A statistical approach to high-throughput screening of predicted orthologs

Orthologs are genes in different species that have diverged from a common ancestral gene after speciation. In contrast, paralogs are genes that have diverged after a gene duplication event. For many comparative analyses, it is of interest to identify orthologs with similar functions. Such orthologs tend to support species divergence (ssd-orthologs) in the sense that they have diverged only due to speciation, to the same relative degree as their species. However, due to incomplete sequencing or gene loss in a species, predicted orthologs can sometimes be paralogs or other non-ssd-orthologs. To increase the specificity of ssd-ortholog prediction, Fulton et al. [Fulton, D., Li, Y., Laird, M., Horsman, B., Roche, F., Brinkman, F., 2006. Improving the specificity of high-throughput ortholog prediction. BMC Bioinformatics 7 (1), 270] developed Ortholuge, a bioinformatics tool that identifies predicted orthologs with atypical genetic divergence. However, when the initial list of putative orthologs contains a non-negligible number of non-ssd-orthologs, the cut-off values that Ortholuge generates for orthology classification are difficult to interpret and can be too high, leading to decreased specificity of ssd-ortholog prediction. Therefore, we propose a complementary statistical approach to determining cut-off values. A benefit of the proposed approach is that it gives the user an estimated conditional probability that a predicted ortholog pair is unusually diverged. This enables the interpretation and selection of cut-off values based on a direct measure of the relative composition of ssd-orthologs versus non-ssd-orthologs. In a simulation comparison of the two approaches, we find that the statistical approach provides more stable cut-off values and improves the specificity of ssd-ortholog prediction for low-quality data sets of predicted orthologs.     

The complementary exponential geometric distribution: Model, properties, and a comparison with its counterpart

In this paper, we proposed a new two-parameter lifetime distribution with increasing failure rate, the complementary exponential geometric distribution, which is complementary to the exponential geometric model proposed by Adamidis and Loukas (1998). The new distribution arises on a latent complementary risks scenario, in which the lifetime associated with a particular risk is not observable; rather, we observe only the maximum lifetime value among all risks. The properties of the proposed distribution are discussed, including a formal proof of its probability density function and explicit algebraic formulas for its reliability and failure rate functions, moments, including the mean and variance, variation coefficient, and modal value. The parameter estimation is based on the usual maximum likelihood approach. We report the results of a misspecification simulation study performed in order to assess the extent of misspecification errors when testing the exponential geometric distribution against our complementary one in the presence of different sample size and censoring percentage. The methodology is illustrated on four real datasets; we also make a comparison between both modeling approaches.     

An alternative objective function for fitting regression trees to functional response variables

Analyses of systems that can be represented by functional responses are becoming common in many scientific disciplines. Functional regression trees (FRT) provide a methodology for modelling such systems. Recent work has focused on fitting models where the response variable is a probability density function, using a splitting criterion that is based on the sum of dissimilarities between the densities. We suggest a different criterion based on deviations of the densities from their mean. We provide motivation and justification for this criterion, and demonstrate its superior performance using an extensive simulation exercise. We discuss the computational aspects of the FRT procedure and show that substantial speed gains can be made through use of a dissimilarity matrix. Our results show that the proposed splitting criterion outperforms both the original and a splitting criterion based on Euclidean distance. Pointwise standard error curves for a predicted functional response can be generated through the fitting procedure, which we demonstrate in a case study with a forestry data set. Supplementary materials are available.     

Optimal allocation of change points in simple step-stress experiments under Type-II censoring

In simple step-stress experiments under Type-II censoring with the cumulative exposure model and exponentially distributed lifetimes, maximum likelihood estimates (MLE) of the expected lifetimes may not exist due to the absence of failure times either before or after the stress change point. For this reason, when planning a step-stress experiment, the change point could be chosen so as to minimize the probability of non-existence of the MLE. These non-existence probabilities are examined and compared in the one- as well as the two-sample situations. Moreover, the optimal allocations of the change points are discussed and the effects of the use of non-optimal choices for the change points are assessed.     

基于QCircuit的BB84窃听仿真与分析

该文研究量子线路模型仿真量子密钥分配协议.基于QCircuit软件运用量子线路模型设计不同攻击模型下的BB84量子密钥分配协议仿真模型,并引入rsec和I(α,E)两个指标,设计指标分析线路模型,仿真分析了不同噪声信道模型下BB84密钥分配协议在P/P、B/P和B/B三种不同截取/重发策略下的有效性及安全性.仿真结果表...     

一种基于FS401的高分辨率视频转换器设计

介绍了VGA高分辨率视频分配设计原理和TV视频转换的系统原理与总体架构.基于FS401视频处理器和VGA视频分配技术的应用,设计开发了一种高分辨率VGA-TV视频转换器.在分析视频格式转换基本原理及FS401芯片功能结构基础上,对视频转换器的硬、软件进行设计,最终开发出视频转换器电路板并应用于实际系统中.实测结果表明,...     

基于多尺度网格模型的物流配送中心选址候选集构建方法

针对物流配送中心选址候选集构建中的地理区域离散化问题,提出一种基于k-增长多尺度网格模型的选址区域离散化方法,根据区域选址敏感度不同,进行尺度差异化网格划分．在此基础上,提出了多尺度网格投影及膨胀算法,识别并剔除“限制性区域”及距其指定范围内的多尺度网格．数值实验表明了所提出的模型及算法的有效性．     

一种求解多维背包问题的混合分布估计算法

针对多维背包问题（MKP）,提出一种基于分布估计算法的混合求解算法,该算法基于优势种群构建概率模型,并基于概率模型采样产生新个体;同时,提出一种基于MKP问题信息的修复机制,有效修复采样后种群中的不可行解．另外,设计了一种自适应的局部搜索操作,以增强算法的局部搜索能力,基于标准测试集的仿真结果和算法比较验证了所提出的混合算法的有效性和鲁棒性．     

基于低频能量分布的掌纹特征提取

提出了一种基于傅里叶变换的掌纹特征提取方法,利用傅里叶变换将空域的掌纹图像变换到频域,选取频域图像的低频能量分布作为掌纹的特征,以此为基础对特征向量进行匹配识别。实验结果表明,该算法实现简单、操作方便,具有较快的反应速度和较高的识别率。     

实时数据分发系统软件的设计与实现

实时数据分发系统指使用实时数据分发服务中间件的分布式系统。实时数据分发服务中间件采用实时发布-订阅协议,通过在数据发布方和订阅方之间配置的服务质量参数,可以实现不同的数据需求和传输方式。该中间件能够跨平台操作,屏蔽底层操作系统的差异,这有利于系统灵活动态地扩展和升级。文中阐述了数据分发服务的思想和模型,以RTI公司的数据分发服务中间件DDS为例,具体研究了该中间件的软件设计和实现。