Comment on "Clustering by passing messages between data points"

Frey and Dueck (Reports, 16 February 2007, p. 972) described an algorithm termed "affinity propagation" (AP) as a promising alternative to traditional data clustering procedures. We demonstrate that a well-established heuristic for the p-median problem often obtains clustering solutions with lower error than AP and produces these solutions in comparable computation time.     

Classic selective sweeps were rare in recent human evolution

Efforts to identify the genetic basis of human adaptations from polymorphism data have sought footprints of "classic selective sweeps" (in which a beneficial mutation arises and rapidly fixes in the population).Yet it remains unknown whether this form of natural selection was common in our evolution. We examined the evidence for classic sweeps in resequencing data from 179 human genomes. As expected under a recurrent-sweep model, we found that diversity levels decrease near exons and conserved noncoding regions. In contrast to expectation, however, the trough in diversity around human-specific amino acid substitutions is no more pronounced than around synonymous substitutions. Moreover, relative to the genome background, amino acid and putative regulatory sites are not significantly enriched in alleles that are highly differentiated between populations. These findings indicate that classic sweeps were not a dominant mode of human adaptation over the past ~250,000 years.     

基于AP聚类算法的图像分割应用与研究

针对传统聚类算法在图像分割中对聚类中心选择敏感,可靠性差的缺点,本文采用AP聚类算法研究图像分割问题。AP(Affinity propagation)聚类算法是通过数据点之间的信息传递产生高质量的聚类中心,避免了聚类初始中心选择难的问题。本文通过与K均值算法和模糊C均值算法在图像分割中的实验比较,得出本算法优于其他两种算法,对图像可取得良好的分割效果。     

基于DBSCAN的VMS数据定置刺网渔船网次提取方法

网次是捕捞努力量计算、渔业资源调查和渔业生产管理中的重要统计参数,定置刺网作业过程中起网状态下的航速与航行、放网时相差较大,可通过阈值进行提取。利用2017年浙临渔12870和浙三渔66666定置刺网渔船VMS数据,首先对其航速及相邻作业点时间差进行统计分析,得到合理的聚类参数,然后采用DBSCAN(Density-Based Spatial Clustering of Application With Noises)算法对定置刺网周围作业点进行聚类,提取作业网次,继而统计各网次作业持续时间与距离。以15 min作为合理误差范围,将各网次起止时间与日志起网时起止时间进行比较验证。结果表明:该方法在网次识别上效果良好,聚类提取的各个网次起网时的起止时间准确率达到80%以上。     

Surface grading of bamboo strips using multi-scale color texture features in eigenspace

In order to achieve high competitive quality of bamboo products, it appears that bamboo strips with naturally different tonalities should be elaborately sorted into different classes according to their global color texture appearance. Inspired by the coarse-to-fine visual perception process of human vision system, this paper proposes a new surface grading approach by integrating the color and texture of bamboo strips based on Gaussian multi-scale space. The multi-scale representations of color texture for the original image of bamboo strips could be obtained and used to construct the multivariate image, each channel of which represents a perceptual observation from different scales. The multivariate image analysis (MIA) techniques are used to extract multi-scale features from the resulting multivariate image data. The characteristic images corresponding to typical classes are selected to build the model of the reference eigenspace. The novel testing images and the training images are all projected onto this reference eigenspace to obtain their representative feature clusters. And the Bhattacharyya distance is used to estimate the similarity of the representative feature clusters between the testing images and the training images in the eigenspace. Then a k-NN classifier is adopted to classify the testing images into the given classes of training images. Comparative experiments have been carried out on a set of actual bamboo strip images and the experimental results verify the effective discrimination of multi-scale color texture eigenspace features and good classification accuracy of the proposed surface grading method.     

具有自我学习机制的网络谣言传播与仿真研究

将社交网络中的个体设为健康者(S)、传播者(I)、反击者(C)和免疫者(R)4种状态,根据不同状态之间的转移机制建立了SICR谣言传播模型.针对"人云亦云"的社会从众心理,引入个体的自我学习机制,基于BA无标度网络仿真分析了自我学习机制以及初始传播者、天然反击者重要性对谣言传播行为的影响.结果显示:自我学习机制能够促进谣言传播;初始传播者越重要,谣言传播范围越广、速度越快;天然反击者的重要性越高,抑制谣言传播的效果越明显.     

Subset selection from multi-experiment data sets with application to milk fatty acid profiles

The development of routine analyses to allow for the handling of large amounts of samples and to avoid cost and time expensive analytical techniques is of high value. These routine analyses most often require calibration using the detailed analyses as reference values. A representative subset reflecting the complete range of the variables of interest is required for this purpose. In this paper this subset selection problem is tackled for multi-experiment data sets. Conventional techniques such as the Kennard and Stone algorithm and OptiSim are compared to a new approach based on Genetic Algorithms. The challenge here is to find an adequate objective function and to modify the standard crossover and mutation operators to keep the number of desired samples fixed. These techniques are applied on a data set containing the concentration of 45 fatty acids, determined by a simplified reference method, in 1033 milk samples, stemming from six different experiments. The objective is to select a subset of 100 samples in which each of the six different experiments is sufficiently represented. While there is no obvious way to generalize the conventional methods for multi-experiment data sets, this can quite easily be accomplished for Genetic Algorithms by modifying the objective function. Our results indicate that Genetic Algorithms are very capable of handling the subset selection problem for multi-experiment data sets.     

Interhemispheric asymmetries of the modular structure in human temporal cortex

Language-relevant processing of auditory signals is lateralized and involves the posterior part of Brodmann area 22. We found that the functional lateralization in this area was accompanied by interhemispheric differences in the organization of the intrinsic microcircuitry. Neuronal tract tracing revealed a modular network of long-range intrinsic connections linking regularly spaced clusters of neurons. Although the cluster diameter was similar in both hemispheres, their spacing was about 20 percent larger in the left hemisphere. Assuming similar relations between functional and anatomical architecture as in visual cortex, the present data suggest that more functionally distinct columnar systems are included per surface unit in the left than in the right area 22.     

High-quality binary protein interaction map of the yeast interactome network

Current yeast interactome network maps contain several hundred molecular complexes with limited and somewhat controversial representation of direct binary interactions. We carried out a comparative quality assessment of current yeast interactome data sets, demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information. Because a large fraction of the yeast binary interactome remains to be mapped, we developed an empirically controlled mapping framework to produce a "second-generation" high-quality, high-throughput Y2H data set covering approximately 20% of all yeast binary interactions. Both Y2H and affinity purification followed by mass spectrometry (AP/MS) data are of equally high quality but of a fundamentally different and complementary nature, resulting in networks with different topological and biological properties. Compared to co-complex interactome models, this binary map is enriched for transient signaling interactions and intercomplex connections with a highly significant clustering between essential proteins. Rather than correlating with essentiality, protein connectivity correlates with genetic pleiotropy.     

Prospects for building the tree of life from large sequence databases

We assess the phylogenetic potential of approximately 300,000 protein sequences sampled from Swiss-Prot and GenBank. Although only a small subset of these data was potentially phylogenetically informative, this subset retained a substantial fraction of the original taxonomic diversity. Sampling biases in the databases necessitate building phylogenetic data sets that have large numbers of missing entries. However, an analysis of two "supermatrices" suggests that even data sets with as much as 92% missing data can provide insights into broad sections of the tree of life.     

Reducing the dimensionality of data with neural networks

High-dimensional data can be converted to low-dimensional codes by training a multilayer neural network with a small central layer to reconstruct high-dimensional input vectors. Gradient descent can be used for fine-tuning the weights in such "autoencoder" networks, but this works well only if the initial weights are close to a good solution. We describe an effective way of initializing the weights that allows deep autoencoder networks to learn low-dimensional codes that work much better than principal components analysis as a tool to reduce the dimensionality of data.     

巨峰葡萄开花前至落果期~(14)C—光合产物的运转分配及与落花落果的关系

在巨峰葡萄开花前,盛花期和落果期．将~(14)CO_2导入不摘心、摘心及花穗用GA_350mL／L,GA_350mL／L＋BA25mL／L处理结果枝花（果）穗的邻近叶中,然后测定新消各部位~(14)C—光合产物的放射性强度。结果表明：1．开花前和盛花期导入~(14)CO_2的两处理,表现出花穗邻近叶的~(14)C—光合产物的运输方向与落果期不同、开花前和盛花期~(14)C—光合产物主要供给花序生长发育,供给枝梢先端极少。而在落果高峰期则大量供应枝梢生长,仅少量供应果穗。2、初花期果枝摘心在落果期能显著促进~(14)C—光合产物运向果穗,同时表现营养生长受抑。3．盛花期用GA_350mL／L、GA_350mL／L＋BA25mL／L处理花穗,可促使~(14)C—光合产物大量运向果穗。     

No specific recognition of leader peptide by SecB, a chaperone involved in protein export

Most proteins destined for export from Escherichia coli are made as precursors containing amino-terminal leader sequences that are essential for export and that are removed during the process. The initial step in export of a subset of proteins, which includes maltose-binding protein, is binding of the precursor by the molecular chaperone SecB. This work shows directly that SecB binds with high affinity to unfolded maltose-binding protein but does not specifically recognize and bind the leader. Rather, the leader modulates folding to expose elements in the remainder of the polypeptide that are recognized by SecB.     

Cyberinfrastructure for e-Science

Here we describe the requirements of an e-Infrastructure to enable faster, better, and different scientific research capabilities. We use two application exemplars taken from the United Kingdom's e-Science Programme to illustrate these requirements and make the case for a service-oriented infrastructure. We provide a brief overview of the UK "plug-and-play composable services" vision and the role of semantics in such an e-Infrastructure.     

Covalent Group IV Atomic Clusters

Atomic clusters containing from two to several hundred atoms offer the possibility of studying the transition from molecules to crystalline solids. The covalent group IV elements carbon, silicon, and germanium are now being examined with this long-range objective. These elements are particularly interesting because of the very different character of their crystalline solids and because they are intermediate between metals and insulators in the nature of their bonding. Small mass-selected atom cluster ions are formed by pulsed laser techniques and identified by time-of-flight methods. Laser photoexcitation is used to study the relative stability of these clusters and their modes of fragmentation. These modes for C(n)(+) clusters, which tend to fragment with a characteristic loss of a neutral C(3), are found to be different from the modes for Si(n)(+) and Ge(n)(+) clusters, which tend to fragment to "magic" clusters such as Si(4)(+), Si(6)(+) and Si(10)(+). These experimental results can be accounted for by recent theoretical calculations of the ground-state structure and stability of small silicon and carbon clusters. Several theoretical approaches give consistent results, showing that small silicon clusters are compact and different from small fragments of the bulk crystal. Calculations show that carbon clusters change from linear structures toward cyclic structures as the cluster size increases, but with significant odd-even differences.     

网络购物物流服务质量评价指标体系的构建(一)以小型B2C和C2C为例

该文介绍了小型B2C和C2C网络购物物流服务质量管理现状,归纳了国内外学者对物流服务质量的研究成果,结合小型B2C和C2C网络购物,采用流程分析法找出其物流服务中与顾客的38个接触点;然后面向网络购物中有签收经验的小型商家制作并发放调查问卷,回收整理所得数据。在验证了调查问卷的信度和效度之后,采用SPSS统计软件对这些接触点均值方差情况进行分析,归纳出如下6个通俗易懂的影响网络购物物流服务质量的代表因子:送货服务水平、接单服务水平、正确安分履行订单能力、时间性、信息服务能力和价格,以期为网络购物物流服务质量评价提供参考。     

The origin of galaxies and clusters of galaxies

Debate on how galaxies and clusters of galaxies formed has reached an interesting stage at which one can find arguments for quite different scenarios. The galaxy distribution has a complex "frothy" character that could be the fossil of a network of protoclusters or pancakes that produced galaxies. However, there are galaxies like our own that seem never to have been in a protocluster but are physically similar to the galaxies in dense clusters. Some clues to be assessed in resolving this dilemma are the possible existence of galaxy filaments, the relative ages of galaxies and clusters of galaxies, and the continuity between cluster and field galaxies and between galaxies and clusters of galaxies.     

基于YOLOv5深度学习的茶叶嫩芽估产方法

针对丘陵地区小规模茶园估产难度高,估产手段少等问题,采用基于YOLOv5的目标检测算法和田间抽样调查法,对丘陵地区小规模茶园估产问题进行研究。在茶园中随机抽取9个有代表性的茶叶生长点;使用目标检测算法识别抽样点茶叶嫩芽数目;利用最小二乘法拟合茶叶嫩芽产量与数目间的线性关系;结合抽样点识别出的嫩芽数目、抽样点面积、线性拟合关系和茶园整体面积估算出茶园茶叶嫩芽产量。结果表明：1)基于YOLOv5的目标检测算法对茶叶嫩芽识别的精度为99.02%,平均准确率为90.14%;2)茶叶嫩芽数目和产量间有高度线性关系,决定系数R²为0.999 8;3)通过算法估计的茶叶嫩芽产量与实际采收产量相对误差为29.56%。本研究能够较为方便的估算出茶园茶叶嫩芽产量,在茶叶生长时期为农户提供产量相关的数据支持,便于茶叶生产的前期管理。     

Evaluation of an analytical method to identify determinants of rice yield components and protein content

Modern information technologies have facilitated the collection of data to assess various aspects of rice production such as yield, quality, soil properties and growth conditions. Currently, farmers can identify any variation of these indicators within a field, between fields or with other farmers. However, a comprehensive analytical method to identify the determinants of variability has not been developed, and the data collected are not efficiently utilized to diagnose and improve the production skills of farmers. Our study focused on the development of an analytical method that can identify the determinants of rice yield and quality. The analytical method used applied cluster analysis (Ward method) to assess the data from 82 paddy fields where rice is produced in various environments and with various management styles. Initially, the 82 paddy fields were classified into 11 clusters based on five indicators of yield components and rice quality; number of panicles, number of spikelets, percentage of ripened grains, 1000-grain weight (GW) and protein content of brown rice. Then, 9 of 11 clusters (two clusters were excluded due to insufficient data to form a cluster) were divided into four groups based on yield capacity. As a result, common characteristics of fertilizer application, meteorological environment and growth conditions were extracted from each cluster. Furthermore, determinants of yield components and protein content were efficiently identified based on the common characteristics extracted.     

农业产业集群的形成机制探析

结合农业产业发展的实际,提出了农业产业集群概念,指出农业资源禀赋差异、合作需求、规模经济以及路径依赖是农业产业集群形成的主要因素,说明了农业产业集群作为一种独特的产业组织形式,是农业产业化发展的一种新形式,在提升整个农业产业竞争力中起着非常重要的促进作用。