Explaining Trained Neural Networks with Semantic Web Technologies: First Steps

The ever increasing prevalence of publicly available structured data on the World Wide Web enables new applications in a variety of domains. In this paper, we provide a conceptual approach that leverages such data in order to explain the input-output behavior of trained artificial neural networks. We apply existing Semantic Web technologies in order to provide an experimental proof of concept

Annotations for Rule-Based Models

The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the associated guidelines for annotating rule-based models of molecular interactions, encoded in the commonly used Kappa and BioNetGen languages, and present prototypes that can be used to extract and query the annotations. An ontology is used to annotate models and facilitate their description

Hybrid Search: Effectively Combining Keywords and Semantic Searches

This paper describes hybrid search, a search method supporting both document and knowledge retrieval via the flexible combination of ontologybased search and keyword-based matching. Hybrid search smoothly copes with lack of semantic coverage of document content, which is one of the main limitations of current semantic search methods. In this paper we define hybrid search formally, discuss its compatibility with the current semantic trends and present a reference implementation: K-Search. We then show how the method outperforms both keyword-based search and pure semantic search in terms of precision and recall in a set of experiments performed on a collection of about 18.000 technical documents. Experiments carried out with professional users show that users understand the paradigm and consider it very powerful and reliable. K-Search has been ported to two applications released at Rolls-Royce plc for searching technical documentation about jet engines

Identification of Design Principles

This report identifies those design principles for a (possibly new) query and transformation language for the Web supporting inference that are considered essential. Based upon these design principles an initial strawman is selected. Scenarios for querying the Semantic Web illustrate the design principles and their reflection in the initial strawman, i.e., a first draft of the query language to be designed and implemented by the REWERSE working group I4

Integration of Biological Sources: Exploring the Case of Protein Homology

Data integration is a key issue in the domain of bioin- formatics, which deals with huge amounts of heteroge- neous biological data that grows and changes rapidly. This paper serves as an introduction in the field of bioinformatics and the biological concepts it deals with, and an exploration of the integration problems a bioinformatics scientist faces. We examine ProGMap, an integrated protein homology system used by bioin- formatics scientists at Wageningen University, and several use cases related to protein homology. A key issue we identify is the huge manual effort required to unify source databases into a single resource. Un- certain databases are able to contain several possi- ble worlds, and it has been proposed that they can be used to significantly reduce initial integration efforts. We propose several directions for future work where uncertain databases can be applied to bioinformatics, with the goal of furthering the cause of bioinformatics integration

AQUA: an ontology driven question answering system

This paper describes AQUA our question answering over the Web. AQUA was designed to work over heterogeneous sources. This means that AQUA is equipped to work as closed domain and in addition to open-domain question answering. As a first instance, AQUA tries to answer a question using a Knowledge base. If a query cannot be satisfied over a knowledge base/database. Then, AQUA tries to find an answer on web pages (i.e. it uses as corpus the internet as resource). Our system uses NLP (Natural Language Processing), First order logic and Information Extraction technologies. AQUA has been tested using an ontology which describes academic life. Keywords Ontologies, Information Extraction, Machine Learnin