TY - JOUR A1 - Steuer, Ralf A1 - Humburg, Peter A1 - Selbig, Joachim T1 - Validation and functional annotation of expression-based clusters based on gene ontology JF - BMC bioinformatics N2 - 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. Y1 - 2006 U6 - https://doi.org/10.1186/1471-2105-7-380 SN - 1471-2105 VL - 7 IS - 380 PB - BioMed Central CY - London ER - TY - JOUR A1 - Laskov, Pavel A1 - Gehl, Christian A1 - Krüger, Stefan A1 - Müller, Klaus-Robert T1 - Incremental support vector learning: analysis, implementation and applications JF - Journal of machine learning research N2 - Incremental Support Vector Machines (SVM) are instrumental in practical applications of online learning. This work focuses on the design and analysis of efficient incremental SVM learning, with the aim of providing a fast, numerically stable and robust implementation. A detailed analysis of convergence and of algorithmic complexity of incremental SVM learning is carried out. Based on this analysis, a new design of storage and numerical operations is proposed, which speeds up the training of an incremental SVM by a factor of 5 to 20. The performance of the new algorithm is demonstrated in two scenarios: learning with limited resources and active learning. Various applications of the algorithm, such as in drug discovery, online monitoring of industrial devices and and surveillance of network traffic, can be foreseen. KW - incremental SVM KW - online learning KW - drug discovery KW - intrusion detection Y1 - 2006 SN - 1532-4435 VL - 7 SP - 1909 EP - 1936 PB - MIT Press CY - Cambridge, Mass. ER - TY - JOUR A1 - Dornhege, Guido A1 - Blankertz, Benjamin A1 - Krauledat, Matthias A1 - Losch, Florian A1 - Curio, Gabriel A1 - Müller, Klaus-Robert T1 - Combined optimization of spatial and temporal filters for improving brain-computer interfacing JF - IEEE transactions on bio-medical electronics N2 - Brain-computer interface (BCI) systems create a novel communication channel from the brain to an output de ice by bypassing conventional motor output pathways of nerves and muscles. Therefore they could provide a new communication and control option for paralyzed patients. Modern BCI technology is essentially based on techniques for the classification of single-trial brain signals. Here we present a novel technique that allows the simultaneous optimization of a spatial and a spectral filter enhancing discriminability rates of multichannel EEG single-trials. The evaluation of 60 experiments involving 22 different subjects demonstrates the significant superiority of the proposed algorithm over to its classical counterpart: the median classification error rate was decreased by 11%. Apart from the enhanced classification, the spatial and/or the spectral filter that are determined by the algorithm can also be used for further analysis of the data, e.g., for source localization of the respective brain rhythms. KW - brain-computer interface KW - common spatial patterns KW - EEG KW - event-related desynchronization KW - single-trial-analysis Y1 - 2006 U6 - https://doi.org/10.1109/TBME.2006.883649 SN - 0018-9294 VL - 53 IS - 11 SP - 2274 EP - 2281 PB - IEEE CY - New York ER - TY - JOUR A1 - Bordihn, Henning A1 - Holzer, Markus T1 - Programmed grammars and their relation to the LBA problem JF - Acta informatica N2 - We consider generating and accepting programmed grammars with bounded degree of non-regulation, that is, the maximum number of elements in success or in failure fields of the underlying grammar. In particular, it is shown that this measure can be restricted to two without loss of descriptional capacity, regardless of whether arbitrary derivations or left-most derivations are considered. Moreover, in some cases, precise characterizations of the linear bounded automaton problem in terms of programmed grammars are obtained. Thus, the results presented in this paper shed new light on some longstanding open problem in the theory of computational complexity. KW - programmed grammars KW - accepting grammars KW - LBA problem KW - degree of non-regulation KW - leftmost derivations Y1 - 2006 U6 - https://doi.org/10.1007/s00236-006-0017-9 SN - 0001-5903 VL - 43 SP - 223 EP - 242 PB - Elsevier CY - New York ER - TY - JOUR A1 - Bordihn, Henning A1 - Fernau, Henning A1 - Holzer, Markus A1 - Manca, Vincenzo A1 - Martin-Vide, Carlos T1 - Iterated sequential transducers as language generating devices JF - Theoretical computer science N2 - 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. KW - finite state sequential transducers KW - state complexity KW - Lindenmayer systems Y1 - 2006 U6 - https://doi.org/10.1016/j.tcs.2006.07.059 SN - 0304-3975 VL - 369 IS - 1 SP - 67 EP - 81 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Jürgensen, Helmut A1 - Konstantinidis, Stavros T1 - (Near-)inverses of sequences N2 - We introduce the notion of a near-inverse of a non-decreasing sequence of positive integers; near-inverses are intended to assume the role of inverses in cases when the latter cannot exist. We prove that the near-inverse of such a sequence is unique; moreover, the relation of being near-inverses of each other is symmetric, i.e. if sequence g is the near-inverse of sequence f, then f is the near-inverse of g. There is a connection, by approximations, between near- inverses of sequences and inverses of continuous strictly increasing real-valued functions which can be exploited to derive simple expressions for near-inverses Y1 - 2006 UR - http://www.informaworld.com/openurl?genre=journal&issn=0020-7160 U6 - https://doi.org/10.1080/00207160500537801 SN - 0020-7160 ER - TY - JOUR A1 - Blankertz, Benjamin A1 - Müller, Klaus-Robert A1 - Krusienski, Dean A1 - Schalk, Gerwin A1 - Wolpaw, Jonathan R. A1 - Schlögl, Alois A1 - Pfurtscheller, Gert A1 - Millan, José del R. A1 - Schröder, Michael A1 - Birbaumer, Niels T1 - The BCI competition III : validating alternative approaches to actual BCI problems N2 - A brain-computer interface (BCI) is a system that allows its users to control external devices with brain activity. Although the proof-of-concept was given decades ago, the reliable translation of user intent into device control commands is still a major challenge. Success requires the effective interaction of two adaptive controllers: the user's brain, which produces brain activity that encodes intent, and the BCI system, which translates that activity into device control commands. In order to facilitate this interaction, many laboratories are exploring a variety of signal analysis techniques to improve the adaptation of the BCI system to the user. In the literature, many machine learning and pattern classification algorithms have been reported to give impressive results when applied to BCI data in offline analyses. However, it is more difficult to evaluate their relative value for actual online use. BCI data competitions have been organized to provide objective formal evaluations of alternative methods. Prompted by the great interest in the first two BCI Competitions, we organized the third BCI Competition to address several of the most difficult and important analysis problems in BCI research. The paper describes the data sets that were provided to the competitors and gives an overview of the results. Y1 - 2006 UR - http://ieeexplore.ieee.org/xpl/RecentIssue.jsp?punumber=7333 U6 - https://doi.org/10.1109/Tnsre.2006.875642 SN - 1534-4320 ER - TY - JOUR A1 - Harmeling, Stefan A1 - Dornhege, Guido A1 - Tax, David A1 - Meinecke, Frank C. A1 - Müller, Klaus-Robert T1 - From outliers to prototypes : Ordering data N2 - We propose simple and fast methods based on nearest neighbors that order objects from high-dimensional data sets from typical points to untypical points. On the one hand, we show that these easy-to-compute orderings allow us to detect outliers (i.e. very untypical points) with a performance comparable to or better than other often much more sophisticated methods. On the other hand, we show how to use these orderings to detect prototypes (very typical points) which facilitate exploratory data analysis algorithms such as noisy nonlinear dimensionality reduction and clustering. Comprehensive experiments demonstrate the validity of our approach. Y1 - 2006 UR - http://www.sciencedirect.com/science/journal/09252312 U6 - https://doi.org/10.1016/j.neucom.2005.05.015 SN - 0925-2312 ER - TY - JOUR A1 - Ocheretnij, Vitalij A1 - Gössel, Michael A1 - Sogomonyan, Egor S. A1 - Marienfeld, Daniel T1 - Modulo p=3 checking for a carry select adder N2 - In this paper a self-checking carry select adder is proposed. The duplicated adder blocks which are inherent to a carry select adder without error detection are checked modulo 3. Compared to a carry select adder without error detection the delay of the MSB of the sum of the proposed adder does not increase. Compared to a self-checking duplicated carry select adder the area is reduced by 20%. No restrictions are imposed on the design of the adder blocks Y1 - 2006 UR - http://www.springerlink.com/content/100286 U6 - https://doi.org/10.1007/s10836-006-6260-8 ER - TY - BOOK A1 - Hüttenrauch, Stefan A1 - Kylau, Uwe A1 - Grund, Martin A1 - Queck, Tobias A1 - Ploskonos, Anna A1 - Schreiter, Torben A1 - Breest, Martin A1 - Haubrock, Sören A1 - Bouche, Paul T1 - Fundamentals of Service-Oriented Engineering BT - Proceedings of the Fall 2006 Workshop of the HPI Research School on Service-Oriented Systems Engineering T3 - Technische Berichte des Hasso-Plattner-Instituts für Softwaresystemtechnik an der Universität Potsdam Y1 - 2006 SN - 3-939469-35-1 SN - 1613-5652 VL - 18 PB - Universitätsverlag Potsdam CY - Potsdam ER -