. These models represent objects as points in some coordinate space such that the observed dissimilarities between objects correspond to the metric distances between the respective points. Practically all analyses of proximity data have been metric in nature, although some (e.g., hierarchical clustering) yield

Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop

Background: Protein evolution gives rise to families of structurally related proteins, within which sequence identities can be extremely low. As a result, structure-based classifications can be effective at identifying unanticipated relationships in known structures and in optimal cases function

formulas are somewhat involved. In this article we present a direct approach which leads immediately to scalar kernels for the unitary ensembles and matrix kernels for the orthogonal and symplectic ensembles, and the representations of the correlation functions, cluster functions, and spacing distributions

A locality sensitive hashing scheme is a distribution on a family F of hash functions operating on a collection of objects, such that for two objects x, y, Prh∈F[h(x) = h(y)] = sim(x,y), where sim(x,y) ∈ [0, 1] is some similarity function defined on the collection of objects. Such a scheme leads

clusters). This formulation is motivated from a document clustering problem in which one has a pairwise similarity function # learned from past data, and the goal is to partition the current set of documents in a way that correlates with # as much as possible; it can also be viewed as a kind of "

algorithm requires much greater functionality in discovering and exploring clusters over different portions of the stream. The widely used practice of viewing data stream clustering algorithms as a class of onepass clustering algorithms is not very useful from an application point of view. For example, a

(JIBS and CESIS) This paper gives an overview of research on economic clusters and clustering and is motivated by the growing intellectual and political interest for the subject. Functional regions have the features that agglomeration of economic activities i.e. clusters, benefit from. Functional

Earlier, we presented evidence that it is possible to predict functional cou-pling between genes based on conservation of gene clusters between genomes. With the rapid increase in availability of prokaryotic sequence data, it has be-come possible to verify and apply the technique. In this paper, we

of the gene regulatory network. We aim here to review datamining and modeling approaches for conceptualizing and unraveling the functional relationships implicit in these datasets. Clustering of co-expression profiles allows us to infer shared regulatory inputs and functional pathways. We discuss various