Fusion rules for merging uncertain information

In previous papers, we have presented a logic-based framework based on fusion rules for merging structured news reports. Structured news reports are XML documents, where the textentries are restricted to individual words or simple phrases, such as names and domain-specific terminology, and numbers and units. We assume structured news reports do not require natural language processing. Fusion rules are a form of scripting language that define how structured news reports should be merged. The antecedent of a fusion rule is a call to investigate the information in the structured news reports and the background knowledge, and the consequent of a fusion rule is a formula specifying an action to be undertaken to form a merged report. It is expected that a set of fusion rules is defined for any given application. In this paper we extend the approach to handling probability values, degrees of beliefs, or necessity measures associated with textentries in the news reports. We present the formal definition for each of these types of uncertainty and explain how they can be handled using fusion rules. We also discuss the methods of detecting inconsistencies among sources.

Development of a Java-based Unified and Flexible Natural Language Discourse System

This paper outlines the design and development of a Java-based, unified and flexible natural language dialogue system that enables users to interact using natural language, e.g. speech. A number of software development issues are considered with the aim of designing an architecture that enables different discourse components to be readily and flexibly combined in a manner that permits information to be easily shared. Use of XML schemas assists this component interaction. The paper describes how a range of Java language features were employed to support the development of the architecture, providing an illustration of how a modern programming language makes tractable the development of a complex dialogue system.

TMAX – a Database System Integrating Tissue Biomarker & Genomic Data

Background: Popular approaches in human tissue-based biomarker discovery include tissue microarrays (TMAs) and DNA Microarrays (DMAs) for protein and gene expression profiling respectively. The data generated by these analytic platforms, together with associated image, clinical and pathological data currently reside on widely different information platforms, making searching and cross-platform analysis difficult. Consequently, there is a strong need to develop a single coherent database capable of correlating all available data types.

Method: This study presents TMAX, a database system to facilitate biomarker discovery tasks. TMAX organises a variety of biomarker discovery-related data into the database. Both TMA and DMA experimental data are integrated in TMAX and connected through common DNA/protein biomarkers. Patient clinical data (including tissue pathological data), computer assisted tissue image and associated analytic data are also included in TMAX to enable the truly high throughput processing of ultra-large digital slides for both TMAs and whole slide tissue digital slides. A comprehensive web front-end was built with embedded XML parser software and predefined SQL queries to enable rapid data exchange in the form of standard XML files.

Results & Conclusion: TMAX represents one of the first attempts to integrate TMA data with public gene expression experiment data. Experiments suggest that TMAX is robust in managing large quantities of data from different sources (clinical, TMA, DMA and image analysis). Its web front-end is user friendly, easy to use, and most importantly allows the rapid and easy data exchange of biomarker discovery related data. In conclusion, TMAX is a robust biomarker discovery data repository and research tool, which opens up the opportunities for biomarker discovery and further integromics research.