Dataset Information

A general method to generate artificial spike train populations matching recorded neurons.

ABSTRACT: We developed a general method to generate populations of artificial spike trains (ASTs) that match the statistics of recorded neurons. The method is based on computing a Gaussian local rate function of the recorded spike trains, which results in rate templates from which ASTs are drawn as gamma distributed processes with a refractory period. Multiple instances of spike trains can be sampled from the same rate templates. Importantly, we can manipulate rate-covariances between spike trains by performing simple algorithmic transformations on the rate templates, such as filtering or amplifying specific frequency bands, and adding behavior related rate modulations. The method was examined for accuracy and limitations using surrogate data such as sine wave rate templates, and was then verified for recorded spike trains from cerebellum and cerebral cortex. We found that ASTs generated with this method can closely follow the firing rate and local as well as global spike time variance and power spectrum. The method is primarily intended to generate well-controlled spike train populations as inputs for dynamic clamp studies or biophysically realistic multicompartmental models. Such inputs are essential to study detailed properties of synaptic integration with well-controlled input patterns that mimic the in vivo situation while allowing manipulation of input rate covariances at different time scales.

SUBMITTER: Abbasi S

PROVIDER: S-EPMC7036336 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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A general method to generate artificial spike train populations matching recorded neurons.

Abbasi Samira S Maran Selva S Jaeger Dieter D

Journal of computational neuroscience 20200123 1

We developed a general method to generate populations of artificial spike trains (ASTs) that match the statistics of recorded neurons. The method is based on computing a Gaussian local rate function of the recorded spike trains, which results in rate templates from which ASTs are drawn as gamma distributed processes with a refractory period. Multiple instances of spike trains can be sampled from the same rate templates. Importantly, we can manipulate rate-covariances between spike trains by perf ...[more]

PMID: 31974719

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Project description:The recent developments in artificial intelligence have the potential to facilitate new research methods in ecology. Especially Deep Convolutional Neural Networks (DCNNs) have been shown to outperform other approaches in automatic image analyses. Here we apply a DCNN to facilitate quantitative wood anatomical (QWA) analyses, where the main challenges reside in the detection of a high number of cells, in the intrinsic variability of wood anatomical features, and in the sample quality. To properly classify and interpret features within the images, DCNNs need to undergo a training stage. We performed the training with images from transversal wood anatomical sections, together with manually created optimal outputs of the target cell areas. The target species included an example for the most common wood anatomical structures: four conifer species; a diffuse-porous species, black alder (Alnus glutinosa L.); a diffuse to semi-diffuse-porous species, European beech (Fagus sylvatica L.); and a ring-porous species, sessile oak (Quercus petraea Liebl.). The DCNN was created in Python with Pytorch, and relies on a Mask-RCNN architecture. The developed algorithm detects and segments cells, and provides information on the measurement accuracy. To evaluate the performance of this tool we compared our Mask-RCNN outputs with U-Net, a model architecture employed in a similar study, and with ROXAS, a program based on traditional image analysis techniques. First, we evaluated how many target cells were correctly recognized. Next, we assessed the cell measurement accuracy by evaluating the number of pixels that were correctly assigned to each target cell. Overall, the "learning process" defining artificial intelligence plays a key role in overcoming the issues that are usually manually solved in QWA analyses. Mask-RCNN is the model that better detects which are the features characterizing a target cell when these issues occur. In general, U-Net did not attain the other algorithms' performance, while ROXAS performed best for conifers, and Mask-RCNN showed the highest accuracy in detecting target cells and segmenting lumen areas of angiosperms. Our research demonstrates that future software tools for QWA analyses would greatly benefit from using DCNNs, saving time during the analysis phase, and providing a flexible approach that allows model retraining.

Project description:IntroductionLinking places to people is a core element of the UK government's geospatial strategy. Matching patient addresses in electronic health records to their Unique Property Reference Numbers (UPRNs) enables spatial linkage for research, innovation and public benefit. Available algorithms are not transparent or evaluated for use with addresses recorded by health care providers.ObjectivesTo describe and quality assure the open-source deterministic ASSIGN address-matching algorithm applied to general practitioner-recorded patient addresses.MethodsBest practice standards were used to report the ASSIGN algorithm match rate, sensitivity and positive predictive value using gold-standard datasets from London and Wales. We applied the ASSIGN algorithm to the recorded addresses of a sample of 1,757,018 patients registered with all general practices in north east London. We examined bias in match results for the study population using multivariable analyses to estimate the likelihood of an address-matched UPRN by demographic, registration, and organisational variables.ResultsWe found a 99.5% and 99.6% match rate with high sensitivity (0.999,0.998) and positive predictive value (0.996,0.998) for the Welsh and London gold standard datasets respectively, and a 98.6% match rate for the study population.The 1.4% of the study population without a UPRN match were more likely to have changed registered address in the last 12 months (match rate: 95.4%), be from a Chinese ethnic background (95.5%), or registered with a general practice using the SystmOne clinical record system (94.4%). Conversely, people registered for more than 6.5 years with their general practitioner were more likely to have a match (99.4%) than those with shorter registration durations.ConclusionsASSIGN is a highly accurate open-source address-matching algorithm with a high match rate and minimal biases when evaluated against a large sample of general practice-recorded patient addresses. ASSIGN has potential to be used in other address-based datasets including those with information relevant to the wider determinants of health.

Dataset Information

A general method to generate artificial spike train populations matching recorded neurons.

Publications

A general method to generate artificial spike train populations matching recorded neurons.

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