布尔网络

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模板:Cleanup

文件:Hou710 BooleanNetwork.svg
State space of a Boolean Network with N=4 nodes and K=1 links per node. Nodes can be either switched on (red) or off (blue). Thin (black) arrows symbolise the inputs of the Boolean function which is a simple "copy"-function for each node. The thick (grey) arrows show what a synchronous update does. Altogether there are 6 (orange) attractors, 4 of them are fixed points.

nodes and K=1 links per node. Nodes can be either switched on (red) or off (blue). Thin (black) arrows symbolise the inputs of the Boolean function which is a simple "copy"-function for each node. The thick (grey) arrows show what a synchronous update does. Altogether there are 6 (orange) attractors, 4 of them are fixed points.]]

节点和每个节点K=1条链路。节点可以被打开(红色)或关闭(蓝色)。细(黑色)箭头象征着布尔函数的输入,布尔函数是每个节点的简单 "复制 "函数。粗(灰色)箭头表示同步更新的功能。总共有6个(橙色)吸引子,其中4个是固定点。


A Boolean network consists of a discrete set of boolean variables each of which has a Boolean function (possibly different for each variable) assigned to it which takes inputs from a subset of those variables and output that determines the state of the variable it is assigned to. This set of functions in effect determines a topology (connectivity) on the set of variables, which then become nodes in a network. Usually, the dynamics of the system is taken as a discrete time series where the state of the entire network at time t+1 is determined by evaluating each variable's function on the state of the network at time t. This may be done synchronously or asynchronously.[1]

A Boolean network consists of a discrete set of boolean variables each of which has a Boolean function (possibly different for each variable) assigned to it which takes inputs from a subset of those variables and output that determines the state of the variable it is assigned to. This set of functions in effect determines a topology (connectivity) on the set of variables, which then become nodes in a network. Usually, the dynamics of the system is taken as a discrete time series where the state of the entire network at time t+1 is determined by evaluating each variable's function on the state of the network at time t. This may be done synchronously or asynchronously.

布尔网络 Boolean Network 由一组离散的布尔变量组成,每个变量都被分配了一个布尔函数(可能每个变量都不同),它从这些变量的子集中获取输入,并输出决定其被分配的变量的状态。 这一组函数实际上决定了变量集上的拓扑结构(连通性),这些变量就成为网络中的节点。通常,系统的动态是以离散时间序列的形式进行的,通过评估每个变量在时间 t 的网络状态上的函数来确定整个网络在时间 t+1的状态,这可能是同步或异步完成的。


Boolean networks have been used in biology to model regulatory networks. Although Boolean networks are a crude simplification of genetic reality where genes are not simple binary switches, there are several cases where they correctly capture the correct pattern of expressed and suppressed genes.[2][3]

Boolean networks have been used in biology to model regulatory networks. Although Boolean networks are a crude simplification of genetic reality where genes are not simple binary switches, there are several cases where they correctly capture the correct pattern of expressed and suppressed genes.

布尔网络在生物学中已被用于模拟调节网络 Regulatory Networks 。虽然布尔网络是对遗传现实的粗略简化,基因不是简单的二进制开关,但在一些情况下,它们正确地捕捉了表达和抑制基因的正确模式。 The seemingly mathematical easy (synchronous) model was only fully understood in the mid 2000s.[4]

The seemingly mathematical easy (synchronous) model was only fully understood in the mid 2000s.

在2000年中期人们才完全理解看似数学上的简易(同步)模型。


Classical model

经典模型

A Boolean network is a particular kind of sequential dynamical system, where time and states are discrete, i.e. both the set of variables and the set of states in the time series each have a bijection onto an integer series. Such systems are like cellular automata on networks, except for the fact that when they are set up each node has a rule that is randomly chosen from all 2模板:Sup possible ones with K inputs. With K=2 class 2 behavior tends to dominate. But for K>2, the behavior one sees quickly approaches what is typical for a random mapping in which the network representing the evolution of the 2模板:Sup states of the N underlying nodes is itself connected essentially randomly.[5]

A Boolean network is a particular kind of sequential dynamical system, where time and states are discrete, i.e. both the set of variables and the set of states in the time series each have a bijection onto an integer series. Such systems are like cellular automata on networks, except for the fact that when they are set up each node has a rule that is randomly chosen from all 2}} possible ones with K inputs. With K=2 class 2 behavior tends to dominate. But for K>2, the behavior one sees quickly approaches what is typical for a random mapping in which the network representing the evolution of the 2 states of the N underlying nodes is itself connected essentially randomly.

布尔网络是一种特殊的顺序动力学系统,其中时间和状态都是离散的,即时间序列中的变量集和状态集都各自有一个偏射到一个整数序列上。这样的系统就像网络上的细胞自动机一样,只是当它们被建立起来时,每个节点都有一个规则,这个规则是从所有 2k 可能的规则中随机选择的,有 K 个输入。在 K=2 时,两类行为往往占主导地位。但对于 K>2 ,人们看到的行为很快就会接近随机映射的典型特征,其中代表 N 个底层节点的 2k 种状态演化的网络本身基本上是随机连接的。


A random Boolean network (RBN) is one that is randomly selected from the set of all possible boolean networks of a particular size, N. One then can study statistically, how the expected properties of such networks depend on various statistical properties of the ensemble of all possible networks. For example, one may study how the RBN behavior changes as the average connectivity is changed.

A random Boolean network (RBN) is one that is randomly selected from the set of all possible boolean networks of a particular size, N. One then can study statistically, how the expected properties of such networks depend on various statistical properties of the ensemble of all possible networks. For example, one may study how the RBN behavior changes as the average connectivity is changed.

随机布尔网络 Random Boolean Network(RBN) 是指从所有可能的特定大小的布尔网络 N 的集合中随机选取的网络。然后,人们可以从统计学上研究,这种网络的预期特性如何依赖于所有可能网络的集合的各种统计特性。 例如,人们可以研究RBN行为如何随着 Average Connectivity 平均连通性 的改变而改变。


The first Boolean networks were proposed by Stuart A. Kauffman in 1969, as random models of genetic regulatory networks[6] but their mathematical understanding only started in the 2000s.[7][8]

The first Boolean networks were proposed by Stuart A. Kauffman in 1969, as random models of genetic regulatory networks but their mathematical understanding only started in the 2000s.

1969年,Stuart A. Kauffman提出了第一个布尔网络,作为遗传调控网络的随机模型,但其数学理解在2000年才开始。

Attractors

吸引子 Attractors


Since a Boolean network has only 2N possible states, a trajectory will sooner or later reach a previously visited state, and thus, since the dynamics are deterministic, the trajectory will fall into a steady state or cycle called an attractor (though in the broader field of dynamical systems a cycle is only an attractor if perturbations from it lead back to it). If the attractor has only a single state it is called a point attractor, and if the attractor consists of more than one state it is called a cycle attractor. The set of states that lead to an attractor is called the basin of the attractor. States which occur only at the beginning of trajectories (no trajectories lead to them), are called garden-of-Eden states[9] and the dynamics of the network flow from these states towards attractors. The time it takes to reach an attractor is called transient time.[4]

Since a Boolean network has only 2N possible states, a trajectory will sooner or later reach a previously visited state, and thus, since the dynamics are deterministic, the trajectory will fall into a steady state or cycle called an attractor (though in the broader field of dynamical systems a cycle is only an attractor if perturbations from it lead back to it). If the attractor has only a single state it is called a point attractor, and if the attractor consists of more than one state it is called a cycle attractor. The set of states that lead to an attractor is called the basin of the attractor. States which occur only at the beginning of trajectories (no trajectories lead to them), are called garden-of-Eden states and the dynamics of the network flow from these states towards attractors. The time it takes to reach an attractor is called transient time.

由于布尔网络只有 2N 种可能的状态,一个轨迹迟早会到达以前访问过的状态,因此,由于动力学是确定性的,轨迹将落入一个稳定状态或周期,称为吸引子(不过在更广泛的动力学系统领域,一个周期只有当来自它的扰动导致回到它时才是吸引子)。如果吸引子只有一个状态,则称为点吸引子,如果吸引子由一个以上的状态组成,则称为周期吸引子。导致吸引子的状态集称为吸引子的盆地。只在轨迹开始时出现的状态(没有轨迹导致它们),称为伊甸园状态

garden-of-Eden states 网络的动态从这些状态流向吸引子。到达吸引子所需的时间称为瞬时 transient time 


With growing computer power and increasing understanding of the seemingly simple model, different authors gave different estimates for the mean number and length of the attractors, here a brief summary of key publications.[10]

With growing computer power and increasing understanding of the seemingly simple model, different authors gave different estimates for the mean number and length of the attractors, here a brief summary of key publications.

随着计算机能力的不断提高,对看似简单的模型的理解也越来越深刻,不同的作者对吸引子的平均数量和长度给出了不同的估计,这里简单总结一下主要的出版物。

{ | class = “ wikitable sortable”
Author Author 作者 Year Year 年份 Mean attractor length Mean attractor length 平均吸引长度 Mean attractor number Mean attractor number 平均吸引子数 comment comment 评论
Kauffmann [6] Kauffmann

考夫曼

1969 1969 1969 [math]\displaystyle{ \langle A\rangle\sim \sqrt{N} }[/math] [math]\displaystyle{ \langle A\rangle\sim \sqrt{N} }[/math] < math > langle a rangle sim sqrt { n } </math > [math]\displaystyle{ \langle\nu\rangle\sim \sqrt{N} }[/math] [math]\displaystyle{ \langle\nu\rangle\sim \sqrt{N} }[/math] < math > langle nu rangle sim sqrt { n } </math >
Bastolla/ Parisi[11] Bastolla/ Parisi Bastolla/ Parisi 1998 1998 1998 faster than a power law, [math]\displaystyle{ \langle A\rangle \gt N^x \forall x }[/math] faster than a power law, [math]\displaystyle{ \langle A\rangle \gt N^x \forall x }[/math] 比幂定律快,< math > langle a rangle > n ^ x for all x </math > faster than a power law, [math]\displaystyle{ \langle\nu\rangle \gt N^x \forall x }[/math] faster than a power law, [math]\displaystyle{ \langle\nu\rangle \gt N^x \forall x }[/math] 比幂定律快,< math > langle nu rangle > n ^ x for all x </math > first numerical evidences first numerical evidences

第一个数字证据

Bilke/ Sjunnesson[12] Bilke/ Sjunnesson Bilke/Sjunnesson 2002 2002 2002 linear with system size, [math]\displaystyle{ \langle\nu\rangle \sim N }[/math] linear with system size, [math]\displaystyle{ \langle\nu\rangle \sim N }[/math] 与系统大小成线性关系
Socolar/Kauffman[13] Socolar/Kauffman Socolar/Kauffman 2003 2003 2003 faster than linear, [math]\displaystyle{ \langle\nu\rangle \gt N^x }[/math] with [math]\displaystyle{ x \gt 1 }[/math] faster than linear, [math]\displaystyle{ \langle\nu\rangle \gt N^x }[/math] with [math]\displaystyle{ x \gt 1 }[/math]

快于线性,< math > langle nu rangle > n ^ x </math > with < math > x > 1 </math >

Samuelsson/Troein[14] Samuelsson/Troein Samuelsson/Troein 2003 2003 2003 superpolynomial growth, [math]\displaystyle{ \langle\nu\rangle \gt N^x \forall x }[/math] superpolynomial growth, [math]\displaystyle{ \langle\nu\rangle \gt N^x \forall x }[/math] 超多项式生长,< math > langle nu rangle > n ^ x for all x </math > mathematical proof mathematical proof

数学证明

Mihaljev/Drossel[15] Mihaljev/Drossel Mihaljev/Drossel 2005 2005 2005 faster than a power law, [math]\displaystyle{ \langle A\rangle \gt N^x \forall x }[/math] faster than a power law, [math]\displaystyle{ \langle A\rangle \gt N^x \forall x }[/math] 比幂定律快,< math > langle a rangle > n ^ x for all x </math > faster than a power law, [math]\displaystyle{ \langle\nu\rangle \gt N^x \forall x }[/math] faster than a power law, [math]\displaystyle{ \langle\nu\rangle \gt N^x \forall x }[/math] 比幂定律快,< math > langle nu rangle > n ^ x for all x </math >

|}

Stability

稳定性 Stability

In dynamical systems theory, the structure and length of the attractors of a network corresponds to the dynamic phase of the network. The stability of Boolean networks depends on the connections of their nodes. A Boolean network can exhibit stable, critical or chaotic behavior. This phenomenon is governed by a critical value of the average number of connections of nodes ([math]\displaystyle{ K_{c} }[/math]), and can be characterized by the Hamming distance as distance measure. In the unstable regime, the distance between two initially close states on average grows exponentially in time, while in the stable regime it decreases exponentially. In this, with "initially close states" one means that the Hamming distance is small compared with the number of nodes ([math]\displaystyle{ N }[/math]) in the network.

In dynamical systems theory, the structure and length of the attractors of a network corresponds to the dynamic phase of the network. The stability of Boolean networks depends on the connections of their nodes. A Boolean network can exhibit stable, critical or chaotic behavior. This phenomenon is governed by a critical value of the average number of connections of nodes ([math]\displaystyle{ K_{c} }[/math]), and can be characterized by the Hamming distance as distance measure. In the unstable regime, the distance between two initially close states on average grows exponentially in time, while in the stable regime it decreases exponentially. In this, with "initially close states" one means that the Hamming distance is small compared with the number of nodes ([math]\displaystyle{ N }[/math]) in the network.

在动力系统理论中,网络的结构和吸引子的长度对应于网络的动态阶段。布尔网络的稳定性取决于其节点的连接。布尔网络可以表现出稳定、临界或混乱的行为。这种现象受节点平均连接数的临界值([math]\displaystyle{ K_{c} }[/math])支配,可以用汉明距离作为距离度量。在非稳定体制下,两个初始接近状态之间的平均距离在时间上呈指数级增长,而在稳定体制下则呈指数级减小。在这其中,用 "最初接近的状态 "意味着汉明距离与网络中的节点数([math]\displaystyle{ N }[/math])相比是很小的。


For N-K-model[16] the network is stable if [math]\displaystyle{ K\lt K_{c} }[/math], critical if [math]\displaystyle{ K=K_{c} }[/math], and unstable if [math]\displaystyle{ K\gt K_{c} }[/math].

For N-K-model the network is stable if [math]\displaystyle{ K\lt K_{c} }[/math], critical if [math]\displaystyle{ K=K_{c} }[/math], and unstable if [math]\displaystyle{ K\gt K_{c} }[/math].

对于N-K模型,如果 [math]\displaystyle{ K\lt K_{c} }[/math] ,网络是稳定的;如果 [math]\displaystyle{ K=K_{c} }[/math] ,网络是临界的;如果 [math]\displaystyle{ K\gt K_{c} }[/math] ,网络是不稳定的。

The state of a given node [math]\displaystyle{ n_{i} }[/math] is updated according to its truth table, whose outputs are randomly populated. [math]\displaystyle{ p_{i} }[/math] denotes the probability of assigning an off output to a given series of input signals.

The state of a given node [math]\displaystyle{ n_{i} }[/math] is updated according to its truth table, whose outputs are randomly populated. [math]\displaystyle{ p_{i} }[/math] denotes the probability of assigning an off output to a given series of input signals.

一个给定节点的状态 [math]\displaystyle{ n_{i} }[/math] 根据其真值表进行更新,真值表的输出是随机填充的。[math]\displaystyle{ p_{i} }[/math] 表示将关闭输出分配给给定系列输入信号的概率。


If [math]\displaystyle{ p_{i}=p=const. }[/math] for every node, the transition between the stable and chaotic range depends on [math]\displaystyle{ p }[/math]. According to Bernard Derrida and Yves Pomeau[17]

If [math]\displaystyle{ p_{i}=p=const. }[/math] for every node, the transition between the stable and chaotic range depends on [math]\displaystyle{ p }[/math]. According to Bernard Derrida and Yves Pomeau

如果 [math]\displaystyle{ p_{i}=p=const. }[/math] 对于每一个节点,稳定和混沌范围之间的转换取决于 [math]\displaystyle{ p }[/math] 。根据伯纳德-德里达和伊夫-波莫的观点 , the critical value of the average number of connections is [math]\displaystyle{ K_{c}=1/[2p(1-p)] }[/math].

, the critical value of the average number of connections is [math]\displaystyle{ K_{c}=1/[2p(1-p)] }[/math].

, 平均连接数的临界值为 [math]\displaystyle{ K_{c}=1/[2p(1-p)] }[/math]


If [math]\displaystyle{ K }[/math] is not constant, and there is no correlation between the in-degrees and out-degrees, the conditions of stability is determined by [math]\displaystyle{ \langle K^{in}\rangle }[/math][18][19][20] The network is stable if [math]\displaystyle{ \langle K^{in}\rangle \lt K_{c} }[/math], critical if [math]\displaystyle{ \langle K^{in}\rangle =K_{c} }[/math], and unstable if [math]\displaystyle{ \langle K^{in}\rangle \gt K_{c} }[/math].

If [math]\displaystyle{ K }[/math] is not constant, and there is no correlation between the in-degrees and out-degrees, the conditions of stability is determined by [math]\displaystyle{ \langle K^{in}\rangle }[/math] The network is stable if [math]\displaystyle{ \langle K^{in}\rangle \lt K_{c} }[/math], critical if [math]\displaystyle{ \langle K^{in}\rangle =K_{c} }[/math], and unstable if [math]\displaystyle{ \langle K^{in}\rangle \gt K_{c} }[/math].

如果 [math]\displaystyle{ K }[/math] 不是常数,且内度和外度之间没有相关性,则稳定性的条件由 [math]\displaystyle{ \langle K^{in}\rangle }[/math] 决定,如果 [math]\displaystyle{ \langle K^{in}\rangle \lt K_{c} }[/math] ,网络是稳定的。如果 [math]\displaystyle{ \langle K^{in}\rangle =K_{c} }[/math] ,则为临界;如果[math]\displaystyle{ \langle K^{in}\rangle \gt K_{c} }[/math] ,则为不稳定。

The conditions of stability are the same in the case of networks with scale-free topology where the in-and out-degree distribution is a power-law distribution: [math]\displaystyle{ P(K) \propto K^{-\gamma} }[/math], and [math]\displaystyle{ \langle K^{in} \rangle=\langle K^{out} \rangle }[/math], since every out-link from a node is an in-link to another.[21]

The conditions of stability are the same in the case of networks with scale-free topology where the in-and out-degree distribution is a power-law distribution: [math]\displaystyle{ P(K) \propto K^{-\gamma} }[/math], and [math]\displaystyle{ \langle K^{in} \rangle=\langle K^{out} \rangle }[/math], since every out-link from a node is an in-link to another.

对于无标度拓扑 scale-free topology 的网络来说,稳定性的条件是一样的,其中的出入度分布是幂律分布。[math]\displaystyle{ P(K) \propto K^{-\gamma} }[/math], 和 [math]\displaystyle{ \langle K^{in}\rangle=\langle K^{out} \rangle }[/math] ,因为从一个节点发出的每一条外链都是到另一个节点的内链。

Sensitivity shows the probability that the output of the Boolean function of a given node changes if its input changes. For random Boolean networks,

Sensitivity shows the probability that the output of the Boolean function of a given node changes if its input changes. For random Boolean networks,

灵敏度显示了给定节点的布尔函数的输出在其输入变化时发生变化的概率。对于随机布尔网络。 [math]\displaystyle{ q_{i}=2p_{i}(1-p_{i}) }[/math]. In the general case, stability of the network is governed by the largest eigenvalue [math]\displaystyle{ \lambda_{Q} }[/math] of matrix [math]\displaystyle{ Q }[/math], where [math]\displaystyle{ Q_{ij}=q_{i}A_{ij} }[/math], and [math]\displaystyle{ A }[/math] is the adjacency matrix of the network.[22] The network is stable if [math]\displaystyle{ \lambda_{Q}\lt 1 }[/math], critical if [math]\displaystyle{ \lambda_{Q}=1 }[/math], unstable if [math]\displaystyle{ \lambda_{Q}\gt 1 }[/math].

[math]\displaystyle{ q_{i}=2p_{i}(1-p_{i}) }[/math]. In the general case, stability of the network is governed by the largest eigenvalue [math]\displaystyle{ \lambda_{Q} }[/math] of matrix [math]\displaystyle{ Q }[/math], where [math]\displaystyle{ Q_{ij}=q_{i}A_{ij} }[/math], and [math]\displaystyle{ A }[/math] is the adjacency matrix of the network. The network is stable if [math]\displaystyle{ \lambda_{Q}\lt 1 }[/math], critical if [math]\displaystyle{ \lambda_{Q}=1 }[/math], unstable if [math]\displaystyle{ \lambda_{Q}\gt 1 }[/math].

[math]\displaystyle{ q_{i}=2p_{i}(1-p_{i}) }[/math]。在一般情况下,网络的稳定性由最大的特征值[math]\displaystyle{ \lambda_{Q} }[/math]来控制。的矩阵 [math]\displaystyle{ Q }[/math],其中[math]\displaystyle{ Q_{ij}=q_{i}A_{ij} }[/math][math]\displaystyle{ A }[/math] 是网络的邻接矩阵。如果 [math]\displaystyle{ \lambda_{Q}\lt 1 }[/math],网络是稳定的;如果 [math]\displaystyle{ \lambda_{Q}=1 }[/math],网络是临界的;如果 [math]\displaystyle{ \lambda_{Q}\gt 1 }[/math],网络是不稳定的。

Variations of the model

模型的变化

Other topologies

其他拓扑性质

One theme is to study different underlying graph topologies.

One theme is to study different underlying graph topologies.

一个主题是研究不同的基础图拓扑结构。

  • The homogeneous case simply refers to a grid which is simply the reduction to the famous Ising model.
  • 同质情况 Homogeneous Case 只是指网格,它只是对著名的伊辛模型 lsing model 的还原。
  • Scale-free topologies may be chosen for Boolean networks.[23] One can distinguish the case where only in-degree distribution in power-law distributed,[24] or only the out-degree-distribution or both.

Other updating schemes

其他更新方案

Classical Boolean networks (sometimes called CRBN, i.e. Classic Random Boolean Network) are synchronously updated. Motivated by the fact that genes don't usually change their state simultaneously,[25] different alternatives have been introduced. A common classification[26] is the following:

Classical Boolean networks (sometimes called CRBN, i.e. Classic Random Boolean Network) are synchronously updated. Motivated by the fact that genes don't usually change their state simultaneously, different alternatives have been introduced. A common classification is the following:

经典布尔网络(有时也称为CRBN,即经典随机布尔网络)是同步更新的。受基因通常不会同时改变其状态这一事实的激励,人们引入了不同的替代方案。常见的分类如下:

  • Deterministic asynchronous updated Boolean networks (DRBNs) are not synchronously updated but a deterministic solution still exists. A node i will be updated when t ≡ Qi (mod Pi) where t is the time step.[27]

t≡Qi(modPi) 其中 t 是时间步长时,i 节点将被更新。确定性异步更新布尔网络(DRBNs)不是同步更新,但确定性解仍然存在。当 t≡Qi(modPi) 时,i 节点将被更新,其中 t 是时间步长。

  • The most general case is full stochastic updating (GARBN, general asynchronous random boolean networks). Here, one (or more) node(s) are selected at each computational step to be updated.
  • 最一般的情况是完全随机更新(GARBN,一般异步随机布尔网络)。在这里,在每个计算步骤中选择一个(或多个)节点进行更新。
  • The Partially-Observed Boolean Dynamical System (POBDS)[28][29][30][31] signal model differs from all previous deterministic and stochastic Boolean network models by removing the assumption of direct observability of the Boolean state vector and allowing uncertainty in the observation process, addressing the scenario encountered in practice.

Application of Boolean Networks

布尔网络的应用


Classification

分类


  • The Scalable Optimal Bayesian Classification[32] developed an optimal classification of trajectories accounting for potential model uncertainty and also proposed a particle-based trajectory classification that is highly scalable for large networks with much lower complexity than the optimal solution.

可伸缩的最佳贝叶斯分类 Scalable Optimal Bayesian Classification [32]开发了一种考虑潜在模型不确定性的轨迹最优分类,还提出了一种基于粒子的轨迹分类,对于大型网络具有高度的可扩展性,复杂度比最优解低得多。

See also

NK模型 NK Model

References

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模板:Stochastic processes

Category:Bioinformatics

类别: 生物信息学

Category:Logic

分类: 逻辑

Category:Spin models

分类: 旋转模型

Category:Exactly solvable models

类别: 完全可解模型

Category:Statistical mechanics

类别: 统计力学


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