基于因果关系挖掘的概率基因调控网络的构建

科学的基因聚类方法是构建基因调控网络的前提,但仅以聚类作为构建网络的主要手段只能找到共同调控的基因,不能精确反映基因之间的相互作用过程。贝叶斯网络模型通过基于图的方式求得多变量之间条件独立的概率因果关系,但因其计算复杂性受到应用层面的限制。该文综合考虑几方面因素,在对基因进行聚类基础上,通过对调控关系的预测获得对目标基因的调控基因组,再利用LCD(local causal relation discovery)方法通过限制搜索条件发现基因间的独立关系,进而获得基因调控网络。实验结果表明了该方法的可行性和有效性。     

使用模型检测解决概率布尔网络优化控制

系统生物学期望对复杂生物系统建立一个真实的、可计算的模型,以便于以系统的角度去理解生物系统的演变过程。在系统生物学中,一个重要的主题是通过外部的干预控制发展关于基因调控网络的控制理论,以作为未来基因治疗技术。目前,布尔网络及其扩展的概率布尔网络已经被广泛用于对基因调控网络进行建模。在控制问题的研究中,概率布尔控制网络的状态迁移本质上构成一条有限状态空间的离散时间马尔科夫决策过程。依据马尔科夫决策过程的理论,通过概率模型检测方法解决网络中有限范围优化控制问题和无限范围优化控制问题。针对带有随机干扰且上下文相关的概率布尔控制网络,使用概率模型检测器PRISM对其进行形式化建模,然后将两类优化控制问题描述为相应的时序逻辑公式,最后通过模型检测寻找出最优解。实验结果表明,提出的方法可以有效地用于生物网络的分析和优化控制。     

进化大规模脉冲神经网络的发育方法

通过自然进化得到的脑包含几十亿的神经元和几万亿的神经连接,并表现出复杂的智能行为.受生物脑进化与发育的启发,研究者给出了进化神经网络的发育编码方法,特点是通过基因重用可在较小的基因空间中进行大规模神经网络的快速搜索.以人工基因组模型为框架描述基因调控网络,用基因表达的动态特性表示细胞命运特化的发育过程,提出了一种进化大规模脉冲神经网络的发育方法.该方法的特点在于可以快速有效地发育生成脉冲神经元、神经连接和突触可塑性.相应的食物采集进化实验突现了以神经驱动的自主智能体的智能行为,并验证了该方法对大规模脉冲神经网络的进化能力.     

胃癌模糊基因调控网络的构建

基因调控网络的研究是以系统的观点为出发点,从基因之间相互作用的角度揭示复杂的生命现象.生命体通过调节差异基因表达来控制其生长、遗传和变异行为.差异表达基因之间的相互作用是构建基因调控网络的纽带,网络中差异表达的基因可以揭示与癌症相关基因的信息.基因网络模型为深入理解生命本质提供了有益的参考,本文提出了一种新颖的方法来预测基因调控网络,即将模糊理论引入基因网络的构建中,阐述了模糊理论基因调控网络建模的机理并初步建立了胃癌模糊基因调控网络,对研究胃癌的发生和发展机理有重要的理论意义和应用价值.     

基于复杂网络模型的基因调控网络的计算模拟

随着大通量基因芯片数据的产生,基因调控机制的网络化研究需求日趋迫切。提出了基于复杂网络理论的基因调控网络的模拟方法,构建了基因调控网络模拟器GN-Simulator。通过分析真实基因调控网络的拓扑特性,提出了对应的矩阵模型,并充分考虑了网络的生物学鲁棒性和动力学稳定性,给出了人工基因网络的生成过程和计算模拟方法。计算实验表明,GN-Simulator能高效地模拟出与真实基因调控网络高度相似的大规模人工网络,并可为不同算法提供无偏验证的多样化人工模拟数据。     

使用稳态系统和粒群优化算法进行基因调控网络推断

基因调控网络模型试图从海量的时序基因表达数据中研究基因的功能,推断基因之间的调控关系,从而揭示复杂的病理现象和生命现象.通过利用时序基因表达数据来推断一个基于稳态系统(S-system)模型的基因网络,提出使用粒群优化算法(PSO)来优化模型参数,从而捕捉基因表达数据中的动力学特性.实验结果表明,该方法能够使模型参数快速得到收敛,配置参数后模型仿真能力好,可以较好地识别基因调控关系.     

基于概率模型检测和遗传算法的基因调控网络的无限范围优化控制

基因调控网络是一类基本且重要的生物网络,通过对其进行控制可以实现生物系统功能的调节。在生物系统中,通过外部的干预控制构造关于基因调控网络的控制理论成为了非常热门的研究主题。目前,作为一种重要的网络模型,带有干扰且上下文相关的概率布尔网络已经被广泛地应用于基因调控网络优化控制问题的研究中。针对无限范围的优化控制问题,文中提出了一种基于概率模型检测和遗传算法的近似最优控制策略的计算方法。首先,该方法将无限范围控制中定义的期望总成本归约为离散时间马尔科夫链上的平稳状态回报;然后,构建包含固定控制策略的带有干扰且上下文相关的概率布尔网络模型,采用带回报属性的时序逻辑公式表示固定控制策略的成本,采用概率模型检测器PRISM进行自动计算。进一步,采用遗传算法,将固定控制策略编码为遗传算法解空间中的个体,基于其控制成本,定义个体的适应度值,将PRISM作为求解器,通过在解空间上迭代地执行遗传操作获取近似最优解。将所提方法应用于WNT5A网络中,实验结果证明了该方法的有效性。     

基于Logistic回归模型的时变结构基因调控网络构建

目前,由大多数基因调控网络的重构方法推导出的网络结构是静态的,即不随时间改变.但在细胞周期或一个有机体的不同生长阶段,调控网络的拓扑结构会发生显著变化.这为深入了解基因调控的时空机制带来困难.因此,文中提出一种基于时延互信息和核权重l1正则化Logistic回归模型学习时变结构基因调控网络的算法.将其应用于两种生物情景数据:黑腹果蝇在不同阶段的肌肉发育和酿酒酵母苯菌灵中毒后的反应.实验结果显示,该方法能反映不同细胞状态对基因间相互作用的影响,有效获取基因调控网络随时间变化的动态效应.     

概率级联布尔网络的集镇定及其应用

随着系统生物学和医学的迅速发展,基因调控网络已经成为一个热点研究领域.布尔网络作为研究生物系统和基因调控网络的一种重要模型,近年来引起了包括生物学家和系统科学家在内的很多学者的广泛关注.本文利用代数状态空间方法,研究了概率级联布尔网络的集镇定问题.首先给出概率级联布尔网络集镇定的定义,并利用矩阵的半张量积给出了概率级联布尔网络的代数表示.其次基于该代数表示,定义了一组合适的概率能达集,并给出了概率级联布尔网络集镇定问题可解的充要条件.最后将所得的理论结果应用于概率级联布尔网络的同步分析及n人随机级联演化布尔博弈的策略一致演化行为分析.     

基因学习算法及其在集合覆盖问题中的应用

在用传统方法解决一些复杂而规模较大的组合优化问题,尤其是NP难题,出现困难时,一些近似算法相继推出。启发式搜索法、模拟退火算法及进化算法等的出现,为解决这些优化问题提供了非常好的手段。近年来,出现了一种概率学习的进化计算模型,如Baluja的PBIL算法与Corno的自私基因算法。概率学习的进化计算模型通过不断地学习每一代的最优个体,最终收敛于最优或较优的解的等位基因概率,其过程描述如下:     

Invariance of the stationary state distribution for mass service networks with multi-regime strategies,different demands,and a “generalized processor sharing” discipline

Mass service networks with multiregime strategies and several types of demands are studied. Single-line nodes can operate in several regimes corresponding to different degrees of performance. The time of existence of each regime has an exponential distribution. The discipline of the demand servicing by the device is the “generalized processor sharing” (GPS) with random channel choice in the node. The amount of work on servicing a demand is a random quantity with an arbitrary distribution function. The invariance of the stationary probability distribution of network states with respect to the functional form of the distribution of the amount of work required for the demand servicing is established.     

Noise tolerance of attractor and feedforward memory models

In short-term memory networks, transient stimuli are represented by patterns of neural activity that persist long after stimulus offset. Here, we compare the performance of two prominent classes of memory networks, feedback-based attractor networks and feedforward networks, in conveying information about the amplitude of a briefly presented stimulus in the presence of gaussian noise. Using Fisher information as a metric of memory performance, we find that the optimal form of network architecture depends strongly on assumptions about the forms of nonlinearities in the network. For purely linear networks, we find that feedforward networks outperform attractor networks because noise is continually removed from feedforward networks when signals exit the network; as a result, feedforward networks can amplify signals they receive faster than noise accumulates over time. By contrast, attractor networks must operate in a signal-attenuating regime to avoid the buildup of noise. However, if the amplification of signals is limited by a finite dynamic range of neuronal responses or if noise is reset at the time of signal arrival, as suggested by recent experiments, we find that attractor networks can outperform feedforward ones. Under a simple model in which neurons have a finite dynamic range, we find that the optimal attractor networks are forgetful if there is no mechanism for noise reduction with signal arrival but nonforgetful (perfect integrators) in the presence of a strong reset mechanism. Furthermore, we find that the maximal Fisher information for the feedforward and attractor networks exhibits power law decay as a function of time and scales linearly with the number of neurons. These results highlight prominent factors that lead to trade-offs in the memory performance of networks with different architectures and constraints, and suggest conditions under which attractor or feedforward networks may be best suited to storing information about previous stimuli.     

On fault tolerance of 3-dimensional mesh networks

In this paper, the concept of k-submesh and k-submesh connectivity fault tolerance model is proposed. And the fault tolerance of 3-D mesh networks is studied under a more realistic model in which each network node has an independent failure probability. It is first observed that if the node failure probability is fixed, then the connectivity probability of 3-D mesh networks can be arbitrarily small when the network size is sufficiently large. Thus, it is practically important for multicomputer system manufacturer to determine the upper bound for node failure probability when the probability of network connectivity and the network size are given. A novel technique is developed to formally derive lower bounds on the connectivity probability for 3-D mesh networks. The study shows that 3-D mesh networks of practical size can tolerate a large number of faulty nodes thus are reliable enough for multicomputer systems. A number of advantages of 3-D mesh networks over other popular network topologies are given.     

多层前向小世界神经网络及其函数逼近

借鉴复杂网络的研究成果, 探讨一种在结构上处于规则和随机连接型神经网络之间的网络模型—-多层前向小世界神经网络. 首先对多层前向规则神经网络中的连接依重连概率p进行重连, 构建新的网络模型, 对其特征参数的分析表明, 当0 < p < 1时, 该网络在聚类系数上不同于Watts-Strogatz 模型; 其次用六元组模型对网络进行描述; 最后, 将不同p值下的小世界神经网络用于函数逼近, 仿真结果表明, 当p = 0:1时, 网络具有最优的逼近性能, 收敛性能对比试验也表明, 此时网络在收敛性能、逼近速度等指标上要优于同规模的规则网络和随机网络.     

Inference in Bayesian Networks with Recursive Probability Trees: Data Structure Definition and Operations

Recursive probability trees (RPTs) are a data structure for representing several types of potentials involved in probabilistic graphical models. The RPT structure improves the modeling capabilities of previous structures (like probability trees or conditional probability tables). These capabilities can be exploited to gain savings in memory space and/or computation time during inference. This paper describes the modeling capabilities of RPTs as well as how the basic operations required for making inference on Bayesian networks operate on them. The performance of the inference process with RPTs is examined with some experiments using the variable elimination algorithm.     

无线传感器网络簇级拓扑演化模型研究

复杂网络理论研究表明,复杂系统的容错能力不仅仅存在于具有冗余组件的系统之中;而且也同样存在于具有无标度(scale-free)特征的网络之中;文章借助于复杂网络理论和偏好依附机制提出一种无线传感器网络簇级拓扑演化模型;拓扑动态分析表明,该模型能够很好地体现无线传感器簇间的拓扑生长过程,由该模型演化成的无线网络拓扑具有无标度网络的性质,所以该拓扑模型具有很强的容错性。     

Large Deviations for Large Capacity Loss Networks with Fixed Routing and Polyhedral Admission Sets

In this paper, we study large deviations of large capacity loss networks with fixed routing. We use two-level modelling for the loss networks: the call level and the cell level. At the call level, a call request is accepted if it succeeds an admission test. The test is based on a polyhedral set of the number of calls in progress when a new call arrives. After being accepted, a call then transmits a sequence of cells (random variables) during its holding period. We show that the fluid limits and the conditional central limit theorems in Kelly (1991) can be extended to the large deviation regime. Moreover, there are corresponding fluid flow explanations for our large deviation results. In particular, we derive the exponential decay rates of the call blocking probability and the cell loss probability. These decay rates are obtained by solving primal and dual convex programming problems.     

基于声望模型的联合呼叫接纳控制算法

为了弥补异构无线网络中呼叫接纳控制研究场景的局限性,降低终端选择接入网时的盲目性,将研究场景从两个接入网延伸为多个接入网,提出一种基于声望模型的联合呼叫接纳控制算法。将声望模型应用于网络选择过程,增加了网络反馈机制。在用户侧,终端根据网络声望值大小选择接入网;在网络侧,采用动态带宽分配和缓冲队列策略来提高接入成功率。仿真结果表明,该算法有效降低了新呼叫阻塞率和切换呼叫掉线率。