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Computational intractability law molds the topology of biological networks
Applied Network Science Pub Date : 2020-07-10 , DOI: 10.1007/s41109-020-00268-0
Ali A. Atiia , Corbin Hopper , Katsumi Inoue , Silvia Vidal , Jérôme Waldispühl

Virtually all molecular interaction networks (MINs), irrespective of organism or physiological context, have a majority of loosely-connected ‘leaf’ genes interacting with at most 1-3 genes, and a minority of highly-connected ‘hub’ genes interacting with at least 10 or more other genes. Previous reports proposed adaptive and non-adaptive hypotheses describing sufficient but not necessary conditions for the origin of this majority-leaves minority-hubs (mLmH) topology. We modelled the evolution of MINs as a computational optimization problem which describes the cost of conserving, deleting or mutating existing genes so as to maximize (minimize) the overall number of beneficial (damaging) interactions network-wide. The model 1) provides sufficient and, assuming \(\mathcal {P}\neq \mathcal {NP}\), necessary conditions for the emergence of mLmH as an adaptation to circumvent computational intractability, 2) predicts the percentage number of genes having d interacting partners, and 3) when employed as a fitness function in an evolutionary algorithm, produces mLmH-possessing synthetic networks whose degree distributions match those of equal-size MINs.

中文翻译:

计算难易定律塑造了生物网络的拓扑

几乎所有分子相互作用网络(MINs),无论是有机体还是生理环境,都具有大部分与最多1-3个基因相互作用的松散连接的“叶子”基因,以及少数与1-3个基因相互作用的高度连接的“集线器”基因至少10个或更多其他基因。先前的报告提出了适应性和非适应性假设,这些假设描述了这种多数叶子少数群体(mLmH)拓扑起源的充分但非必要条件。我们将MIN的进化模型建模为一个计算优化问题,该问题描述了保存,删除或变异现有基因的成本,以便最大化(最小化)整个网络中有益(有害)相互作用的总数。模型1)提供了足够的,并假设\(\ mathcal {P} \ neq \ mathcal {NP} \),mLmH的出现作为适应规避计算难点的必要条件,2)预测具有d个相互作用伴侣的基因的百分比,3)在进化算法中用作适应度函数时,会产生具有mLmH的合成网络度分布与MIN大小相等的分布相匹配。
更新日期:2020-07-10
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