Modelling sequential data is important in many areas of science and engineering. Hidden Markov models (HMMs) and Kalman filter models (KFMs) are popular for this because they are simple and flexible. For example, HMMs have been used for speech recognition and bio-sequence analysis, and KFMs have

due to the lack of a systematic framework that can accommodate noise, variability, and low replication often typical of microarray data. Results: We develop a Bayesian probabilistic framework for microarray data analysis. At the simplest level, we model log-expression values by independent normal

. For each experimental run, we first gen erated random CPTs. We then sampled from the joint distribution defined by the network and clamped the observed nodes (all nodes in the bottom layer) to their sampled value. Given a structure and observations, we then ran three inference algorithms -junction tree

The central proposal of this article is that verbal reports are data. Accounting for verbal reports, as for other kinds of data, requires explication of the mech-anisms by which the reports are generated, and the ways in which they are sensitive to experimental factors (instructions, tasks, etc

evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure, but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when

to be shortest paths. The algorithm and its analysis are simple and intuitive, yet the algorithm runs as fast as any other known method on dense. graphs, achieving an O(n³) time bound on an n-vertex graph. By incorporating the dynamic tree data structure of Sleator and Tarjan, we obtain a version

a notion of hyperlinked communities on the www through an analysis of the link topology. Byinvoking a simple, mathematically clean method for de ning and exposing the structure of these communities, we are able to derive anumber of themes: The communities can be viewed as containing a core

into account the dependence structure between the gene expression levels. No specific parametric form is assumed for the distribution of the test statistics and a permutation procedure is used to estimate adjusted p-values. Several data displays are suggested for the visual identification of differentially

to compute the affinity between each pair of points. This local scaling leads to better clustering especially when the data includes multiple scales and when the clusters are placed within a cluttered background. We further suggest exploiting the structure of the eigenvectors to infer automatically

that the distributions of packet features (IP addresses and ports) observed in flow traces reveals both the presence and the structure of a wide range of anomalies. Using entropy as a summarization tool, we show that the analysis of feature distributions leads to significant advances on two fronts: (1) it enables highly