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| | ==批判 Criticism== | | ==批判 Criticism== |
| − | An assumption (sometimes more sometimes less implicit) behind the preservation of a topological sub-structure is that it is of a particular functional importance. This assumption has recently been questioned. Some authors have argued that motifs, like ''bi-fan motifs'', might show a variety depending on the network context, and therefore,<ref name="ad">{{cite journal |vauthors=Ingram PJ, Stumpf MP, Stark J |title=Network motifs: structure does not determine function |journal=BMC Genomics |volume=7 |pages=108 |year=2006 |pmid=16677373 |pmc=1488845 |doi=10.1186/1471-2164-7-108 }} {{open access}}</ref> structure of the motif does not necessarily determine function. Network structure certainly does not always indicate function; this is an idea that has been around for some time, for an example see the Sin operon.<ref>{{cite journal |vauthors=Voigt CA, Wolf DM, Arkin AP |title=The ''Bacillus subtilis'' sin operon: an evolvable network motif |journal=Genetics |volume=169 |issue=3 |pages=1187–202 |date=March 2005 |pmid=15466432 |pmc=1449569 |doi=10.1534/genetics.104.031955 |url=http://www.genetics.org/cgi/pmidlookup?view=long&pmid=15466432}}</ref>
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| | 关于拓扑子结构的一个（某种程度上隐含的）前提性假设是其具有特定的功能重要性。但这个假设最近遭到质疑，有人提出在不同的网络环境下模体可能表现出多样性，例如双扇模体，所以<ref name="ad">{{cite journal |vauthors=Ingram PJ, Stumpf MP, Stark J |title=Network motifs: structure does not determine function |journal=BMC Genomics |volume=7 |pages=108 |year=2006 |pmid=16677373 |pmc=1488845 |doi=10.1186/1471-2164-7-108 }} {{open access}}</ref>模体的结构不必然决定功能，网络结构也不当然能揭示其功能；这种见解由来已久，可参见【Sin 操纵子】</font>。<ref>{{cite journal |vauthors=Voigt CA, Wolf DM, Arkin AP |title=The ''Bacillus subtilis'' sin operon: an evolvable network motif |journal=Genetics |volume=169 |issue=3 |pages=1187–202 |date=March 2005 |pmid=15466432 |pmc=1449569 |doi=10.1534/genetics.104.031955 |url=http://www.genetics.org/cgi/pmidlookup?view=long&pmid=15466432}}</ref> | | 关于拓扑子结构的一个（某种程度上隐含的）前提性假设是其具有特定的功能重要性。但这个假设最近遭到质疑，有人提出在不同的网络环境下模体可能表现出多样性，例如双扇模体，所以<ref name="ad">{{cite journal |vauthors=Ingram PJ, Stumpf MP, Stark J |title=Network motifs: structure does not determine function |journal=BMC Genomics |volume=7 |pages=108 |year=2006 |pmid=16677373 |pmc=1488845 |doi=10.1186/1471-2164-7-108 }} {{open access}}</ref>模体的结构不必然决定功能，网络结构也不当然能揭示其功能；这种见解由来已久，可参见【Sin 操纵子】</font>。<ref>{{cite journal |vauthors=Voigt CA, Wolf DM, Arkin AP |title=The ''Bacillus subtilis'' sin operon: an evolvable network motif |journal=Genetics |volume=169 |issue=3 |pages=1187–202 |date=March 2005 |pmid=15466432 |pmc=1449569 |doi=10.1534/genetics.104.031955 |url=http://www.genetics.org/cgi/pmidlookup?view=long&pmid=15466432}}</ref> |
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| − | Most analyses of motif function are carried out looking at the motif operating in isolation. Recent research<ref>{{cite journal |vauthors=Knabe JF, Nehaniv CL, Schilstra MJ |title=Do motifs reflect evolved function?—No convergent evolution of genetic regulatory network subgraph topologies |journal=BioSystems |volume=94 |issue=1–2 |pages=68–74 |year=2008 |pmid=18611431 |doi=10.1016/j.biosystems.2008.05.012 }}</ref> provides good evidence that network context, i.e. the connections of the motif to the rest of the network, is too important to draw inferences on function from local structure only — the cited paper also reviews the criticisms and alternative explanations for the observed data. An analysis of the impact of a single motif module on the global dynamics of a network is studied in.<ref>{{cite journal |vauthors=Taylor D, Restrepo JG |title=Network connectivity during mergers and growth: Optimizing the addition of a module |journal=Physical Review E |volume=83 |issue=6 |year=2011 |page=66112 |doi=10.1103/PhysRevE.83.066112 |pmid=21797446 |bibcode=2011PhRvE..83f6112T |arxiv=1102.4876 }}</ref> Yet another recent work suggests that certain topological features of biological networks naturally give rise to the common appearance of canonical motifs, thereby questioning whether frequencies of occurrences are reasonable evidence that the structures of motifs are selected for their functional contribution to the operation of networks.<ref>{{cite journal|last1=Konagurthu|first1=Arun S.|last2=Lesk|first2=Arthur M.|title=Single and multiple input modules in regulatory networks|journal=Proteins: Structure, Function, and Bioinformatics|date=23 April 2008|volume=73|issue=2|pages=320–324|doi=10.1002/prot.22053|pmid=18433061}}</ref><ref>{{cite journal |vauthors=Konagurthu AS, Lesk AM |title=On the origin of distribution patterns of motifs in biological networks |journal=BMC Syst Biol |volume=2 |pages=73 |year=2008 |pmid=18700017 |pmc=2538512 |doi=10.1186/1752-0509-2-73 }} {{open access}}</ref>
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| − | | + | 模体的研究主要应用于静态复杂网络，而时变复杂网络的研究<ref>Braha, D., & Bar‐Yam, Y. (2006). [https://static1.squarespace.com/static/5b68a4e4a2772c2a206180a1/t/5c5de3faf4e1fc43e7b3d21e/1549657083988/Complexity_Braha_Original_w_Cover.pdf From centrality to temporary fame: Dynamic centrality in complex networks]. Complexity, 12(2), 59-63. </ref>对网络模体的提出了重大的新解释，并介绍了'''时变网络模体'''的概念。Braha和Bar-Yam<ref> Braha D., Bar-Yam Y. (2009) [https://s3.amazonaws.com/academia.edu.documents/4892116/Adaptive_Networks__Theory__Models_and_Applications__Understanding_Complex_Systems_.pdf?response-content-disposition=inline%3B%20filename%3DRedes_teoria.pdf&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWOWYYGZ2Y53UL3A%2F20191111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20191111T173250Z&X-Amz-Expires=3600&X-Amz-SignedHeaders=host&X-Amz-Signature=89d08c9e92b88ed817e4eb0f87c480757ef79c4b865919a5e0890cbefa164c61#page=55 Time-Dependent Complex Networks: Dynamic Centrality, Dynamic Motifs, and Cycles of Social Interactions]. In: Gross T., Sayama H. (eds) Adaptive Networks. Understanding Complex Systems. Springer, Berlin, Heidelberg </ref>研究了 |
| − | While the study of motifs was mostly applied to static complex networks, research of temporal complex networks<ref>Braha, D., & Bar‐Yam, Y. (2006). [https://static1.squarespace.com/static/5b68a4e4a2772c2a206180a1/t/5c5de3faf4e1fc43e7b3d21e/1549657083988/Complexity_Braha_Original_w_Cover.pdf From centrality to temporary fame: Dynamic centrality in complex networks]. Complexity, 12(2), 59-63. </ref> suggested a significant reinterpretation of network motifs, and introduced the concept of '''temporal network motifs'''. Braha and Bar-Yam<ref> Braha D., Bar-Yam Y. (2009) [https://s3.amazonaws.com/academia.edu.documents/4892116/Adaptive_Networks__Theory__Models_and_Applications__Understanding_Complex_Systems_.pdf?response-content-disposition=inline%3B%20filename%3DRedes_teoria.pdf&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWOWYYGZ2Y53UL3A%2F20191111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20191111T173250Z&X-Amz-Expires=3600&X-Amz-SignedHeaders=host&X-Amz-Signature=89d08c9e92b88ed817e4eb0f87c480757ef79c4b865919a5e0890cbefa164c61#page=55 Time-Dependent Complex Networks: Dynamic Centrality, Dynamic Motifs, and Cycles of Social Interactions]. In: Gross T., Sayama H. (eds) Adaptive Networks. Understanding Complex Systems. Springer, Berlin, Heidelberg </ref> studied the dynamics of local motif structure in time-dependent/temporal networks, and find recurrent patterns that might provide empirical evidence for cycles of social interaction. Counter to the perspective of stable motifs and motif profiles in complex networks, they demonstrated that for temporal networks the local structure is time-dependent and might evolve over time. Braha and Bar-Yam further suggested that analyzing the temporal local structure might provide important information about the dynamics of system-level task and functionality.
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| − | 模体的研究主要应用于静态复杂网络，而时变复杂网络的研究<ref>Braha, D., & Bar‐Yam, Y. (2006). [https://static1.squarespace.com/static/5b68a4e4a2772c2a206180a1/t/5c5de3faf4e1fc43e7b3d21e/1549657083988/Complexity_Braha_Original_w_Cover.pdf From centrality to temporary fame: Dynamic centrality in complex networks]. Complexity, 12(2), 59-63. </ref>对网络模体的提出了重大的新解释，并介绍了时变网络模体的概念。Braha和Bar-Yam<ref> Braha D., Bar-Yam Y. (2009) [https://s3.amazonaws.com/academia.edu.documents/4892116/Adaptive_Networks__Theory__Models_and_Applications__Understanding_Complex_Systems_.pdf?response-content-disposition=inline%3B%20filename%3DRedes_teoria.pdf&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWOWYYGZ2Y53UL3A%2F20191111%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20191111T173250Z&X-Amz-Expires=3600&X-Amz-SignedHeaders=host&X-Amz-Signature=89d08c9e92b88ed817e4eb0f87c480757ef79c4b865919a5e0890cbefa164c61#page=55 Time-Dependent Complex Networks: Dynamic Centrality, Dynamic Motifs, and Cycles of Social Interactions]. In: Gross T., Sayama H. (eds) Adaptive Networks. Understanding Complex Systems. Springer, Berlin, Heidelberg </ref>研究了
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| | 本地模体结构在时间依赖网络/时变网络的动力学，发现的一些反复模式有望成为社会互动周期的经验论据。他们证明了对于时变网络，其本地结构是时间依赖的且可能随时间演变，作为对复杂网络中稳定模体观及的模体表达观的反论，Braha和Bar-Yam进一步提出，对时变本地结构的分析有可能找到关于系统级任务和功能方面的动力学的重要信息。 | | 本地模体结构在时间依赖网络/时变网络的动力学，发现的一些反复模式有望成为社会互动周期的经验论据。他们证明了对于时变网络，其本地结构是时间依赖的且可能随时间演变，作为对复杂网络中稳定模体观及的模体表达观的反论，Braha和Bar-Yam进一步提出，对时变本地结构的分析有可能找到关于系统级任务和功能方面的动力学的重要信息。 |
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