motivation: Advances in molecular biological, analytical and computational technologies are enabling us to systematically investigate the complex molecular processes underlying biological systems. In particular, using highthroughput gene expression assays, we are able to measure the output 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 aspects of clustering, ranging from distance measures to clustering algorithms and multiple-cluster memberships. More advanced analysis aims to infer causal connections between genes directly, i.e. who is regulating whom and how. We discuss several approaches to the problem of reverse engineering of genetic networks, from discrete Boolean networks, to continuous linear and non-linear models. We conclude that the combination of predictive modeling with systematic experimental verification will be required to gain a deeper insight into living organisms, therapeutic targeting and bioengineering.

Hierarchical clustering is a common method used to determine clusters of similar data points in multidimensional spaces. O(n 2 ) algorithms are known for this problem [3, 4, 10, 18]. This paper reviews important results for sequential algorithms and describes previous work on parallel algorithms for hierarchical clustering. Parallel algorithms to perform hierarchical clustering using several distance metrics are then described. Optimal PRAM algorithms using n log n processors are given for the average link, complete link, centroid, median, and minimum variance metrics. Optimal butterfly and tree algorithms using n log n processors are given for the centroid, median, and minimum variance metrics. Optimal asymptotic speedups are achieved for the best practical algorithm to perform clustering using the single link metric on a n log n processor PRAM, butterfly, or tree. Keywords. Hierarchical clustering, pattern analysis, parallel algorithm, butterfly network, PRAM algorithm. 1 In...

We consider the problem of organizing and browsing the top ranked portion of the documents returned by an information retrieval system. We study the effectiveness of a document organization in helping a user to locate the relevant material among the retrieved documents as quickly as possible. In this context we examine a set of clustering algorithms and experimentally show that a clustering of the retrieved documents can be significantly more effective than traditional ranked list approach. We also show that the clustering approach can be as effective as the interactive relevance feedback based on query expansion while retaining an important advantage -- it provides the user with a valuable sense of control over the feedback process.

Abstract. An exact algorithm is proposed for minimum sum-of-squares nonhierarchical clustering, i.e., for partitioning a given set of points from a Euclidean m-space into a given number of clusters in order to minimize the sum of squared distances from all points to the centroid of the cluster to which they belong. This problem is expressed as a constrained hyperbolic program in 0-1 variables. The resolution method combines an interior point algorithm, i.e., a weighted analytic center column generation method, with branch-and-bound. The auxiliary problem of determining the entering column (i.e., the oracle) is an unconstrained hyperbolic program in 0-1 variables with a quadratic numerator and linear denominator. It is solved through a sequence of unconstrained quadratic programs in 0-1 variables. To accelerate resolution, variable neighborhood search heuristics are used both to get a good initial solution and to solve quickly the auxiliary problem as long as global optimality is not reached. Estimated bounds for the dual variables are deduced from the heuristic solution and used in the resolution process as a trust region. Proved minimum sum-of-squares partitions are determined for the first time for several fairly large data sets from the literature, including Fisher’s 150 iris. Key words. classification and discrimination, cluster analysis, interior-point methods, combinatorial optimization

In this paper, we describe a unique new paradigm for video database management known as ViBE (Video Indexing and Browsing Environment). ViBE is a browseable/searchable paradigm for organizing video data containing a large number of sequences. We describe how ViBE performs on a database of MPEG sequences.

Abstract--Description of the morphology of organisms is mostly done in terms of features assuming cer-tain states. Biological patterns are subjected to certain constraints imposed on them by the fact that they all are developed from a single cell. Using a model in which some of the constraints of biological develop-ment are incorporated we investigate the relation between different modes of description of such patterns. Pattern generation Pattern recognition Numerical taxonomy Parallel rewriting sys-tems L-systems I.

In this paper we address the problem of building object class representations based on local features and fast matching in a large database. We propose an efficient algorithm for hierarchical agglomerative clustering. We examine different agglomerative and partitional clustering strategies and compare the quality of obtained clusters. Our combination of partitional-agglomerative clustering gives significant improvement in terms of efficiency while maintaining the same quality of clusters. We also propose a method for building data structures for fast matching in high dimensional feature spaces. These improvements allow to deal with large sets of training data typically used in recognition of multiple object classes. 1

Clustering is ill-defined. Unlike supervised learning where labels lead to crisp performance criteria such as accuracy and squared error, clustering quality depends on how the clusters will be used. Devising clustering criteria that capture what users need is difficult. Most clustering algorithms search for optimal clusterings based on a pre-specified clustering criterion. Our approach differs. We search for many alternate clusterings of the data, and then allow users to select the clustering(s) that best fit their needs. Meta clustering first finds a variety of clusterings and then clusters this diverse set of clusterings so that users must only examine a small number of qualitatively different clusterings. We present methods for automatically generating a diverse set of alternate clusterings, as well as methods for grouping clusterings into meta clusters. We evaluate meta clustering on four test problems and two case studies. Surprisingly, clusterings that would be of most interest to users often are not very compact clusterings. 1.

We present a hierarchical partitioning of images using a pairwise similarity function on a graph-based representation of an image. This function measures the difference along the boundary of two components relative to a measure of differences of the components' internal differences. This definition tries to encapsulate the intuitive notion of contrast. Two components are merged if there is a low-cost connection between them. Each component's internal difference is represented by the maximum edge weight of its minimum spanning tree. External differences are the smallest weight of edges connecting components. We use this idea for building a minimum spanning tree to find region borders quickly and effortlessly in a bottom-up way, based on local differences in a specific feature.

The region's internal properties (color, texture, ...) help to identify them and their external relations (adjacency, inclusion, ...) are used to build groups of regions having a particular consistent meaning in a more abstract context. Low-level cue image segmentation in a bottom-up way, cannot and should not produce a complete final "good" segmentation. We present a hierarchical partitioning of images using a pairwise similarity function on a graph-based representation of an image.