On Region Algebras, XML Databases, and Information Retrieval

This paper describes some new ideas on developing a logical algebra for databases that manage textual data and support information retrieval functionality. We describe a first prototype of such a system

Investigating modularity in the analysis of process algebra models of biochemical systems

Compositionality is a key feature of process algebras which is often cited as one of their advantages as a modelling technique. It is certainly true that in biochemical systems, as in many other systems, model construction is made easier in a formalism which allows the problem to be tackled compositionally. In this paper we consider the extent to which the compositional structure which is inherent in process algebra models of biochemical systems can be exploited during model solution. In essence this means using the compositional structure to guide decomposed solution and analysis. Unfortunately the dynamic behaviour of biochemical systems exhibits strong interdependencies between the components of the model making decomposed solution a difficult task. Nevertheless we believe that if such decomposition based on process algebras could be established it would demonstrate substantial benefits for systems biology modelling. In this paper we present our preliminary investigations based on a case study of the pheromone pathway in yeast, modelling in the stochastic process algebra Bio-PEPA

Exploiting Query Structure and Document Structure to Improve Document Retrieval Effectiveness

In this paper we present a systematic analysis of document retrieval using unstructured and structured queries within the score region algebra (SRA) structured retrieval framework. The behavior of di®erent retrieval models, namely Boolean, tf.idf, GPX, language models, and Okapi, is tested using the transparent SRA framework in our three-level structured retrieval system called TIJAH. The retrieval models are implemented along four elementary retrieval aspects: element and term selection, element score computation, score combination, and score propagation. The analysis is performed on a numerous experiments evaluated on TREC and CLEF collections, using manually generated unstructured and structured queries. Unstructured queries range from the short title queries to long title + description + narrative queries. For generating structured queries we exploit the knowledge of the document structure and the content used to semantically describe or classify documents. We show that such structured information can be utilized in retrieval engines to give more precise answers to user queries then when using unstructured queries