• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法,用中文像聊天一样搜索,搜遍4000万医学文献。AI智能推荐,让科研检索更轻松。

立即免费搜索

文件翻译

保留排版,准确专业,支持PDF/Word/PPT等文件格式,支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述,25分钟生成高质量综述,智能提取关键信息,辅助科研写作。

立即免费体验

从节点的动态信号推断网络。

Inferring a network from dynamical signals at its nodes.

机构信息

Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA.

Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.

出版信息

PLoS Comput Biol. 2020 Nov 30;16(11):e1008435. doi: 10.1371/journal.pcbi.1008435. eCollection 2020 Nov.

DOI:10.1371/journal.pcbi.1008435
PMID:33253160
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7728228/
Abstract

We give an approximate solution to the difficult inverse problem of inferring the topology of an unknown network from given time-dependent signals at the nodes. For example, we measure signals from individual neurons in the brain, and infer how they are inter-connected. We use Maximum Caliber as an inference principle. The combinatorial challenge of high-dimensional data is handled using two different approximations to the pairwise couplings. We show two proofs of principle: in a nonlinear genetic toggle switch circuit, and in a toy neural network.

摘要

我们给出了一个从节点上给定的时变信号推断未知网络拓扑结构的困难逆问题的近似解。例如,我们测量大脑中单个神经元的信号,并推断它们是如何相互连接的。我们使用最大口径作为推断原理。使用两种不同的方法来处理高维数据的组合挑战。我们展示了两个原理证明:在非线性遗传开关电路和玩具神经网络中。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3818/7728228/f0c5de605aa3/pcbi.1008435.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3818/7728228/1c5d0e5fb33c/pcbi.1008435.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3818/7728228/5047bf536c3c/pcbi.1008435.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3818/7728228/314d5fc4df0b/pcbi.1008435.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3818/7728228/f0c5de605aa3/pcbi.1008435.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3818/7728228/1c5d0e5fb33c/pcbi.1008435.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3818/7728228/5047bf536c3c/pcbi.1008435.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3818/7728228/314d5fc4df0b/pcbi.1008435.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3818/7728228/f0c5de605aa3/pcbi.1008435.g004.jpg

相似文献

1
Inferring a network from dynamical signals at its nodes.从节点的动态信号推断网络。
PLoS Comput Biol. 2020 Nov 30;16(11):e1008435. doi: 10.1371/journal.pcbi.1008435. eCollection 2020 Nov.
2
MICRAT: a novel algorithm for inferring gene regulatory networks using time series gene expression data.MICRAT:一种使用时间序列基因表达数据推断基因调控网络的新算法。
BMC Syst Biol. 2018 Dec 14;12(Suppl 7):115. doi: 10.1186/s12918-018-0635-1.
3
Reconstructing gene regulatory networks of biological function using differential equations of multilayer perceptrons.使用多层感知机的微分方程重建生物功能的基因调控网络。
BMC Bioinformatics. 2022 Nov 24;23(1):503. doi: 10.1186/s12859-022-05055-5.
4
Identifying the pulsed neuron networks' structures by a nonlinear Granger causality method.利用非线性格兰杰因果关系方法识别脉冲神经元网络的结构。
BMC Neurosci. 2020 Feb 12;21(1):7. doi: 10.1186/s12868-020-0555-z.
5
Periodic synchronization of isolated network elements facilitates simulating and inferring gene regulatory networks including stochastic molecular kinetics.周期性同步孤立网络元素有助于模拟和推断基因调控网络,包括随机分子动力学。
BMC Bioinformatics. 2022 Jan 5;23(1):13. doi: 10.1186/s12859-021-04541-6.
6
Data-Driven Boolean Network Inference Using a Genetic Algorithm With Marker-Based Encoding.基于标记编码的遗传算法的数据驱动布尔网络推断。
IEEE/ACM Trans Comput Biol Bioinform. 2022 May-Jun;19(3):1558-1569. doi: 10.1109/TCBB.2021.3055646. Epub 2022 Jun 3.
7
Convolutional Neural Networks as Summary Statistics for Approximate Bayesian Computation.卷积神经网络作为近似贝叶斯计算的汇总统计量。
IEEE/ACM Trans Comput Biol Bioinform. 2022 Nov-Dec;19(6):3353-3365. doi: 10.1109/TCBB.2021.3108695. Epub 2022 Dec 8.
8
Systematic errors in connectivity inferred from activity in strongly recurrent networks.从强重复网络中的活动推断出的连接中的系统误差。
Nat Neurosci. 2020 Oct;23(10):1286-1296. doi: 10.1038/s41593-020-0699-2. Epub 2020 Sep 7.
9
An algebra-based method for inferring gene regulatory networks.一种基于代数的基因调控网络推断方法。
BMC Syst Biol. 2014 Mar 26;8:37. doi: 10.1186/1752-0509-8-37.
10
Inference of gene networks from gene expression time series using recurrent neural networks and sparse MAP estimation.使用递归神经网络和稀疏最大后验估计从基因表达时间序列推断基因网络。
J Bioinform Comput Biol. 2018 Aug;16(4):1850009. doi: 10.1142/S0219720018500099. Epub 2018 Apr 26.

引用本文的文献

1
The maximum entropy principle for compositional data.组合数据的最大熵原理。
BMC Bioinformatics. 2022 Oct 29;23(1):449. doi: 10.1186/s12859-022-05007-z.
2
Quantifying biochemical reaction rates from static population variability within incompletely observed complex networks.从复杂网络中不完全观测到的静态群体变异性定量生化反应速率。
PLoS Comput Biol. 2022 Jun 22;18(6):e1010183. doi: 10.1371/journal.pcbi.1010183. eCollection 2022 Jun.
3
SiGMoiD: A super-statistical generative model for binary data.SiGMoiD:一种用于二值数据的超统计生成模型。

本文引用的文献

1
The Maximum Caliber Variational Principle for Nonequilibria.非平衡态的最大口径变分原理。
Annu Rev Phys Chem. 2020 Apr 20;71:213-238. doi: 10.1146/annurev-physchem-071119-040206. Epub 2020 Feb 19.
2
Maximum Entropy Framework for Predictive Inference of Cell Population Heterogeneity and Responses in Signaling Networks.最大熵框架用于预测信号网络中细胞群体异质性和反应的预测推理。
Cell Syst. 2020 Feb 26;10(2):204-212.e8. doi: 10.1016/j.cels.2019.11.010. Epub 2019 Dec 18.
3
Maximum Caliber Can Build and Infer Models of Oscillation in a Three-Gene Feedback Network.
PLoS Comput Biol. 2021 Aug 6;17(8):e1009275. doi: 10.1371/journal.pcbi.1009275. eCollection 2021 Aug.
最大口径可以构建和推断三基因反馈网络中的振荡模型。
J Phys Chem B. 2019 Jan 17;123(2):343-355. doi: 10.1021/acs.jpcb.8b07465. Epub 2019 Jan 9.
4
Maximum Caliber Can Characterize Genetic Switches with Multiple Hidden Species.最大口径可表征具有多个隐藏种的遗传开关。
J Phys Chem B. 2018 May 31;122(21):5666-5677. doi: 10.1021/acs.jpcb.7b12251. Epub 2018 Feb 15.
5
Perspective: Maximum caliber is a general variational principle for dynamical systems.观点:最大口径是动力系统的一个通用变分原理。
J Chem Phys. 2018 Jan 7;148(1):010901. doi: 10.1063/1.5012990.
6
Inverse statistical physics of protein sequences: a key issues review.蛋白质序列的反统计物理学:关键问题综述。
Rep Prog Phys. 2018 Mar;81(3):032601. doi: 10.1088/1361-6633/aa9965.
7
Building Predictive Models of Genetic Circuits Using the Principle of Maximum Caliber.利用最大口径原理构建遗传电路的预测模型。
Biophys J. 2017 Nov 7;113(9):2121-2130. doi: 10.1016/j.bpj.2017.08.057.
8
Dynamical criticality in the collective activity of a population of retinal neurons.视网膜神经元群体集体活动中的动力学临界性。
Phys Rev Lett. 2015 Feb 20;114(7):078105. doi: 10.1103/PhysRevLett.114.078105.
9
Searching for collective behavior in a large network of sensory neurons.在大型感觉神经元网络中寻找集体行为。
PLoS Comput Biol. 2014 Jan;10(1):e1003408. doi: 10.1371/journal.pcbi.1003408. Epub 2014 Jan 2.
10
Perturbation biology: inferring signaling networks in cellular systems.扰动生物学:推断细胞系统中的信号网络。
PLoS Comput Biol. 2013;9(12):e1003290. doi: 10.1371/journal.pcbi.1003290. Epub 2013 Dec 19.