000 Informatik, Informationswissenschaft, allgemeine Werke
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Background: The biological interpretation of large-scale gene expression data is one of the paramount challenges in current bioinformatics. In particular, placing the results in the context of other available functional genomics data, such as existing bio-ontologies, has already provided substantial improvement for detecting and categorizing genes of interest. One common approach is to look for functional annotations that are significantly enriched within a group or cluster of genes, as compared to a reference group. Results: In this work, we suggest the information-theoretic concept of mutual information to investigate the relationship between groups of genes, as given by data-driven clustering, and their respective functional categories. Drawing upon related approaches (Gibbons and Roth, Genome Research 12: 1574-1581, 2002), we seek to quantify to what extent individual attributes are sufficient to characterize a given group or cluster of genes. Conclusion: We show that the mutual information provides a systematic framework to assess the relationship between groups or clusters of genes and their functional annotations in a quantitative way. Within this framework, the mutual information allows us to address and incorporate several important issues, such as the interdependence of functional annotations and combinatorial combinations of attributes. It thus supplements and extends the conventional search for overrepresented attributes within a group or cluster of genes. In particular taking combinations of attributes into account, the mutual information opens the way to uncover specific functional descriptions of a group of genes or clustering result. All datasets and functional annotations used in this study are publicly available. All scripts used in the analysis are provided as additional files.
Dynamic service adaptation
(2006)
Change can be observed in our environment and in the technology we build. While changes in the environment happen continuously and implicitly, our technology has to be kept in sync with the changing world around it. Although we can prepare for some of the changes for most of them we cannot. This is especially true for next-generation mobile communication systems that are expected to support the creation of a ubiquitous society where virtually everything is connected and made available within an organic information network. Resources will frequently join or leave the network, new types of media or new combinations of existing types will be used to interact and cooperate, and services will be tailored to preferences and needs of individual customers to better meet their needs. This paper outlines our research in the area of dynamic service adaptation to provide concepts and technologies allowing for such environments. Copyright (C) 2006 John Wiley & Sons, Ltd.
Iterated finite state sequential transducers are considered as language generating devices. The hierarchy induced by the size of the state alphabet is proved to collapse to the fourth level. The corresponding language families are related to the families of languages generated by Lindenmayer systems and Chomsky grammars. Finally, some results on deterministic and extended iterated finite state transducers are established.