scholarly journals NetPyNE: a tool for data-driven multiscale modeling of brain circuits

2018 ◽  
Author(s):  
Salvador Dura-Bernal ◽  
Benjamin A Suter ◽  
Padraig Gleeson ◽  
Matteo Cantarelli ◽  
Adrian Quintana ◽  
...  

AbstractBiophysical modeling of neuronal networks helps to integrate and interpret rapidly growing and disparate experimental datasets at multiple scales. The NetPyNE tool (www.netpyne.org) provides both programmatic and graphical interfaces to develop data-driven multiscale network models in NEURON. NetPyNE clearly separates model parameters from implementation code. Users provide specifications at a high level via a standardized declarative language, e.g., a connectivity rule, instead of tens of loops to create millions of cell-to-cell connections. Users can then generate the NEURON network, run efficiently parallelized simulations, optimize and explore network parameters through automated batch runs, and use built-in functions for visualization and analysis – connectivity matrices, voltage traces, raster plots, local field potentials, and information theoretic measures. NetPyNE also facilitates model sharing by exporting and importing using NeuroML and SONATA standardized formats. NetPyNE is already being used to teach computational neuroscience students and by modelers to investigate different brain regions and phenomena.

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Salvador Dura-Bernal ◽  
Benjamin A Suter ◽  
Padraig Gleeson ◽  
Matteo Cantarelli ◽  
Adrian Quintana ◽  
...  

Biophysical modeling of neuronal networks helps to integrate and interpret rapidly growing and disparate experimental datasets at multiple scales. The NetPyNE tool (www.netpyne.org) provides both programmatic and graphical interfaces to develop data-driven multiscale network models in NEURON. NetPyNE clearly separates model parameters from implementation code. Users provide specifications at a high level via a standardized declarative language, for example connectivity rules, to create millions of cell-to-cell connections. NetPyNE then enables users to generate the NEURON network, run efficiently parallelized simulations, optimize and explore network parameters through automated batch runs, and use built-in functions for visualization and analysis – connectivity matrices, voltage traces, spike raster plots, local field potentials, and information theoretic measures. NetPyNE also facilitates model sharing by exporting and importing standardized formats (NeuroML and SONATA). NetPyNE is already being used to teach computational neuroscience students and by modelers to investigate brain regions and phenomena.


2020 ◽  
Vol 14 ◽  
Author(s):  
Amelie Schäfer ◽  
Elizabeth C. Mormino ◽  
Ellen Kuhl

Alzheimer's disease is associated with the cerebral accumulation of neurofibrillary tangles of hyperphosphorylated tau protein. The progressive occurrence of tau aggregates in different brain regions is closely related to neurodegeneration and cognitive impairment. However, our current understanding of tau propagation relies almost exclusively on postmortem histopathology, and the precise propagation dynamics of misfolded tau in the living brain remain poorly understood. Here we combine longitudinal positron emission tomography and dynamic network modeling to test the hypothesis that misfolded tau propagates preferably along neuronal connections. We follow 46 subjects for three or four annual positron emission tomography scans and compare their pathological tau profiles against brain network models of intracellular and extracellular spreading. For each subject, we identify a personalized set of model parameters that characterizes the individual progression of pathological tau. Across all subjects, the mean protein production rate was 0.21 ± 0.15 and the intracellular diffusion coefficient was 0.34 ± 0.43. Our network diffusion model can serve as a tool to detect non-clinical symptoms at an earlier stage and make informed predictions about the timeline of neurodegeneration on an individual personalized basis.


2019 ◽  
Author(s):  
Matthew F. Singh ◽  
Todd S. Braver ◽  
Michael W. Cole ◽  
ShiNung Ching

AbstractA key challenge for neuroscience is to develop generative, causal models of the human nervous system in an individualized, data-driven manner. Previous initiatives have either constructed biologically-plausible models that are not constrained by individual-level human brain activity or used data-driven statistical characterizations of individuals that are not mechanistic. We aim to bridge this gap through the development of a new modeling approach termed Mesoscale Individualized Neurodynamic (MINDy) modeling, wherein we fit nonlinear dynamical systems models directly to human brain imaging data. The MINDy framework is able to produce these data-driven network models for hundreds to thousands of interacting brain regions in just 1-3 minutes per subject. We demonstrate that the models are valid, reliable, and robust. We show that MINDy models are predictive of individualized patterns of resting-state brain dynamical activity. Furthermore, MINDy is better able to uncover the mechanisms underlying individual differences in resting state activity than functional connectivity methods.


Author(s):  
Abdulla Ghani ◽  
Isaac Boxx ◽  
Carrie Noren

Abstract This paper presents a data-driven identification framework with the objective to retrieve a flame model from the nonlinear limit cycle. The motivation is to identify a flame model for configurations, which do not allow the determination of the flame dynamics: that is commonly for industrial applications where (i) optical access for non-intrusive measurements of velocity and heat release fluctuations are not feasible and (ii) unstable combustion is monitored via multiple pressure recordings. To demonstrate the usefulness of the method, we chose three test cases: (i) a classical Rijke tube; (ii) an experiment of a laminar flame (EM2C case) (iii) and a high-pressure, turbulent premixed flame (DLR case). The procedure is as follows: First, acoustic network models for the three cases are generated for which the in-house software taX is employed. Next, the acoustic network models are embedded in an optimization framework with the objective to identify flame parameters that match the experimental limit cycle data: based on the instability frequency and pressure amplitudes, we formulate physical constraints and an objective function in order to identify the flame model parameters gain nopt and time delay τopt in the nonlinear regime. We demonstrate for the three cases that the identified flame parameters reproduce the unstable combustion processes and highlight the usefulness of the method for control purposes.


2020 ◽  
Vol 142 (12) ◽  
Author(s):  
Abdulla Ghani ◽  
Isaac Boxx ◽  
Carrie Noren

Abstract This paper presents a data-driven identification framework with the objective to retrieve a flame model from the nonlinear limit cycle. The motivation is to identify a flame model for configurations, which do not allow the determination of the flame dynamics: that is commonly for industrial applications where (i) optical access for nonintrusive measurements of velocity and heat release fluctuations are not feasible and (ii) unstable combustion is monitored via multiple pressure recordings. To demonstrate the usefulness of the method, we chose three test cases: (i) a classical Rijke tube; (ii) an experiment of a laminar flame (EM2C case), (iii) and a high-pressure, turbulent premixed flame (German Aerospace Center (DLR) case). The procedure is as follows: First, acoustic network models for the three cases are generated for which the in-house software taX is employed. Next, the acoustic network models are embedded in an optimization framework with the objective to identify flame parameters that match the experimental limit cycle data: based on the instability frequency and pressure amplitudes, we formulate physical constraints and an objective function in order to identify the flame model parameters gain nopt and time delay τopt in the nonlinear regime. We demonstrate for the three cases that the identified flame parameters reproduce the unstable combustion processes and highlight the usefulness of the method for control purposes.


2019 ◽  
Author(s):  
Jan-Eirik W. Skaar ◽  
Alexander J. Stasik ◽  
Espen Hagen ◽  
Torbjørn V. Ness ◽  
Gaute T. Einevoll

AbstractMost modeling in systems neuroscience has beendescriptivewhere neural representations, that is, ‘receptive fields’, have been found by statistically correlating neural activity to sensory input. In the traditional physics approach to modelling, hypotheses are represented bymechanisticmodels based on the underlying building blocks of the system, and candidate models are validated by comparing with experiments. Until now validation of mechanistic cortical network models has been based on comparison with neuronal spikes, found from the high-frequency part of extracellular electrical potentials. In this computational study we investigated to what extent the low-frequency part of the signal, the local field potential (LFP), can be used to infer properties of the neuronal network. In particular, we asked the question whether the LFP can be used to accurately estimate synaptic connection weights in the underlying network. We considered the thoroughly analysed Brunel network comprising an excitatory and an inhibitory population of recurrently connected integrate-and-fire (LIF) neurons. This model exhibits a high diversity of spiking network dynamics depending on the values of only three synaptic weight parameters. The LFP generated by the network was computed using a hybrid scheme where spikes computed from the point-neuron network were replayed on biophysically detailed multicompartmental neurons. We assessed how accurately the three model parameters could be estimated from power spectra of stationary ‘background’ LFP signals by application of convolutional neural nets (CNNs). All network parameters could be very accurately estimated, suggesting that LFPs indeed can be used for network model validation.Significance statementMost of what we have learned about brain networksin vivohave come from the measurement of spikes (action potentials) recorded by extracellular electrodes. The low-frequency part of these signals, the local field potential (LFP), contains unique information about how dendrites in neuronal populations integrate synaptic inputs, but has so far played a lesser role. To investigate whether the LFP can be used to validate network models, we computed LFP signals for a recurrent network model (the Brunel network) for which the ground-truth parameters are known. By application of convolutional neural nets (CNNs) we found that the synaptic weights indeed could be accurately estimated from ‘background’ LFP signals, suggesting a future key role for LFP in development of network models.


Author(s):  
Xiaoling Luo ◽  
Adrian Cottam ◽  
Yao-Jan Wu ◽  
Yangsheng Jiang

Trip purpose information plays a significant role in transportation systems. Existing trip purpose information is traditionally collected through human observation. This manual process requires many personnel and a large amount of resources. Because of this high cost, automated trip purpose estimation is more attractive from a data-driven perspective, as it could improve the efficiency of processes and save time. Therefore, a hybrid-data approach using taxi operations data and point-of-interest (POI) data to estimate trip purposes was developed in this research. POI data, an emerging data source, was incorporated because it provides a wealth of additional information for trip purpose estimation. POI data, an open dataset, has the added benefit of being readily accessible from online platforms. Several techniques were developed and compared to incorporate this POI data into the hybrid-data approach to achieve a high level of accuracy. To evaluate the performance of the approach, data from Chengdu, China, were used. The results show that the incorporation of POI information increases the average accuracy of trip purpose estimation by 28% compared with trip purpose estimation not using the POI data. These results indicate that the additional trip attributes provided by POI data can increase the accuracy of trip purpose estimation.


2021 ◽  
pp. 1-14
Author(s):  
Debo Dong ◽  
Dezhong Yao ◽  
Yulin Wang ◽  
Seok-Jun Hong ◽  
Sarah Genon ◽  
...  

Abstract Background Schizophrenia has been primarily conceptualized as a disorder of high-order cognitive functions with deficits in executive brain regions. Yet due to the increasing reports of early sensory processing deficit, recent models focus more on the developmental effects of impaired sensory process on high-order functions. The present study examined whether this pathological interaction relates to an overarching system-level imbalance, specifically a disruption in macroscale hierarchy affecting integration and segregation of unimodal and transmodal networks. Methods We applied a novel combination of connectome gradient and stepwise connectivity analysis to resting-state fMRI to characterize the sensorimotor-to-transmodal cortical hierarchy organization (96 patients v. 122 controls). Results We demonstrated compression of the cortical hierarchy organization in schizophrenia, with a prominent compression from the sensorimotor region and a less prominent compression from the frontal−parietal region, resulting in a diminished separation between sensory and fronto-parietal cognitive systems. Further analyses suggested reduced differentiation related to atypical functional connectome transition from unimodal to transmodal brain areas. Specifically, we found hypo-connectivity within unimodal regions and hyper-connectivity between unimodal regions and fronto-parietal and ventral attention regions along the classical sensation-to-cognition continuum (voxel-level corrected, p < 0.05). Conclusions The compression of cortical hierarchy organization represents a novel and integrative system-level substrate underlying the pathological interaction of early sensory and cognitive function in schizophrenia. This abnormal cortical hierarchy organization suggests cascading impairments from the disruption of the somatosensory−motor system and inefficient integration of bottom-up sensory information with attentional demands and executive control processes partially account for high-level cognitive deficits characteristic of schizophrenia.


Author(s):  
Leijin Long ◽  
Feng He ◽  
Hongjiang Liu

AbstractIn order to monitor the high-level landslides frequently occurring in Jinsha River area of Southwest China, and protect the lives and property safety of people in mountainous areas, the data of satellite remote sensing images are combined with various factors inducing landslides and transformed into landslide influence factors, which provides data basis for the establishment of landslide detection model. Then, based on the deep belief networks (DBN) and convolutional neural network (CNN) algorithm, two landslide detection models DBN and convolutional neural-deep belief network (CDN) are established to monitor the high-level landslide in Jinsha River. The influence of the model parameters on the landslide detection results is analyzed, and the accuracy of DBN and CDN models in dealing with actual landslide problems is compared. The results show that when the number of neurons in the DBN is 100, the overall error is the minimum, and when the number of learning layers is 3, the classification error is the minimum. The detection accuracy of DBN and CDN is 97.56% and 97.63%, respectively, which indicates that both DBN and CDN models are feasible in dealing with landslides from remote sensing images. This exploration provides a reference for the study of high-level landslide disasters in Jinsha River.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Giuseppe Giacopelli ◽  
Domenico Tegolo ◽  
Emiliano Spera ◽  
Michele Migliore

AbstractThe brain’s structural connectivity plays a fundamental role in determining how neuron networks generate, process, and transfer information within and between brain regions. The underlying mechanisms are extremely difficult to study experimentally and, in many cases, large-scale model networks are of great help. However, the implementation of these models relies on experimental findings that are often sparse and limited. Their predicting power ultimately depends on how closely a model’s connectivity represents the real system. Here we argue that the data-driven probabilistic rules, widely used to build neuronal network models, may not be appropriate to represent the dynamics of the corresponding biological system. To solve this problem, we propose to use a new mathematical framework able to use sparse and limited experimental data to quantitatively reproduce the structural connectivity of biological brain networks at cellular level.


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