Single Linkage Clustering Algorithm Research Articles

Symbolic hierarchical analysis in currency markets: An application to contagion in currency crises

In this paper we introduce a new method to describe dynamical patterns of the real exchange rate co-movements time series and to analyze contagion in currency crisis. The method combines the tools of symbolic time series analysis with the nearest neighbor single linkage clustering algorithm. Data symbolization allows us obtaining a metric distance between two different time series that is used to construct an ultrametric distance. By analyzing the data of various countries, we derive a hierarchical organization, constructing minimal-spanning and hierarchical trees. From these trees we detect different clusters of countries according to their proximity. We show that this methodology permits us to construct a structural and dynamic topology that is useful to study interdependence and contagion effects among financial time series.

Small Molecule Antagonizes Autoinhibition and Activates AMP-activated Protein Kinase in Cells

AMP-activated protein kinase (AMPK) serves as an energy sensor and is considered a promising drug target for treatment of type II diabetes and obesity. A previous report has shown that mammalian AMPK alpha1 catalytic subunit including autoinhibitory domain was inactive. To test the hypothesis that small molecules can activate AMPK through antagonizing the autoinhibition in alpha subunits, we screened a chemical library with inactive human alpha1(394) (alpha1, residues 1-394) and found a novel small-molecule activator, PT1, which dose-dependently activated AMPK alpha1(394), alpha1(335), alpha2(398), and even heterotrimer alpha1beta1gamma1. Based on PT1-docked AMPK alpha1 subunit structure model and different mutations, we found PT1 might interact with Glu-96 and Lys-156 residues near the autoinhibitory domain and directly relieve autoinhibition. Further studies using L6 myotubes showed that the phosphorylation of AMPK and its downstream substrate, acetyl-CoA carboxylase, were dose-dependently and time-dependently increased by PT1 with-out an increase in cellular AMP:ATP ratio. Moreover, in HeLa cells deficient in LKB1, PT1 enhanced AMPK phosphorylation, which can be inhibited by the calcium/calmodulin-dependent protein kinase kinases inhibitor STO-609 and AMPK inhibitor compound C. PT1 also lowered hepatic lipid content in a dose-dependent manner through AMPK activation in HepG2 cells, and this effect was diminished by compound C. Taken together, these data indicate that this small-molecule activator may directly activate AMPK via antagonizing the autoinhibition in vitro and in cells. This compound highlights the effort to discover novel AMPK activators and can be a useful tool for elucidating the mechanism responsible for conformational change and autoinhibitory regulation of AMPK.

PhyloPat: phylogenetic pattern analysis of eukaryotic genes

BackgroundPhylogenetic patterns show the presence or absence of certain genes or proteins in a set of species. They can also be used to determine sets of genes or proteins that occur only in certain evolutionary branches. Phylogenetic patterns analysis has routinely been applied to protein databases such as COG and OrthoMCL, but not upon gene databases. Here we present a tool named PhyloPat which allows the complete Ensembl gene database to be queried using phylogenetic patterns.DescriptionPhyloPat is an easy-to-use webserver, which can be used to query the orthologies of all complete genomes within the EnsMart database using phylogenetic patterns. This enables the determination of sets of genes that occur only in certain evolutionary branches or even single species. We found in total 446,825 genes and 3,164,088 orthologous relationships within the EnsMart v40 database. We used a single linkage clustering algorithm to create 147,922 phylogenetic lineages, using every one of the orthologies provided by Ensembl. PhyloPat provides the possibility of querying with either binary phylogenetic patterns (created by checkboxes) or regular expressions. Specific branches of a phylogenetic tree of the 21 included species can be selected to create a branch-specific phylogenetic pattern. Users can also input a list of Ensembl or EMBL IDs to check which phylogenetic lineage any gene belongs to. The output can be saved in HTML, Excel or plain text format for further analysis. A link to the FatiGO web interface has been incorporated in the HTML output, creating easy access to functional information. Finally, lists of omnipresent, polypresent and oligopresent genes have been included.ConclusionPhyloPat is the first tool to combine complete genome information with phylogenetic pattern querying. Since we used the orthologies generated by the accurate pipeline of Ensembl, the obtained phylogenetic lineages are reliable. The completeness and reliability of these phylogenetic lineages will further increase with the addition of newly found orthologous relationships within each new Ensembl release.

Stream segregation algorithm for pattern matching in polyphonic music databases

As music can be represented symbolically, most of the existing methods extend some string matching algorithms to retrieve musical patterns in a music database. However, not all retrieved patterns are perceptually significant because some of them are, in fact, inaudible. Music is perceived in groupings of musical notes called streams. The process of grouping musical notes into streams is called stream segregation. Stream-crossing musical patterns are perceptually insignificant and should be pruned from the retrieval results. This can be done if all musical notes in a music database are segregated into streams and musical patterns are retrieved from the streams. Findings in auditory psychology are utilized in this paper, in which stream segregation is modelled as a clustering process and an adapted single-link clustering algorithm is proposed. Supported by experiments on real music data, streams are identified by the proposed algorithm with considerable accuracy.

Machine grouping in cellular manufacturing

Recent productivity gains enjoyed by Japan and other European countries have prompted more manufacturers from other countries to explore the use of advanced technologies as a means of improving their competitive edge in the world market. This paper presents a brief review of two of these technologies: robotics and group technologies (GT). Various research issues are discussed for each technology together with the strengths and weaknesses of the papers reviewed. As a means of integrating the two technologies, a group technology-based model for selecting robots for manufacturing cells is presented. An appropriate definition of similarity measure for the weighted codes of coding and classification analysis in GT is presented using a robot coding system example. A single linkage clustering algorithm is then proposed for use in finding robot clusters for a manufacturing cell. Finally a numerical example is presented to illustrate the model.

Concurrent formation of part families and machine cells based on the fuzzy set theory

Abstract The goal of this research is to develop a group technology (GT) cell formation methodology, with the inclusion of fuzziness usually found in industry. Three studies are conducted. The first study establishes a procedure through which a nonbinary machine-component matrix is constructed. This matrix forms the basis of the following two studies. The second study applies the nonbinary matrix concept to the single linkage clustering algorithm. The third study focuses on a modified rank order clustering algorithm that involves fuzzy set theory. The modified single linkage and modified rank order clustering algorithm are compared and the strengths and weaknesses are discussed. The flexibility provided by the fuzzy set-based method is presented.

Automated conformational analysis from crystallographic data. 1. A symmetry-modified single-linkage clustering algorithm for three-dimensional pattern recognition

Single-linkage cluster analysis is used to identify discrete conformational subgroups for a chemical fragment from crystal structure data. Fragment conformations are defined by N, torsion angles for N/ occurrences of the fragment in the Cambridge Structural Database. Conformational analysis is complicated by (a) the 2D topological symmetry of the fragment, giving rise to permutations of torsion

Detection of diffuse clusters in noise background

The paper presents a method for the detection of a two-dimensional extended pattern of points in a flat background. The method is based on the statistical properties of a single-link clustering algorithm, which allows to select the most significant clusters. Its calibration is based on simulated data. An application on real X-ray astronomical is also shown.

Bicriterion Cluster Analysis

Cluster analysis is concerned with the problem of partitioning a given set of entities into homogeneous and well-separated subsets called clusters. The concepts of homogeneity and of separation can be made precise when a measure of dissimilarity between the entities is given. Let us define the diameter of a partition of the given set of entities into clusters as the maximum dissimilarity between any pair of entities in the same cluster and the split of a partition as the minimum dissimilarity between entities in different clusters. The problems of determining a partition into a given number of clusters with minimum diameter (i.e., a partition of maximum homogeneity) or with maximum split (i.e., a partition of maximum separation) are first considered. It is shown that the latter problem can be solved by the classical single-link clustering algorithm, while the former can be solved by a graph-theoretic algorithm involving the optimal coloration of a sequence of partial graphs, described in more detail in a previous paper. A partition into a given number of clusters will be called efficient if and only if there exists no partition into at most the same number of clusters with smaller diameter and not smaller split or with larger split and not larger diameter. Two efficient partitions are called equivalent if and only if they have the same values for the split and for the diameter.