Farshad Fotouhi

Learn More
Data from large-scale protein interaction screens for humans and model eukaryotes have been invaluable for developing systems-level models of biological processes. Despite this value, only a limited amount of interaction data is available for prokaryotes. Here we report the systematic identification of protein interactions for the bacterium Campylobacter(More)
Scientific workflows have recently emerged as a new paradigm for scientists to formalize and structure complex and distributed scientific processes to enable and accelerate many scientific discoveries. In contrast to business workflows, which are typically control flow oriented, scientific workflows tend to be dataflow oriented, introducing a new set of(More)
In this paper, we propose a new clustering algorithm called <i>Fast Genetic K-means Algorithm (FGKA)</i>. FGKA is inspired by the Genetic K-means Algorithm (GKA) proposed by Krishna and Murty in 1999 but features several improvements over GKA. Our experiments indicate that, while K-means algorithm might converge to a local optimum, both FGKA and GKA always(More)
In an annotated image database, keywords are usually associated with images instead of individual regions, which poses a major challenge for any region based image annotation algorithm. In this paper, we propose to learn the correspondence between image regions and keywords through Multiple-Instance Learning (MIL). After a representative image region has(More)
Storing and querying XML documents using a RDBMS is a challenging problem since one needs to resolve the conflict between the hierarchical, ordered nature of the XML data model and the flat, unordered nature of the relational data model. This conflict can be resolved by the following XML-to-Relational mappings: schema mapping, data mapping and query(More)
Article history: Received 12 October 2008 Received in revised form 8 March 2010 Accepted 11 March 2010 Available online 23 March 2010 Provenance metadata has become increasingly important to support scientific discovery reproducibility, result interpretation, and problem diagnosis in scientific workflow environments. The provenance management problem(More)
In recent years, clustering algorithms have been effectively applied in molecular biology for gene expression data analysis. With the help of clustering algorithms such as K-means, hierarchical clustering, SOM, etc, genes are partitioned into groups based on the similarity between their expression profiles. In this way, functionally related genes are(More)
In this demo, we present current status of our VIsual sciEntific Workflow management system called VIEW, highlighting the following two features: (i) the use of Semantic Web technology to represent, store, and query provenance metadata, leading to an interoperable and extensible provenance system, and (ii) the support of visualization of various provenance(More)