Knowledge discovery programs in the biological sciences require flexibility in the use of symbolic data and semantic information. Thus, the framework for the discovery program must facilitate proposing and selecting the next task to perform and performing the selected tasks. The framework we describe, called the agenda- and justificationbased framework, has several properties that are desirable in semiautonomous discovery systems: It provides a mechanism for estimating the plausibility of tasks, it uses heuristics to propose and perform tasks, and it facilitates the encoding of general discovery strategies and the use of background knowledge. Our results demonstrate that both reasons given for performing tasks and estimates of the interestingness of the concepts and hypotheses examined by HAMB contribute to its performance and that the program can discover novel, interesting relationships in biological data.

Within computational biology, algorithms are constructed with the aim of extracting knowledge from biological data, in particular, data generated by the large genome projects, where gene and protein sequences are produced in high volume. In this article, we explore new ways of representing protein-sequence information, using machine learning strategies, where the primary goal is the discovery of novel powerful representations for use in AI techniques. In the case of proteins and the 20 different amino acids they typically contain, it is also a secondary goal to discover how the current selection of amino acids -- which now are common in proteins -- might have emerged from simpler selections, or alphabets, in use earlier during the evolution of living organisms.

The rate at which expert annotators add the experimental information into more or less controlled vocabularies of databases snails along at an even slower pace. Most methods that annotate protein function exploit sequence similarity by transferring experimental information for homologues. A crucial development aiding such transfer is large-scale, work- and management-intensive projects aimed at developing a comprehensive ontology for gene-protein function, such as the Gene Ontology project. Some of these tools target parsing controlled vocabulary from databases; others venture at mining free texts from MEDLINE abstracts or full scientific papers.

EUROLAN, which has been held biennially since 1993, is one of the most significant European summer schools in the area of natural language processing. Each of the EUROLAN sessions has focused on an area of timely interest to researchers in the field; this year's EUROLAN involved students in tutorials and hands-on sessions concerned with semantic web technologies as applied to language processing, ontology creation and use, and consideration of the semantic web's potential and limitations.

However, the amount of data this new technology produces is more than one can manually analyze. Hence, the need for automated analysis of microarray data offers an opportunity for machine learning to have a significant impact on biology and medicine. This article describes microarray technology, the data it produces, and the types of machine learning tasks that naturally arise with these data. It also reviews some of the recent prominent applications of machine learning to gene-chip data, points to related tasks where machine learning might have a further impact on biology and medicine, and describes additional types of interesting data that recent advances in biotechnology allow biomedical researchers to collect.

The Second International Joint Conference on Autonomous Agents and Multiagent Systems (AAMAS-03) was held in Melbourne, Australia, in July 2003. Attracting nearly 500 delegates, the event confirmed AAMAS as the academic main event for researchers with an interest in multiagent systems. We summarize the conference highlights and report on the associated workshops, tutorials, and emerging trends.

Case-based reasoning (CBR) is a computational reasoning paradigm that involves the storage and retrieval of past experiences to solve novel problems. It is an approach that is particularly relevant in scientific domains, where there is a wealth of data but often a lack of theories or general principles. This article describes several CBR systems that have been developed to carry out planning, analysis, and prediction in the domain of molecular biology.

This science seeks to understand how the complete complement of molecular components of living organisms (nucleic acid, protein, small molecules, and so on) interact together to form living organisms. Functional genomics is of interest to AI because the relationship between machines and living organisms is central to AI and because the field is an instructive and fun domain to apply and sharpen AI tools and ideas, requiring complex knowledge representation, reasoning, learning, and so on. This article describes two machine learning (inductive logic programming [ILP])-based approaches to the bioinformatic problem of predicting protein function from amino acid sequence. The second approach used protein-functional ontologies to provide function classes and a hybrid ILP method to predict function directly from sequence.

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