Brian2GeNN: accelerating spiking neural network simulations with graphics hardware

“Brian” is a popular Python-based simulator for spiking neural networks, commonly used in computational neuroscience. GeNN is a C++-based meta-compiler for accelerating spiking neural network simulations using consumer or high performance grade graphics processing units (GPUs). Here we introduce a new software package, Brian2GeNN, that connects the two systems so that users can make use of GeNN GPU acceleration when developing their models in Brian, without requiring any technical knowledge about GPUs, C++ or GeNN. The new Brian2GeNN software uses a pipeline of code generation to translate Brian scripts into C++ code that can be used as input to GeNN, and subsequently can be run on suitable NVIDIA GPU accelerators. From the user’s perspective, the entire pipeline is invoked by adding two simple lines to their Brian scripts. We have shown that using Brian2GeNN, two non-trivial models from the literature can run tens to hundreds of times faster than on CPU

Equation-oriented specification of neural models for simulations

Simulating biological neuronal networks is a core method of research in computational neuroscience. A full specification of such a network model includes a description of the dynamics and state changes of neurons and synapses, as well as the synaptic connectivity patterns and the initial values of all parameters. A standard approach in neuronal modeling software is to build network models based on a library of pre-defined components and mechanisms; if a model component does not yet exist, it has to be defined in a special-purpose or general low-level language and potentially be compiled and linked with the simulator. Here we propose an alternative approach that allows flexible definition of models by writing textual descriptions based on mathematical notation. We demonstrate that this approach allows the definition of a wide range of models with minimal syntax. Furthermore, such explicit model descriptions allow the generation of executable code for various target languages and devices, since the description is not tied to an implementation. Finally, this approach also has advantages for readability and reproducibility, because the model description is fully explicit, and because it can be automatically parsed and transformed into formatted descriptions. The presented approach has been implemented in the Brian2 simulator

The use of the development and well-being assessment (DAWBA) in clinical practice: a randomized trial

The development and well-being assessment (DAWBA) has been used in various epidemiological studies, whereas the clinical value of the instrument needs support from further studies. In particular, it is important to document how the use of the DAWBA influences clinical decision-making. The present study employed the DAWBA in a consecutive series of 270 new referrals to a large public child and adolescent psychiatric service in Zurich, Switzerland. ICD-10 based diagnoses were obtained from clinicians for all patients and reliability of DAWBA expert raters was calculated. The DAWBA diagnoses were randomly disclosed (n=144) or not disclosed (n=126) before clinical decision-making. The reliability of DAWBA expert diagnoses was very satisfactory and the agreement under the disclosed versus the non-disclosed condition amounted to 77 versus 68% for internalizing disorders and to 63 versus 71% for externalizing disorders. The increment in agreement due to disclosure of the DAWBA diagnosis was significant for internalizing disorders. Access to DAWBA information was more likely to prompt clinicians to add an extra diagnosis. Professional background and degree of clinical experience did not affect diagnostic agreement. Overall, diagnostic agreements between DAWBA expert diagnoses and clinical diagnoses were in the fair to moderate range and comparable to previous studies with other structured diagnostic interviews. The inclusion of the DAWBA into the clinical assessment process had an impact on diagnostic decision-making regarding internalizing disorders but not regarding externalizing disorder

The contribution of parent and youth information to identify mental health disorders or problems in adolescents

BACKGROUND Discrepancies between multiple informants often create considerable uncertainties in delivering services to youth. The present study assessed the ability of the parent and youth scales of the Strength and Difficulties Questionnaire (SDQ) to predict mental health problems/disorders across several mental health domains as validated against two contrasting indices of validity for psychopathology derived from the Development and Well Being Assessment (DAWBA): (1) an empirically derived computer algorithm and (2) expert based ICD-10 diagnoses. METHODS Ordinal and logistic regressions were used to predict any problems/disorders, emotional problems/disorders and behavioural problems/disorders in a community sample (n = 252) and in a clinic sample (n = 95). RESULTS The findings were strikingly similar in both samples. Parent and youth SDQ scales were related to any problem/disorder. Youth SDQ symptom and impact had the strongest association with emotional problems/disorder and parent SDQ symptom score were most strongly related to behavioural problems/disorders. Both the SDQ total and the impact scores significantly predicted emotional problems/disorders in males whereas this was the case only for the total SDQ score in females. CONCLUSION The present study confirms and expands previous findings on parent and youth informant validity. Clinicians should include both parent and youth for identifying any mental health problems/disorders, youth information for detecting emotional problems/disorders, and parent information to detect behavioural problems/disorders. Not only symptom scores but also impact measures may be useful to detect emotional problems/disorders, particularly in male youth

Risk of Population Extinction from Periodic and Abrupt Changes of Environment

A simulation model of a population having internal (genetic) structure is presented. The population is subject to selection pressure coming from the environment which is the same in the whole system but changes in time. Reproduction has a sexual character with recombination and mutation. Two cases are considered - oscillatory changes of the environment and abrupt ones (catastrophes). We show how the survival chance of a population depends on maximum allowed size of the population, the length of the genotypes characterising individuals, selection pressure and the characteristics of the climate changes, either their period of oscillations or the scale of the abrupt shift.Comment: 8 pages, 25 references, 10 figures; preliminary version to be submitted to Physica

SpineML and Brian 2.0 interfaces for using GPU enhanced Neuronal Networks (GeNN)

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Hyperlexia in a 4-year-old boy with Autistic Spectrum Disorder

This paper presents a case study of a 4-year-old boy with Autistic Spectrum Disorder and a mental age of approximately 1:5 who demonstrates precocious oral-reading behaviour in the absence of spontaneous speech. Tests of reading regular and irregular words, pseudowords, homographic heterophones, single sentences and texts were carried out. Performance on a variety of reading tasks suggests the ability to use grapheme–phoneme correspondences and whole word reading for decoding single words. In addition, successful reading of some homographic heterophones and semantic paraphrasing of texts suggests a level of lexical, syntactic, semantic and pragmatic development far beyond his mental or chronological age. The realisation of highly developed reading ability is paradoxical in the context of profound impairment in cognitive development and an absence of spoken language

Routine delivery of artemisinin-based combination treatment at fixed health facilities reduces malaria prevalence in Tanzania: an observational study

BACKGROUND Artemisinin-based combination therapy (ACT) has been promoted as a means to reduce malaria transmission due to their ability to kill both asexual blood stages of malaria parasites, which sustain infections over long periods and the immature derived sexual stages responsible for infecting mosquitoes and onward transmission. Early studies reported a temporal association between ACT introduction and reduced malaria transmission in a number of ecological settings. However, these reports have come from areas with low to moderate malaria transmission, been confounded by the presence of other interventions or environmental changes that may have reduced malaria transmission, and have not included a comparison group without ACT. This report presents results from the first large-scale observational study to assess the impact of case management with ACT on population-level measures of malaria endemicity in an area with intense transmission where the benefits of effective infection clearance might be compromised by frequent and repeated re-infection. METHODS A pre-post observational study with a non-randomized comparison group was conducted at two sites in Tanzania. Both sites used sulphadoxine-pyrimethamine (SP) monotherapy as a first-line anti-malarial from mid-2001 through 2002. In 2003, the ACT, artesunate (AS) co-administered with SP (AS + SP), was introduced in all fixed health facilities in the intervention site, including both public and registered non-governmental facilities. Population-level prevalence of Plasmodium falciparum asexual parasitaemia and gametocytaemia were assessed using light microscopy from samples collected during representative household surveys in 2001, 2002, 2004, 2005 and 2006. FINDINGS Among 37,309 observations included in the analysis, annual asexual parasitaemia prevalence in persons of all ages ranged from 11% to 28% and gametocytaemia prevalence ranged from <1% to 2% between the two sites and across the five survey years. A multivariable logistic regression model was fitted to adjust for age, socioeconomic status, bed net use and rainfall. In the presence of consistently high coverage and efficacy of SP monotherapy and AS + SP in the comparison and intervention areas, the introduction of ACT in the intervention site was associated with a modest reduction in the adjusted asexual parasitaemia prevalence of 5 percentage-points or 23% (p < 0.0001) relative to the comparison site. Gametocytaemia prevalence did not differ significantly (p = 0.30). INTERPRETATION The introduction of ACT at fixed health facilities only modestly reduced asexual parasitaemia prevalence. ACT is effective for treatment of uncomplicated malaria and should have substantial public health impact on morbidity and mortality, but is unlikely to reduce malaria transmission substantially in much of sub-Saharan Africa where individuals are rapidly re-infected.Financial support for IMPACT-Tz came primarily from CDC, the U.S. Agency for International Development and the Wellcome Trust

Analysis of patient flows for orthopedic procedures using small area analysis in Switzerland

BACKGROUND: In general cantons regulate and control the Swiss health service system; patient flows within and between cantons are thereby partially disregarded. This paper develops an alternative spatial model, based upon the construction of orthopedic hospital service areas (HSA(O)s), and introduces indices for the analysis of patient streams in order to identify areas, irrespective of canton, with diverse characteristics, importance, needs, or demands. METHODS: HSA(O)s were constructed using orthopedic discharge data. Patient streams between the HSA(O)s were analysed by calculating three indices: the localization index (% local residents discharged locally), the netindex (the ratio of discharges of nonlocal incoming residents to outgoing local residents), and the market share index (% of local resident discharges of all discharges in local hospitals). RESULTS: The 85 orthopedic HSA(O)s show a median localization index of 60.8%, a market share index of 75.1%, and 30% of HSA(O)s have a positive netindex. Insurance class of bed, admission type, and patient age are partially but significantly associated with those indicators. A trend to more centrally provided health services can be observed not only in large urban HSA(O)s such as Geneva, Bern, Basel, and Zurich, but also in HSA(O)s in mountain sport areas such as Sion, Davos, or St.Moritz. Furthermore, elderly and emergency patients are more frequently treated locally than younger people or those having elective procedures. CONCLUSION: The division of Switzerland into HSA(O)s provides an alternative spatial model for analysing and describing patient streams for health service utilization. Because this small area model allows more in-depth analysis of patient streams both within and between cantons, it may improve support and planning of resource allocation of in-patient care in the Swiss healthcare system