利用 PymoNNto 和 PymoNNtorch 加速尖峰神经网络仿真

IF 2.5 4区 医学 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Frontiers in Neuroinformatics Pub Date : 2024-02-20 DOI:10.3389/fninf.2024.1331220
Marius Vieth, Ali Rahimi, Ashena Gorgan Mohammadi, Jochen Triesch, Mohammad Ganjtabesh
{"title":"利用 PymoNNto 和 PymoNNtorch 加速尖峰神经网络仿真","authors":"Marius Vieth, Ali Rahimi, Ashena Gorgan Mohammadi, Jochen Triesch, Mohammad Ganjtabesh","doi":"10.3389/fninf.2024.1331220","DOIUrl":null,"url":null,"abstract":"Spiking neural network simulations are a central tool in Computational Neuroscience, Artificial Intelligence, and Neuromorphic Engineering research. A broad range of simulators and software frameworks for such simulations exist with different target application areas. Among these, PymoNNto is a recent Python-based toolbox for spiking neural network simulations that emphasizes the embedding of custom code in a modular and flexible way. While PymoNNto already supports GPU implementations, its backend relies on NumPy operations. Here we introduce PymoNNtorch, which is natively implemented with PyTorch while retaining PymoNNto's modular design. Furthermore, we demonstrate how changes to the implementations of common network operations in combination with PymoNNtorch's native GPU support can offer speed-up over conventional simulators like NEST, ANNarchy, and Brian 2 in certain situations. Overall, we show how PymoNNto's modular and flexible design in combination with PymoNNtorch's GPU acceleration and optimized indexing operations facilitate research and development of spiking neural networks in the Python programming language.","PeriodicalId":12462,"journal":{"name":"Frontiers in Neuroinformatics","volume":"45 1","pages":""},"PeriodicalIF":2.5000,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Accelerating spiking neural network simulations with PymoNNto and PymoNNtorch\",\"authors\":\"Marius Vieth, Ali Rahimi, Ashena Gorgan Mohammadi, Jochen Triesch, Mohammad Ganjtabesh\",\"doi\":\"10.3389/fninf.2024.1331220\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Spiking neural network simulations are a central tool in Computational Neuroscience, Artificial Intelligence, and Neuromorphic Engineering research. A broad range of simulators and software frameworks for such simulations exist with different target application areas. Among these, PymoNNto is a recent Python-based toolbox for spiking neural network simulations that emphasizes the embedding of custom code in a modular and flexible way. While PymoNNto already supports GPU implementations, its backend relies on NumPy operations. Here we introduce PymoNNtorch, which is natively implemented with PyTorch while retaining PymoNNto's modular design. Furthermore, we demonstrate how changes to the implementations of common network operations in combination with PymoNNtorch's native GPU support can offer speed-up over conventional simulators like NEST, ANNarchy, and Brian 2 in certain situations. Overall, we show how PymoNNto's modular and flexible design in combination with PymoNNtorch's GPU acceleration and optimized indexing operations facilitate research and development of spiking neural networks in the Python programming language.\",\"PeriodicalId\":12462,\"journal\":{\"name\":\"Frontiers in Neuroinformatics\",\"volume\":\"45 1\",\"pages\":\"\"},\"PeriodicalIF\":2.5000,\"publicationDate\":\"2024-02-20\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Frontiers in Neuroinformatics\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.3389/fninf.2024.1331220\",\"RegionNum\":4,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"MATHEMATICAL & COMPUTATIONAL BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Frontiers in Neuroinformatics","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.3389/fninf.2024.1331220","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"MATHEMATICAL & COMPUTATIONAL BIOLOGY","Score":null,"Total":0}
引用次数: 0

摘要

尖峰神经网络模拟是计算神经科学、人工智能和神经形态工程研究的核心工具。针对不同的目标应用领域,有多种用于此类模拟的模拟器和软件框架。其中,PymoNNto 是最近推出的一款基于 Python 的尖峰神经网络仿真工具箱,它强调以模块化和灵活的方式嵌入自定义代码。虽然 PymoNNto 已经支持 GPU 实现,但其后台依赖于 NumPy 操作。在这里,我们将介绍 PymoNNtorch,它是用 PyTorch 原生实现的,同时保留了 PymoNNto 的模块化设计。此外,我们还展示了如何通过改变常见网络操作的实现方式,结合 PymoNNtorch 的原生 GPU 支持,在某些情况下实现比 NEST、ANNarchy 和 Brian 2 等传统模拟器更快的速度。总之,我们展示了 PymoNNto 的模块化和灵活设计如何与 PymoNNtorch 的 GPU 加速和优化索引操作相结合,促进了 Python 编程语言中尖峰神经网络的研究与开发。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
Accelerating spiking neural network simulations with PymoNNto and PymoNNtorch
Spiking neural network simulations are a central tool in Computational Neuroscience, Artificial Intelligence, and Neuromorphic Engineering research. A broad range of simulators and software frameworks for such simulations exist with different target application areas. Among these, PymoNNto is a recent Python-based toolbox for spiking neural network simulations that emphasizes the embedding of custom code in a modular and flexible way. While PymoNNto already supports GPU implementations, its backend relies on NumPy operations. Here we introduce PymoNNtorch, which is natively implemented with PyTorch while retaining PymoNNto's modular design. Furthermore, we demonstrate how changes to the implementations of common network operations in combination with PymoNNtorch's native GPU support can offer speed-up over conventional simulators like NEST, ANNarchy, and Brian 2 in certain situations. Overall, we show how PymoNNto's modular and flexible design in combination with PymoNNtorch's GPU acceleration and optimized indexing operations facilitate research and development of spiking neural networks in the Python programming language.
求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Frontiers in Neuroinformatics
Frontiers in Neuroinformatics MATHEMATICAL & COMPUTATIONAL BIOLOGY-NEUROSCIENCES
CiteScore
4.80
自引率
5.70%
发文量
132
审稿时长
14 weeks
期刊介绍: Frontiers in Neuroinformatics publishes rigorously peer-reviewed research on the development and implementation of numerical/computational models and analytical tools used to share, integrate and analyze experimental data and advance theories of the nervous system functions. Specialty Chief Editors Jan G. Bjaalie at the University of Oslo and Sean L. Hill at the École Polytechnique Fédérale de Lausanne are supported by an outstanding Editorial Board of international experts. This multidisciplinary open-access journal is at the forefront of disseminating and communicating scientific knowledge and impactful discoveries to researchers, academics and the public worldwide. Neuroscience is being propelled into the information age as the volume of information explodes, demanding organization and synthesis. Novel synthesis approaches are opening up a new dimension for the exploration of the components of brain elements and systems and the vast number of variables that underlie their functions. Neural data is highly heterogeneous with complex inter-relations across multiple levels, driving the need for innovative organizing and synthesizing approaches from genes to cognition, and covering a range of species and disease states. Frontiers in Neuroinformatics therefore welcomes submissions on existing neuroscience databases, development of data and knowledge bases for all levels of neuroscience, applications and technologies that can facilitate data sharing (interoperability, formats, terminologies, and ontologies), and novel tools for data acquisition, analyses, visualization, and dissemination of nervous system data. Our journal welcomes submissions on new tools (software and hardware) that support brain modeling, and the merging of neuroscience databases with brain models used for simulation and visualization.
期刊最新文献
Quantitative assessment of neurodevelopmental maturation: a comprehensive systematic literature review of artificial intelligence-based brain age prediction in pediatric populations. Spectral graph convolutional neural network for Alzheimer's disease diagnosis and multi-disease categorization from functional brain changes in magnetic resonance images. Commentary: Accelerating spiking neural network simulations with PymoNNto and PymoNNtorch. Fuzzy C-means clustering algorithm applied in computed tomography images of patients with intracranial hemorrhage. Early detection of mild cognitive impairment through neuropsychological tests in population screenings: a decision support system integrating ontologies and machine learning.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1