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MIIND : A Model-Agnostic Simulator of Neural Populations.

ABSTRACT: MIIND is a software platform for easily and efficiently simulating the behaviour of interacting populations of point neurons governed by any 1D or 2D dynamical system. The simulator is entirely agnostic to the underlying neuron model of each population and provides an intuitive method for controlling the amount of noise which can significantly affect the overall behaviour. A network of populations can be set up quickly and easily using MIIND's XML-style simulation file format describing simulation parameters such as how populations interact, transmission delays, post-synaptic potentials, and what output to record. During simulation, a visual display of each population's state is provided for immediate feedback of the behaviour and population activity can be output to a file or passed to a Python script for further processing. The Python support also means that MIIND can be integrated into other software such as The Virtual Brain. MIIND's population density technique is a geometric and visual method for describing the activity of each neuron population which encourages a deep consideration of the dynamics of the neuron model and provides insight into how the behaviour of each population is affected by the behaviour of its neighbours in the network. For 1D neuron models, MIIND performs far better than direct simulation solutions for large populations. For 2D models, performance comparison is more nuanced but the population density approach still confers certain advantages over direct simulation. MIIND can be used to build neural systems that bridge the scales between an individual neuron model and a population network. This allows researchers to maintain a plausible path back from mesoscopic to microscopic scales while minimising the complexity of managing large numbers of interconnected neurons. In this paper, we introduce the MIIND system, its usage, and provide implementation details where appropriate.

SUBMITTER: Osborne H

PROVIDER: S-EPMC8291130 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundExcess adiposity in children is strongly correlated with obesity-related metabolic disease in adulthood, including diabetes, cardiovascular disease, and 13 types of cancer. Despite the many long-term health risks of childhood obesity, body mass index (BMI) Z-score is typically the only adiposity marker used in pediatric studies and clinical applications. The effects of regional adiposity are not captured in a single scalar measurement, and their effects on short- and long-term metabolic health are largely unknown. However, clinicians and researchers rarely deploy gold-standard methods for measuring compartmental fat such as magnetic resonance imaging (MRI) and dual X-ray absorptiometry (DXA) on children and adolescents due to cost or radiation concerns. Three-dimensional optical (3DO) scans are relatively inexpensive to obtain and use non-invasive and radiation-free imaging techniques to capture the external surface geometry of a patient's body. This 3D shape contains cues about the body composition that can be learned from a structured correlation between 3D body shape parameters and reference DXA scans obtained on a sample population.Study aimThis study seeks to introduce a radiation-free, automated 3D optical imaging solution for monitoring body shape and composition in children aged 5-17.MethodsWe introduce an automated, linear learning method to predict total and regional body composition of children aged 5-17 from 3DO scans. We collected 145 male and 206 female 3DO scans on children between the ages of 5 and 17 with three scanners from independent manufacturers. We used an automated shape templating method first introduced on an adult population to fit a topologically consistent 60,000 vertex (60 k) mesh to 3DO scans of arbitrary scanning source and mesh topology. We constructed a parameterized body shape space using principal component analysis (PCA) and estimated a regression matrix between the shape parameters and their associated DXA measurements. We automatically fit scans of 30 male and 38 female participants from a held-out test set and predicted 12 body composition measurements.ResultsThe coefficient of determination (R2) between 3DO predicted body composition and DXA measurements was at least 0.85 for all measurements with the exception of visceral fat on 3D scan predictions. Precision error was 1-4 times larger than that of DXA. No predicted variable was significantly different from DXA measurement except for male trunk lean mass.ConclusionOptical imaging can quickly, safely, and inexpensively estimate regional body composition in children aged 5-17. Frequent repeat measurements can be taken to chart changes in body adiposity over time without risk of radiation overexposure.

Project description:MotivationNew low-coverage single-cell DNA sequencing technologies enable the measurement of copy number profiles from thousands of individual cells within tumors. From this data, one can infer the evolutionary history of the tumor by modeling transformations of the genome via copy number aberrations. Copy number aberrations alter multiple adjacent genomic loci, violating the standard phylogenetic assumption that loci evolve independently. Thus, specialized models to infer copy number phylogenies have been introduced. A widely used model is the copy number transformation (CNT) model in which a genome is represented by an integer vector and a copy number aberration is an event that either increases or decreases the number of copies of a contiguous segment of the genome. The CNT distance between a pair of copy number profiles is the minimum number of events required to transform one profile to another. While this distance can be computed efficiently, no efficient algorithm has been developed to find the most parsimonious phylogeny under the CNT model.ResultsWe introduce the zero-agnostic copy number transformation (ZCNT) model, a simplification of the CNT model that allows the amplification or deletion of regions with zero copies. We derive a closed form expression for the ZCNT distance between two copy number profiles and show that, unlike the CNT distance, the ZCNT distance forms a metric. We leverage the closed-form expression for the ZCNT distance and an alternative characterization of copy number profiles to derive polynomial time algorithms for two natural relaxations of the small parsimony problem on copy number profiles. While the alteration of zero copy number regions allowed under the ZCNT model is not biologically realistic, we show on both simulated and real datasets that the ZCNT distance is a close approximation to the CNT distance. Extending our polynomial time algorithm for the ZCNT small parsimony problem, we develop an algorithm, Lazac, for solving the large parsimony problem on copy number profiles. We demonstrate that Lazac outperforms existing methods for inferring copy number phylogenies on both simulated and real data.

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MIIND : A Model-Agnostic Simulator of Neural Populations.

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