación entre un conjunto de variables ambientales y la riqueza de especies nativas (NFSR), y evaluar la eficacia de potenciales acciones de restauración para mejorar la NFSR en la cuenca del río Júcar. Para ello se aplicó un enfoque de modelación de red neuronal artificial (ANN), utilizando en la fase de entrenamiento el algoritmo Levenberg-Marquardt. Se aplicó el método de las derivadas parciales para determinar la importancia relativa de las variables ambientales. Según los resultados, el modelo de ANN combina variables que describen la calidad de ribera, la calidad del agua y el hábitat físico, y ayudó a identificar los principales factores que condicionan el patrón de distribución de la NFSR en los ríos Mediterráneos. En la segunda parte del estudio, el modelo fue utilizado para evaluar la eficacia de dos acciones de restauración en el río Júcar: la eliminación de dos azudes abandonados, con el consiguiente incremento de la proporción de corrientes. Estas simulaciones indican que la riqueza aumenta con el incremento de la longitud libre de barreras artificiales y la proporción del mesohabitat de corriente, y demostró la utilidad de las ANN como una poderosa herramienta para apoyar la toma de decisiones en el manejo y restauración ecológica de los ríos Mediterráneos. El segundo artículo tiene como objetivo determinar la importancia relativa de los dos principales factores que controlan la reducción de la riqueza de peces (NFSR), es decir, las interacciones entre las especies acuáticas, variables del hábitat (incluyendo la conectividad fluvial) y biológicas (incluidas las especies invasoras) en los ríos Júcar, Cabriel y Turia. Con este fin, tres modelos de ANN fueron analizados: el primero fue construido solamente con variables biológicas, el segundo se construyó únicamente con variables de hábitat y el tercero con la combinación de estos dos grupos de variables. Los resultados muestran que las variables de hábitat son los ¿drivers¿ más importantes para la distribución de NFSR, y demuestran la importancia ecológica de los modelos desarrollados. Los resultados de este estudio destacan la necesidad de proponer medidas de mitigación relacionadas con la mejora del hábitat (incluyendo la variabilidad de caudales en el río) como medida para conservar y restaurar los ríos Mediterráneos. El tercer artículo busca comparar la fiabilidad y relevancia ecológica de dos modelos predictivos de NFSR, basados en redes neuronales artificiales (ANN) y random forests (RF). La relevancia de las variables seleccionadas por cada modelo se evaluó a partir del conocimiento ecológico y apoyado por otras investigaciones. Los dos modelos fueron desarrollados utilizando validación cruzada k-fold y su desempeño fue evaluado a través de tres índices: el coeficiente de determinación (R2 ), el error cuadrático medio (MSE) y el coeficiente de determinación ajustado (R2 adj). Según los resultados, RF obtuvo el mejor desempeño en entrenamiento. Pero, el procedimiento de validación cruzada reveló que ambas técnicas generaron resultados similares (R2 = 68% para RF y R2 = 66% para ANN). La comparación de diferentes métodos de machine learning es muy útil para el análisis crítico de los resultados obtenidos a través de los modelos. El cuarto artículo tiene como objetivo evaluar la capacidad de las ANN para identificar los factores que afectan a la densidad y la presencia/ausencia de Luciobarbus guiraonis en la demarcación hidrográfica del Júcar. Se utilizó una red neuronal artificial multicapa de tipo feedforward (ANN) para representar relaciones no lineales entre descriptores de L. guiraonis con variables biológicas y de hábitat. El poder predictivo de los modelos se evaluó con base en el índice Kappa (k), la proporción de casos correctamente clasificados (CCI) y el área bajo la curva (AUC) característica operativa del receptor (ROC). La presencia/ausencia de L. guiraonis fue bien predicha por el modelo ANN (CCI = 87%, AUC = 0.85 y k = 0.66). La predicción de la densidad fue moderada (CCI = 62%, AUC = 0.71 y k = 0.43). Las variables más importantes que describen la presencia/ausencia fueron: radiación solar, área de drenaje y la proporción de especies exóticas de peces con un peso relativo del 27.8%, 24.53% y 13.60% respectivamente. En el modelo de densidad, las variables más importantes fueron el coeficiente de variación de los caudales medios anuales con una importancia relativa del 50.5% y la proporción de especies exóticas de peces con el 24.4%. Los modelos proporcionan información importante acerca de la relación de L. guiraonis con variables bióticas y de hábitat, este nuevo conocimiento podría utilizarse para apoyar futuros estudios y para contribuir en la toma de decisiones para la conservación y manejo de especies en los en los ríos Júcar, Cabriel y Turia.Olaya Marín, EJ. (2013). Ecological models at fish community and species level to support effective river restoration [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/28853TESI

Differentiating noise and modulators in artificial neural networks

Research in Computational Neural Networks is currently taking place at many different levels; from coarse-grain symbolic models to fine-grain representations of neurons and cell processes. One feature that the different approaches share, is that they are all in relative infancy. Thus, most research concentrates on gross aspects of neural communication and methods of computational simulation. Recently, some clues have been found which point to more subtle mechanisms underlying the information processing capability of neural 'nodes'. These clues are the improvement in network operation by the injection of random noise; and the neurobiological finding that neuropeptides may exist as slower Signal transmission channels between neurons. This study concerns the difference between random noise injection, and directed, low-level, activity injections which are postulated to be produced by neuromodulators such as neuropeptides. The findings of this study are that random noise does, indeed, enhance the operation of coarse-grain neural models; and that a 'neuropeptidergic' analogue also enhances operation; but to a different extent, and probably through a different mechanism. Further testing of a medium-grain computer model gives some indication of how a neuropeptidergic modulation might affect real neurons, by extending the time-course of the activation of the neuron. This appears to be a similar mechanism to that postulated for the coarse-grain 'neuropeptidergic' simulation model. Given these findings, is it possible that signal transmission in real nervous systems assume these mechanisms? If so, it may be possible that a process of concurrent propagation, through different signal channels, also occurs in real nervous systems, making the nervous system much more complex than current models allow

Water Pipeline Leakage Detection Based on Machine Learning and Wireless Sensor Networks

The detection of water pipeline leakage is important to ensure that water supply networks can operate safely and conserve water resources. To address the lack of intelligent and the low efficiency of conventional leakage detection methods, this paper designs a leakage detection method based on machine learning and wireless sensor networks (WSNs). The system employs wireless sensors installed on pipelines to collect data and utilizes the 4G network to perform remote data transmission. A leakage triggered networking method is proposed to reduce the wireless sensor network’s energy consumption and prolong the system life cycle effectively. To enhance the precision and intelligence of leakage detection, we propose a leakage identification method that employs the intrinsic mode function, approximate entropy, and principal component analysis to construct a signal feature set and that uses a support vector machine (SVM) as a classifier to perform leakage detection. Simulation analysis and experimental results indicate that the proposed leakage identification method can effectively identify the water pipeline leakage and has lower energy consumption than the networking methods used in conventional wireless sensor networks

Designing of Collagen Based Poly(3-hydroxybutyrate-co-4-hydroxybutyrate) Scaffolds for Tissue Engineering

P(3HB-co-4HB) copolymer was modified using collagen by adapting dual solvent system. The surface properties of samples were characterized by Fourier transforminfrared spectroscopy (FTIR), scanning electron microscopy (SEM), organic elemental analysis (CHN analysis), and water contact angle measurements.The effects of collagen concentration, scaffold thickness, and 4HB molar fraction on the hydrophilicitywere optimized by the Taguchi method.The orthogonal array experiment was conducted to obtain the response for a hydrophilic scaffold. Analysis of variance (ANOVA) was used to determine the significant parameters and determine the optimal level for each parameter. The results also showed that the hydrophilicity of P(3HB-co-4HB)/collagen blend scaffolds increased as the collagen concentration increased up to 15 wt% with a molar fraction of 50mol% at 0.1mm scaffold thickness. The biocompatibility of the P(3HB-co-4HB)/collagen blend surface was evaluated by fibroblast cell (L929) culture.The collagen blend scaffold surfaces showed significant cell adhesion and growth as compared to P(3HB-co-4HB) copolymer scaffolds

Computational methods toward early detection of neuronal deterioration

In today's world, because of developments in medical sciences, people are living longer, particularly in the advanced countries. This increasing of the lifespan has caused the prevalence of age-related diseases like Alzheimer’s and dementia. Researches show that ion channel disruptions, especially the formation of permeable pores to cations by Aβ plaques, play an important role in the occurrence of these types of diseases. Therefore, early detection of such diseases, particularly using non-invasive tools can aid both patients and those scientists searching for a cure. To achieve the goal toward early detection, the computational analysis of ion channels, ion imbalances in the presence of Aβ pores in neurons and fault detection is done. Any disruption in the membrane of the neuron, like the formation of permeable pores to cations by Aβ plaques, causes ionic imbalance and, as a result, faults occur in the signalling of the neuron.The first part of this research concentrates on ion channels, ion imbalances and their impacts on the signalling behaviour of the neuron. This includes investigating the role of Aβ channels in the development of neurodegenerative diseases. Results revealed that these types of diseases can lead to ionic imbalances in the neuron. Ion imbalances can change the behaviour of neuronal signalling. Therefore, by identifying the pattern of these changes, the disease can be detected in the very early stages. Then the role of coupling and synchronisation effects in such diseases were studied. After that, a novel method to define minimum requirements for synchronicity between two coupled neurons is proposed. Further, a new computational model of Aβ channels is proposed and developed which mimics the behaviour of a neuron in the course of Alzheimer's disease. Finally, both fault computation and disease detection are carried out using a residual generation method, where the residuals from two observers are compared to assess their performance

EDEN: A high-performance, general-purpose, NeuroML-based neural simulator

Modern neuroscience employs in silico experimentation on ever-increasing and more detailed neural networks. The high modelling detail goes hand in hand with the need for high model reproducibility, reusability and transparency. Besides, the size of the models and the long timescales under study mandate the use of a simulation system with high computational performance, so as to provide an acceptable time to result. In this work, we present EDEN (Extensible Dynamics Engine for Networks), a new general-purpose, NeuroML-based neural simulator that achieves both high model flexibility and high computational performance, through an innovative model-analysis and code-generation technique. The simulator runs NeuroML v2 models directly, eliminating the need for users to learn yet another simulator-specific, model-specification language. EDEN's functional correctness and computational performance were assessed through NeuroML models available on the NeuroML-DB and Open Source Brain model repositories. In qualitative experiments, the results produced by EDEN were verified against the established NEURON simulator, for a wide range of models. At the same time, computational-performance benchmarks reveal that EDEN runs up to 2 orders-of-magnitude faster than NEURON on a typical desktop computer, and does so without additional effort from the user. Finally, and without added user effort, EDEN has been built from scratch to scale seamlessly over multiple CPUs and across computer clusters, when available.Comment: 29 pages, 9 figure

Retinal drug delivery: rethinking outcomes for the efficient replication of retinal behavior

The retina is a highly organized structure that is considered to be "an approachable part of the brain." It is attracting the interest of development scientists, as it provides a model neurovascular system. Over the last few years, we have been witnessing significant development in the knowledge of the mechanisms that induce the shape of the retinal vascular system, as well as knowledge of disease processes that lead to retina degeneration. Knowledge and understanding of how our vision works are crucial to creating a hardware-adaptive computational model that can replicate retinal behavior. The neuronal system is nonlinear and very intricate. It is thus instrumental to have a clear view of the neurophysiological and neuroanatomic processes and to take into account the underlying principles that govern the process of hardware transformation to produce an appropriate model that can be mapped to a physical device. The mechanistic and integrated computational models have enormous potential toward helping to understand disease mechanisms and to explain the associations identified in large model-free data sets. The approach used is modulated and based on different models of drug administration, including the geometry of the eye. This work aimed to review the recently used mathematical models to map a directed retinal network.The authors acknowledge the financial support received from the Portuguese Science and Technology Foundation (FCT/MCT) and the European Funds (PRODER/COMPETE) for the project UIDB/04469/2020 (strategic fund), co-financed by FEDER, under the Partnership Agreement PT2020. The authors also acknowledge FAPESP – São Paulo Research Foundation, for the financial support for the publication of the article.info:eu-repo/semantics/publishedVersio

Modeling and Simulation in Engineering

The Special Issue Modeling and Simulation in Engineering, belonging to the section Engineering Mathematics of the Journal Mathematics, publishes original research papers dealing with advanced simulation and modeling techniques. The present book, “Modeling and Simulation in Engineering I, 2022”, contains 14 papers accepted after peer review by recognized specialists in the field. The papers address different topics occurring in engineering, such as ferrofluid transport in magnetic fields, non-fractal signal analysis, fractional derivatives, applications of swarm algorithms and evolutionary algorithms (genetic algorithms), inverse methods for inverse problems, numerical analysis of heat and mass transfer, numerical solutions for fractional differential equations, Kriging modelling, theory of the modelling methodology, and artificial neural networks for fault diagnosis in electric circuits. It is hoped that the papers selected for this issue will attract a significant audience in the scientific community and will further stimulate research involving modelling and simulation in mathematical physics and in engineering