Suppr超能文献

缺失和虚假交互以及复杂网络的重构。

Missing and spurious interactions and the reconstruction of complex networks.

机构信息

Department of Chemical and Biological Engineering and Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208, USA.

出版信息

Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22073-8. doi: 10.1073/pnas.0908366106. Epub 2009 Dec 14.

Abstract

Network analysis is currently used in a myriad of contexts, from identifying potential drug targets to predicting the spread of epidemics and designing vaccination strategies and from finding friends to uncovering criminal activity. Despite the promise of the network approach, the reliability of network data is a source of great concern in all fields where complex networks are studied. Here, we present a general mathematical and computational framework to deal with the problem of data reliability in complex networks. In particular, we are able to reliably identify both missing and spurious interactions in noisy network observations. Remarkably, our approach also enables us to obtain, from those noisy observations, network reconstructions that yield estimates of the true network properties that are more accurate than those provided by the observations themselves. Our approach has the potential to guide experiments, to better characterize network data sets, and to drive new discoveries.

摘要

网络分析目前被应用于许多领域,从识别潜在的药物靶点到预测传染病的传播和设计疫苗接种策略,从寻找朋友到发现犯罪活动。尽管网络方法有很大的前景,但在研究复杂网络的所有领域中,网络数据的可靠性都是一个令人担忧的问题。在这里,我们提出了一个通用的数学和计算框架来处理复杂网络中数据可靠性的问题。特别是,我们能够可靠地识别噪声网络观测中缺失和虚假的相互作用。值得注意的是,我们的方法还使我们能够从这些噪声观测中获得网络重建,从而获得比观测本身提供的更准确的真实网络特性的估计。我们的方法有可能指导实验,更好地描述网络数据集,并推动新的发现。

相似文献

1
Missing and spurious interactions and the reconstruction of complex networks.
Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22073-8. doi: 10.1073/pnas.0908366106. Epub 2009 Dec 14.
3
4
Dynamics and control of diseases in networks with community structure.
PLoS Comput Biol. 2010 Apr 8;6(4):e1000736. doi: 10.1371/journal.pcbi.1000736.
5
A Bayesian Framework for Combining Protein and Network Topology Information for Predicting Protein-Protein Interactions.
IEEE/ACM Trans Comput Biol Bioinform. 2015 May-Jun;12(3):538-50. doi: 10.1109/TCBB.2014.2359441.
6
Immunization strategies in networks with missing data.
PLoS Comput Biol. 2020 Jul 9;16(7):e1007897. doi: 10.1371/journal.pcbi.1007897. eCollection 2020 Jul.
7
Using indirect protein-protein interactions for protein complex prediction.
J Bioinform Comput Biol. 2008 Jun;6(3):435-66. doi: 10.1142/s0219720008003497.
8
FALCON or how to compute measures time efficiently on dynamically evolving dense complex networks?
J Biomed Inform. 2014 Feb;47:62-70. doi: 10.1016/j.jbi.2013.09.005. Epub 2013 Sep 21.
9
ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context.
BMC Bioinformatics. 2006 Mar 20;7 Suppl 1(Suppl 1):S7. doi: 10.1186/1471-2105-7-S1-S7.
10
Network inference with ensembles of bi-clustering trees.
BMC Bioinformatics. 2019 Oct 28;20(1):525. doi: 10.1186/s12859-019-3104-y.

引用本文的文献

1
Deciphering Probabilistic Species Interaction Networks.
Ecol Lett. 2025 Jun;28(6):e70161. doi: 10.1111/ele.70161.
2
A Generalized Bayesian Stochastic Block Model for Microbiome Community Detection.
Stat Med. 2025 Feb 10;44(3-4):e10291. doi: 10.1002/sim.10291.
3
Link prediction of heterogeneous complex networks based on an improved embedding learning algorithm.
PLoS One. 2025 Jan 7;20(1):e0315507. doi: 10.1371/journal.pone.0315507. eCollection 2025.
4
Inconsistency among evaluation metrics in link prediction.
PNAS Nexus. 2024 Nov 6;3(11):pgae498. doi: 10.1093/pnasnexus/pgae498. eCollection 2024 Nov.
5
A One Health framework for exploring zoonotic interactions demonstrated through a case study.
Nat Commun. 2024 Jul 15;15(1):5650. doi: 10.1038/s41467-024-49967-7.
6
The effectiveness of intervention measures on MERS-CoV transmission by using the contact networks reconstructed from link prediction data.
Front Public Health. 2024 May 17;12:1386495. doi: 10.3389/fpubh.2024.1386495. eCollection 2024.
8
The maximum capability of a topological feature in link prediction.
PNAS Nexus. 2024 Mar 13;3(3):pgae113. doi: 10.1093/pnasnexus/pgae113. eCollection 2024 Mar.
9
On the complexity of quantum link prediction in complex networks.
Sci Rep. 2024 Jan 10;14(1):1026. doi: 10.1038/s41598-023-49906-4.
10
Link prediction based on spectral analysis.
PLoS One. 2024 Jan 2;19(1):e0287385. doi: 10.1371/journal.pone.0287385. eCollection 2024.

本文引用的文献

1
The structure of the nervous system of the nematode Caenorhabditis elegans.
Philos Trans R Soc Lond B Biol Sci. 1986 Nov 12;314(1165):1-340. doi: 10.1098/rstb.1986.0056.
2
A general pipeline for quality and statistical assessment of protein interaction data using R and Bioconductor.
Nat Protoc. 2009;4(4):535-46. doi: 10.1038/nprot.2009.26. Epub 2009 Mar 26.
3
High-quality binary protein interaction map of the yeast interactome network.
Science. 2008 Oct 3;322(5898):104-10. doi: 10.1126/science.1158684. Epub 2008 Aug 21.
4
5
A truer measure of our ignorance.
Proc Natl Acad Sci U S A. 2008 May 13;105(19):6795-6. doi: 10.1073/pnas.0802459105. Epub 2008 May 12.
6
Estimating the size of the human interactome.
Proc Natl Acad Sci U S A. 2008 May 13;105(19):6959-64. doi: 10.1073/pnas.0708078105. Epub 2008 May 12.
7
Hierarchical structure and the prediction of missing links in networks.
Nature. 2008 May 1;453(7191):98-101. doi: 10.1038/nature06830.
8
Extracting the hierarchical organization of complex systems.
Proc Natl Acad Sci U S A. 2007 Sep 25;104(39):15224-9. doi: 10.1073/pnas.0703740104. Epub 2007 Sep 19.
9
A network-based method for target selection in metabolic networks.
Bioinformatics. 2007 Jul 1;23(13):1616-22. doi: 10.1093/bioinformatics/btm150. Epub 2007 Apr 26.
10
Synchronization reveals topological scales in complex networks.
Phys Rev Lett. 2006 Mar 24;96(11):114102. doi: 10.1103/PhysRevLett.96.114102. Epub 2006 Mar 22.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验