@article{LaskovGehlKruegeretal.2006, author = {Laskov, Pavel and Gehl, Christian and Kr{\"u}ger, Stefan and M{\"u}ller, Klaus-Robert}, title = {Incremental support vector learning: analysis, implementation and applications}, series = {Journal of machine learning research}, volume = {7}, journal = {Journal of machine learning research}, publisher = {MIT Press}, address = {Cambridge, Mass.}, issn = {1532-4435}, pages = {1909 -- 1936}, year = {2006}, abstract = {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.}, language = {en} } @article{SteuerHumburgSelbig2006, author = {Steuer, Ralf and Humburg, Peter and Selbig, Joachim}, title = {Validation and functional annotation of expression-based clusters based on gene ontology}, series = {BMC bioinformatics}, volume = {7}, journal = {BMC bioinformatics}, number = {380}, publisher = {BioMed Central}, address = {London}, issn = {1471-2105}, doi = {10.1186/1471-2105-7-380}, pages = {12}, year = {2006}, abstract = {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.}, language = {en} } @article{BordihnFernauHolzeretal.2006, author = {Bordihn, Henning and Fernau, Henning and Holzer, Markus and Manca, Vincenzo and Martin-Vide, Carlos}, title = {Iterated sequential transducers as language generating devices}, series = {Theoretical computer science}, volume = {369}, journal = {Theoretical computer science}, number = {1}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3975}, doi = {10.1016/j.tcs.2006.07.059}, pages = {67 -- 81}, year = {2006}, abstract = {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.}, language = {en} } @article{GrellSchaubSelbig2006, author = {Grell, Susanne and Schaub, Torsten H. and Selbig, Joachim}, title = {Modelling biological networks by action languages via set programming}, issn = {0302-9743}, doi = {10.1007/11799573}, year = {2006}, language = {en} } @article{DelgrandeSchaubTompits2006, author = {Delgrande, James Patrick and Schaub, Torsten H. and Tompits, Hans}, title = {A Preference-Based Framework for Updating logic Programs : preliminary reports}, year = {2006}, language = {en} } @article{GressmannJanhunenMerceretal.2006, author = {Gressmann, Jean and Janhunen, Tomi and Mercer, Robert E. and Schaub, Torsten H. and Thiele, Sven and Tichy, Richard}, title = {On probing and multi-threading in platypus}, year = {2006}, language = {en} } @article{AngerGebserSchaub2006, author = {Anger, Christian and Gebser, Martin and Schaub, Torsten H.}, title = {Approaching the core of unfounded sets}, year = {2006}, language = {en} } @article{ShenoyKrauledatBlankertzetal.2006, author = {Shenoy, Pradeep and Krauledat, Matthias and Blankertz, Benjamin and Rao, Rajesh P. N. and M{\"u}ller, Klaus-Robert}, title = {Towards adaptive classification for BCI}, doi = {10.1088/1741-2560/3/1/R02}, year = {2006}, abstract = {Non-stationarities are ubiquitous in EEG signals. They are especially apparent in the use of EEG-based brain- computer interfaces (BCIs): (a) in the differences between the initial calibration measurement and the online operation of a BCI, or (b) caused by changes in the subject's brain processes during an experiment (e.g. due to fatigue, change of task involvement, etc). In this paper, we quantify for the first time such systematic evidence of statistical differences in data recorded during offline and online sessions. Furthermore, we propose novel techniques of investigating and visualizing data distributions, which are particularly useful for the analysis of (non-) stationarities. Our study shows that the brain signals used for control can change substantially from the offline calibration sessions to online control, and also within a single session. In addition to this general characterization of the signals, we propose several adaptive classification schemes and study their performance on data recorded during online experiments. An encouraging result of our study is that surprisingly simple adaptive methods in combination with an offline feature selection scheme can significantly increase BCI performance}, language = {en} } @article{BlankertzDornhegeKrauledatetal.2006, author = {Blankertz, Benjamin and Dornhege, Guido and Krauledat, Matthias and M{\"u}ller, Klaus-Robert and Kunzmann, Volker and Losch, Florian and Curio, Gabriel}, title = {The Berlin brain-computer interface : EEG-based communication without subject training}, issn = {1534-4320}, doi = {10.1109/Tnsre.2006.875557}, year = {2006}, abstract = {The Berlin Brain-Computer Interface (BBCI) project develops a noninvasive BCI system whose key features are 1) the use of well-established motor competences as control paradigms, 2) high-dimensional features from 128-channel electroencephalogram (EEG), and 3) advanced machine learning techniques. As reported earlier, our experiments demonstrate that very high information transfer rates can be achieved using the readiness potential (RP) when predicting the laterality of upcoming left-versus right-hand movements in healthy subjects. A more recent study showed that the RP similarily accompanies phantom movements in arm amputees, but the signal strength decreases with longer loss of the limb. In a complementary approach, oscillatory features are used to discriminate imagined movements (left hand versus right hand versus foot). In a recent feedback study with six healthy subjects with no or very little experience with BCI control, three subjects achieved an information transfer rate above 35 bits per minute (bpm), and further two subjects above 24 and 15 bpm, while one subject could not achieve any BCI control. These results are encouraging for an EEG-based BCI system in untrained subjects that is independent of peripheral nervous system activity and does not rely on evoked potentials even when compared to results with very well-trained subjects operating other BCI systems}, language = {en} } @article{WilligMitschke2006, author = {Willig, Andreas and Mitschke, Robert}, title = {Results of bit error measurements with sensor nodes and casuistic consequences for design of energy-efficient error control schemes}, isbn = {978-3-540-32158-3}, year = {2006}, abstract = {For the proper design of energy-efficient error control schemes some insight into channel error patterns is needed. This paper presents bit error and packet loss measurements taken with sensor nodes running the popular RFM}, language = {en} } @article{RozinatVanderAalst2006, author = {Rozinat, A and Van der Aalst, Wil M. P.}, title = {Conformance testing: Measuring the fit and appropriateness of event logs and process models}, year = {2006}, abstract = {Most information systems log events (e.g., transaction logs, audit traits) to audit and monitor the processes they support. At the same time, many of these processes have been explicitly modeled. For example, SAP R/3 logs events in transaction logs and there are EPCs (Event-driven Process Chains) describing the so-called reference models. These reference models describe how the system should be used. The coexistence of event logs and process models raises an interesting question: "Does the event log conform to the process model and vice versa?". This paper demonstrates that there is not a simple answer to this question. To tackle the problem, we distinguish two dimensions of conformance: fitness (the event log may be the result of the process modeled) and appropriateness (the model is a likely candidate from a structural and behavioral point of view). Different metrics have been defined and a Conformance Checker has been implemented within the ProM Framework}, language = {en} } @article{GerbserSchaub2006, author = {Gerbser, Martin and Schaub, Torsten H.}, title = {Tableau calculi for answer set programming}, issn = {0302-9743}, doi = {10.1007/11799573}, year = {2006}, language = {en} } @article{Konczak2006, author = {Konczak, Kathrin}, title = {Voting Theory in Answer Set Programming}, year = {2006}, language = {en} } @article{AngerGebserJanhunenetal.2006, author = {Anger, Christian and Gebser, Martin and Janhunen, Tomi and Schaub, Torsten H.}, title = {What's a head without a body?}, year = {2006}, language = {en} } @article{GerbserLeeLierler2006, author = {Gerbser, Martin and Lee, Joohyung and Lierler, Yuliya}, title = {Elementary sets for logic programs}, isbn = {978-1-57735-281-5}, year = {2006}, language = {en} } @article{GerbserSchaub2006, author = {Gerbser, Martin and Schaub, Torsten H.}, title = {Characterizing (ASP) inferences by unit propagation}, year = {2006}, language = {en} } @article{Konczak2006, author = {Konczak, Kathrin}, title = {Weak order equivalence for Logic Programs with Prefernces}, year = {2006}, language = {en} } @article{KonczakLinkeSchaub2006, author = {Konczak, Kathrin and Linke, Thomas and Schaub, Torsten H.}, title = {Graphs and colorings for answer set programming}, issn = {1471-0684}, doi = {10.1017/S1471068405002528}, year = {2006}, abstract = {We investigate the usage of rule dependency graphs and their colorings for characterizing and computing answer sets of logic programs. This approach provides us with insights into the interplay between rules when inducing answer sets. We start with different characterizations of answer sets in terms of totally colored dependency graphs that differ ill graph-theoretical aspects. We then develop a series of operational characterizations of answer sets in terms of operators on partial colorings. In analogy to the notion of a derivation in proof theory, our operational characterizations are expressed as (non-deterministically formed) sequences of colorings, turning an uncolored graph into a totally colored one. In this way, we obtain an operational framework in which different combinations of operators result in different formal properties. Among others, we identify the basic strategy employed by the noMoRe system and justify its algorithmic approach. Furthermore, we distinguish operations corresponding to Fitting's operator as well as to well-founded semantics}, language = {en} } @article{CordesKaiserSelbig2006, author = {Cordes, Frank and Kaiser, Rolf and Selbig, Joachim}, title = {Bioinformatics approach to predicting HIV drug resistance}, issn = {1473-7159}, doi = {10.1586/14737159.6.2.207}, year = {2006}, abstract = {The emergence of drug resistance remains one of the most challenging issues in the treatment of HIV-1 infection. The extreme replication dynamics of HIV facilitates its escape from the selective pressure exerted by the human immune system and by the applied combination drug therapy. This article reviews computational methods whose combined use can support the design of optimal antiretroviral therapies based on viral genotypic and phenotypic data. Genotypic assays are based on the analysis of mutations associated with reduced drug susceptibility, but are difficult to interpret due to the numerous mutations and mutational patterns that confer drug resistance. Phenotypic resistance or susceptibility can be experimentally evaluated by measuring the inhibition of the viral replication in cell culture assays. However, this procedure is expensive and time consuming}, language = {en} } @article{LemmCurioHlushchuketal.2006, author = {Lemm, Steven and Curio, Gabriel and Hlushchuk, Yevhen and M{\"u}ller, Klaus-Robert}, title = {Enhancing the signal-to-noise ratio of ICA-based extracted ERPs}, issn = {0018-9294}, doi = {10.1109/Tbme.2006.870258}, year = {2006}, abstract = {When decomposing single trial electroencephalography it is a challenge to incorporate prior physiological knowledge. Here, we develop a method that uses prior information about the phase-locking property of event-related potentials in a regularization framework to bias a blind source separation algorithm toward an improved separation of single-trial phase-locked responses in terms of an increased signal-to-noise ratio. In particular, we suggest a transformation of the data, using weighted average of the single trial and trial-averaged response, that redirects the focus of source separation methods onto the subspace of event-related potentials. The practical benefit with respect to an improved separation of such components from ongoing background activity and extraneous noise is first illustrated on artificial data and finally verified in a real-world application of extracting single-trial somatosensory evoked potentials from multichannel EEG-recordings}, language = {en} }