The K-Space segmentation tool set

In this paper we describe two applications, created as part of the K-Space Network of Excellence, designed to allow researchers to use and experiment with state-of-the-art methods for spatial segmentation of images and video sequences. The first of these tools is an _Interactive Segmentation Tool_, developed to allow accurate human-guided segmentation of semantic objects from images using different segmentation algorithms. The tool is particularly useful for generating ground-truth segmentations, extracting objects for further processing, and as a general image processing application.The second tool we developed is designed for fully automatic spatial region segmentation of image and video. The tool is web-based; usage only requires a browser. Both the automatic and interactive segmentation tools have been made available online; we anticipate they will be a valuable resource for other researchers

Application of regulatory sequence analysis and metabolic network analysis to the interpretation of gene expression data

We present two complementary approaches for the interpretation of clusters of co-regulated genes, such as those obtained from DNA chips and related methods. Starting from a cluster of genes with similar expression profiles, two basic questions can be asked: 1. Which mechanism is responsible for the coordinated transcriptional response of the genes? This question is approached by extracting motifs that are shared between the upstream sequences of these genes. The motifs extracted are putative cis-acting regulatory elements. 2. What is the physiological meaning for the cell to express together these genes? One way to answer the question is to search for potential metabolic pathways that could be catalyzed by the products of the genes. This can be done by selecting the genes from the cluster that code for enzymes, and trying to assemble the catalyzed reactions to form metabolic pathways. We present tools to answer these two questions, and we illustrate their use with selected examples in the yeast Saccharomyces cerevisiae. The tools are available on the web (http://ucmb.ulb.ac.be/bioinformatics/rsa-tools/; http://www.ebi.ac.uk/research/pfbp/; http://www.soi.city.ac.uk/~msch/)

Determining the Unithood of Word Sequences using Mutual Information and Independence Measure

Most works related to unithood were conducted as part of a larger effort for the determination of termhood. Consequently, the number of independent research that study the notion of unithood and produce dedicated techniques for measuring unithood is extremely small. We propose a new approach, independent of any influences of termhood, that provides dedicated measures to gather linguistic evidence from parsed text and statistical evidence from Google search engine for the measurement of unithood. Our evaluations revealed a precision and recall of 98.68% and 91.82% respectively with an accuracy at 95.42% in measuring the unithood of 1005 test cases.Comment: More information is available at http://explorer.csse.uwa.edu.au/reference

Wrapper Maintenance: A Machine Learning Approach

The proliferation of online information sources has led to an increased use of wrappers for extracting data from Web sources. While most of the previous research has focused on quick and efficient generation of wrappers, the development of tools for wrapper maintenance has received less attention. This is an important research problem because Web sources often change in ways that prevent the wrappers from extracting data correctly. We present an efficient algorithm that learns structural information about data from positive examples alone. We describe how this information can be used for two wrapper maintenance applications: wrapper verification and reinduction. The wrapper verification system detects when a wrapper is not extracting correct data, usually because the Web source has changed its format. The reinduction algorithm automatically recovers from changes in the Web source by identifying data on Web pages so that a new wrapper may be generated for this source. To validate our approach, we monitored 27 wrappers over a period of a year. The verification algorithm correctly discovered 35 of the 37 wrapper changes, and made 16 mistakes, resulting in precision of 0.73 and recall of 0.95. We validated the reinduction algorithm on ten Web sources. We were able to successfully reinduce the wrappers, obtaining precision and recall values of 0.90 and 0.80 on the data extraction task