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In this paper we report about the recently completed porting of GAMMA to the Netgear GA621 Gigabit Ethernet adapter, and provide a comparison among GAMMA, MPI/GAMMA, TCP/IP, and MPICH/TCP, based on the Netgear GA621 and the older Netgear GA620 network adapters and using different device drivers, in a Gigabit Ethernet cluster of PCs running Linux 2.4. GAMMA (the Genoa Active Message MAchine) is a lightweight messaging system based on an Active Message-like paradigm, originally designed for efficient exploitation of Fast Ethernet interconnects. The comparison includes simple latency/hspace{0pt}bandwidth evaluation of the messaging systems on both adapters, as well as performance comparisons based on the NAS NPB and an end-user fluid dynamics application called Modular Ocean Model (MOM). The analysis of results provides useful hints concerning the efficient use of Gigabit Ethernet with clusters of PCs. In particular, it emerges that GAMMA on the GA621 adapter, with a combination of low end-to-end latency (8.5 $mu$s) and high throughput (118.4 MByte/s), provides a performing, cost-effective alternative to proprietary high-speed networks, e.g.~Myrinet, for a wide range of cluster computing applications.
More on nomore
(2002)
A polynomial translation of logic programs with nested expressions into disjunctive logic programs
(2002)
More on nomore
(2002)
Preferred well-founded semantics for logic programming by alternating fixpoints : preliminary report
(2002)
The integration of preferences into answer set programming constitutes an important practical device for distinguishing certain preferred answer sets from non-preferred ones. To this end, we elaborate upon rule dependency graphs and their colorings for characterizing different preference handling strategies found in the literature. We start from a characterization of (three types of) preferred answer sets in terms of totally colored dependency graphs. In particular, we demonstrate that this approach allows us to capture all three approaches to preferences in a uniform setting by means of the concept of a height function. In turn, we exemplarily develop an operational characterization of preferred answer sets in terms of operators on partial colorings for one particular strategy. In analogy to the notion of a derivation in proof theory, our operational characterization is expressed as a (non-deterministically formed) sequence of colorings, gradually turning an uncolored graph into a totally colored one
Antwortmengenprogrammierung
(2003)
In order to take full advantage of Grid environments, applications need to be able to run on various heterogeneous platforms. Distributed runs across several clusters or supercomputers for example, require matching binaries at each site. Thus, at some stage, each Grid enabled application needs to be recompiled for every platform. Up to now, creating matching binaries on different platforms was a manual, sequential, slow, and very error-prone process. Developers had to log into each machine, transfer source code, check consistency and recompile if necessary. This cumbersome procedure is surely one reason for the (still existing) lack of production Grid computing. Gridmake, a tool to automate and speed up this procedure is presented in this paper.
Characterizing Grids
(2003)
We present a new data model approach to describe the various objects that either represent the Grid infrastructure or make use of it. The data model is based on the experiences and experiments conducted in heterogeneous Grid environments. While very sophisticated data models exist to describe and characterize e.g. compute capacities or web services, we will show that a general description, which combines {em all} of these aspects, is needed to give an adequate representation of objects on a Grid. The Grid Object Description Language (GODsL)} is a generic and extensible approach to unify the various aspects that an object on a Grid can have. GODsL provides the content for the XML based communication in Grid migration scenarios, carried out in the GridLab project. We describe the data model architecture on a general level and focus on the Grid application scenarios.
We propose two methods that reduce the post-nonlinear blind source separation problem (PNL-BSS) to a linear BSS problem. The first method is based on the concept of maximal correlation: we apply the alternating conditional expectation (ACE) algorithm-a powerful technique from nonparametric statistics-to approximately invert the componentwise nonlinear functions. The second method is a Gaussianizing transformation, which is motivated by the fact that linearly mixed signals before nonlinear transformation are approximately Gaussian distributed. This heuristic, but simple and efficient procedure works as good as the ACE method. Using the framework provided by ACE, convergence can be proven. The optimal transformations obtained by ACE coincide with the sought-after inverse functions of the nonlinearitics. After equalizing the nonlinearities, temporal decorrelation separation (TDSEP) allows us to recover the source signals. Numerical simulations testing "ACE-TD" and "Gauss-TD" on realistic examples are performed with excellent results
A well-known result by Stein (1956) shows that in particular situations, biased estimators can yield better parameter estimates than their generally preferred unbiased counterparts. This letter follows the same spirit, as we will stabilize the unbiased generalization error estimates by regularization and finally obtain more robust model selection criteria for learning. We trade a small bias against a larger variance reduction, which has the beneficial effect of being more precise on a single training set. We focus on the subspace information criterion (SIC), which is an unbiased estimator of the expected generalization error measured by the reproducing kernel Hilbert space norm. SIC can be applied to the kernel regression, and it was shown in earlier experiments that a small regularization of SIC has a stabilization effect. However, it remained open how to appropriately determine the degree of regularization in SIC. In this article, we derive an unbiased estimator of the expected squared error, between SIC and the expected generalization error and propose determining the degree of regularization of SIC such that the estimator of the expected squared error is minimized. Computer simulations with artificial and real data sets illustrate that the proposed method works effectively for improving the precision of SIC, especially in the high-noise-level cases. We furthermore compare the proposed method to the original SIC, the cross-validation, and an empirical Bayesian method in ridge parameter selection, with good results
Recently blind source separation (BSS) methods have been highly successful when applied to biomedical data. This paper reviews the concept of BSS and demonstrates its usefulness in the context of event-related MEG measurements. In a first experiment we apply BSS to artifact identification of raw MEG data and discuss how the quality of the resulting independent component projections can be evaluated. The second part of our study considers averaged data of event-related magnetic fields. Here, it is particularly important to monitor and thus avoid possible overfitting due to limited sample size. A stability assessment of the BSS decomposition allows to solve this task and an additional grouping of the BSS components reveals interesting structure, that could ultimately be used for gaining a better physiological modeling of the data
We present a new technique for uniquely identifying a single failing vector in an interval of test vectors. This technique is applicable to combinational circuits and for scan-BIST in sequential circuits with multiple scan chains. The proposed method relies on the linearity properties of the MISR and on the use of two test sequences, which are both applied to the circuit under test. The second test sequence is derived from the first in a straightforward manner and the same test pattern source is used for both test sequences. If an interval contains only a single failing vector, the algebraic analysis is guaranteed to identify it. We also show analytically that if an interval contains two failing vectors, the probability that this case is interpreted as one failing vector is very low. We present experimental results for the ISCAS benchmark circuits to demonstrate the use of the proposed method for identifying failing test vectors
In this paper, we show how an approach to belief revision and belief contraction can be axiomatized by means of quantified Boolean formulas. Specifically, we consider the approach of belief change scenarios, a general framework that has been introduced for expressing different forms of belief change. The essential idea is that for a belief change scenario (K, R, C), the set of formulas K, representing the knowledge base, is modified so that the sets of formulas R and C are respectively true in, and consistent with the result. By restricting the form of a belief change scenario, one obtains specific belief change operators including belief revision, contraction, update, and merging. For both the general approach and for specific operators, we give a quantified Boolean formula such that satisfying truth assignments to the free variables correspond to belief change extensions in the original approach. Hence, we reduce the problem of determining the results of a belief change operation to that of satisfiability. This approach has several benefits. First, it furnishes an axiomatic specification of belief change with respect to belief change scenarios. This then leads to further insight into the belief change framework. Second, this axiomatization allows us to identify strict complexity bounds for the considered reasoning tasks. Third, we have implemented these different forms of belief change by means of existing solvers for quantified Boolean formulas. As well, it appears that this approach may be straightforwardly applied to other specific approaches to belief change
Usually, noise is considered to be destructive. We present a new method that constructively injects noise to assess the reliability and the grouping structure of empirical ICA component estimates. Our method can be viewed as a Monte-Carlo-style approximation of the curvature of some performance measure at the solution. Simulations show that the true root-mean-squared angle distances between the real sources and the source estimates can be approximated well by our method. In a toy experiment, we see that we are also able to reveal the underlying grouping structure of the extracted ICA components. Furthermore, an experiment with fetal ECG data demonstrates that our approach is useful for exploratory data analysis of real-world data. (C) 2003 Elsevier B.V. All rights reserved
Motivation: Continued development of analytical techniques based on gas chromatography and mass spectrometry now facilitates the generation of larger sets of metabolite concentration data. An important step towards the understanding of metabolite dynamics is the recognition of stable states where metabolite concentrations exhibit a simple behaviour. Such states can be characterized through the identification of significant thresholds in the concentrations. But general techniques for finding discretization thresholds in continuous data prove to be practically insufficient for detecting states due to the weak conditional dependences in concentration data. Results: We introduce a method of recognizing states in the framework of decision tree induction. It is based upon a global analysis of decision forests where stability and quality are evaluated. It leads to the detection of thresholds that are both comprehensible and robust. Applied to metabolite concentration data, this method has led to the discovery of hidden states in the corresponding variables. Some of these reflect known properties of the biological experiments, and others point to putative new states
We present a general approach for representing and reasoning with sets of defaults in default logic, focusing on reasoning about preferences among sets of defaults. First, we consider how to control the application of a set of defaults so that either all apply (if possible) or none do (if not). From this, an approach to dealing with preferences among sets of default rules is developed. We begin with an ordered default theory, consisting of a standard default theory, but with possible preferences on sets of rules. This theory is transformed into a second, standard default theory wherein the preferences are respected. The approach differs from other work, in that we obtain standard default theories and do not rely on prioritized versions of default logic. In practical terms this means we can immediately use existing default logic theorem provers for an implementation. Also, we directly generate just those extensions containing the most preferred applied rules; in contrast, most previous approaches generate all extensions, then select the most preferred. In a major application of the approach, we show how semimonotonic default theories can be encoded so that reasoning can be carried out at the object level. With this, we can reason about default extensions from within the framework of a standard default logic. Hence one can encode notions such as skeptical and credulous conclusions, and can reason about such conclusions within a single extension
In recent years, there has been a large amount of disparate work concerning the representation and reasoning with qualitative preferential information by means of approaches to nonmonotonic reasoning. Given the variety of underlying systems, assumptions, motivations, and intuitions, it is difficult to compare or relate one approach with another. Here, we present an overview and classification for approaches to dealing with preference. A set of criteria for classifying approaches is given, followed by a set of desiderata that an approach might be expected to satisfy. A comprehensive set of approaches is subsequently given and classified with respect to these sets of underlying principles
Interest in developing a new method of man-to-machine communication-a brain-computer interface (BCI)-has grown steadily over the past few decades. BCIs create a new communication channel between the brain and an output device by bypassing conventional motor output pathways of nerves and muscles. These systems use signals recorded from the scalp, the surface of the cortex, or from inside the brain to enable users to control a variety of applications including simple word-processing software and orthotics. BCI technology could therefore provide a new communication and control option for individuals who cannot otherwise express their wishes to the outside world. Signal processing and classification methods are essential tools in the development of improved BCI technology. We organized the BCI Competition 2003 to evaluate the current state of the art of these tools. Four laboratories well versed in EEG-based BCI research provided six data sets in a documented format. We made these data sets (i.e., labeled training sets and unlabeled test sets) and their descriptions available on the Internet. The goal in the competition was to maximize the performance measure for the test labels. Researchers worldwide tested their algorithms and competed for the best classification results. This paper describes the six data sets and the results and function of the most successful algorithms
Noninvasive electroencephalogram (EEG) recordings provide for easy and safe access to human neocortical processes which can be exploited for a brain-computer interface (BCI). At present, however, the use of BCIs is severely limited by low bit-transfer rates. We systematically analyze and develop two recent concepts, both capable of enhancing the information gain from multichannel scalp EEG recordings: 1) the combination of classifiers, each specifically tailored for different physiological phenomena, e.g., slow cortical potential shifts, such as the premovement Bereitschaftspotential or differences in spatio-spectral distributions of brain activity (i.e., focal event-related desynchronizations) and 2) behavioral paradigms inducing the subjects to generate one out of several brain states (multiclass approach) which all bare a distinctive spatio-temporal signature well discriminable in the standard scalp EEG. We derive information-theoretic predictions and demonstrate their relevance in experimental data. We will show that a suitably arranged interaction between these concepts can significantly boost BCI performances
The power of a language L is the set of all powers of the words in L. In this paper, the following decision problem is investigated. Given a context-free language L, is the power of L context-free? We show that this problem is decidable for languages over unary alphabets, but it is undecidable whenever languages over alphabets with at least two letters are considered. (C) 2003 Elsevier B.V. All rights reserved
Untitled
(2004)
With the success of wireless technologies in consumer electronics, standard wireless technologies are envisioned for the deployment in industrial environments as well. Industrial applications involving mobile subsystems or just the desire to save cabling make wireless technologies attractive. Nevertheless, these applications often have stringent requirements on reliability and timing. In wired environments, timing and reliability are well catered for by fieldbus systems (which are a mature technology designed to enable communication between digital controllers and the sensors and actuators interfacing to a physical process). When wireless links are included, reliability and timing requirements are significantly more difficult to meet, due to the adverse properties of the radio channels. In this paper we thus discuss some key issues coming up in wireless fieldbus and wireless industrial communication systems:1)fundamental problems like achieving timely and reliable transmission despite channel errors; 2) the usage of existing wireless technologies for this specific field of applications; and 3) the creation of hybrid systems in which wireless stations are included into existing wired systems
Motivation: Visualizing and analysing the potential non-linear structure of a dataset is becoming an important task in molecular biology. This is even more challenging when the data have missing values. Results: Here, we propose an inverse model that performs non-linear principal component analysis (NLPCA) from incomplete datasets. Missing values are ignored while optimizing the model, but can be estimated afterwards. Results are shown for both artificial and experimental datasets. In contrast to linear methods, non-linear methods were able to give better missing value estimations for non-linear structured data. Application: We applied this technique to a time course of metabolite data from a cold stress experiment on the model plant Arabidopsis thaliana, and could approximate the mapping function from any time point to the metabolite responses. Thus, the inverse NLPCA provides greatly improved information for better understanding the complex response to cold stress
This paper proposes a new independent component analysis (ICA) method which is able to unmix overcomplete mixtures of sparce or structured signals like speech, music or images. Furthermore, the method is designed to be robust against outliers, which is a favorable feature for ICA algorithms since most of them are extremely sensitive to outliers. Our approach is based on a simple outlier index. However, instead of robustifying an existing algorithm by some outlier rejection technique we show how this index can be used directly to solve the ICA problem for super-Gaussian sources. The resulting inlier-based ICA (IBICA) is outlier-robust by construction and can be used for standard ICA as well as for overcomplete ICA (i.e. more source signals than observed signals). (c) 2005 Wiley Periodicals, Inc
Data recorded in electroencephalogram (EEG)-based brain-computer interface experiments is generally very noisy, non-stationary, and contaminated with artifacts that can deteriorate discrimination/classification methods. In this paper, we extend the common spatial pattern (CSP) algorithm with the aim to alleviate these adverse effects. In particular, we suggest an extension of CSP to the state space, which utilizes the method of time delay embedding. As we will show, this allows for individually tuned frequency filters at each electrode position and, thus, yields an improved and more robust machine learning procedure. The advantages of the proposed method over the original CSP method are verified in terms of an improved information transfer rate (bits per trial) on a set of EEG-recordings from experiments of imagined limb movements
Phase synchronization is an important phenomenon that occurs in a wide variety of complex oscillatory processes. Measuring phase synchronization can therefore help to gain fundamental insight into nature. In this Letter we point out that synchronization analysis techniques can detect spurious synchronization, if they are fed with a superposition of signals such as in electroencephalography or magnetoencephalography data. We show how techniques from blind source separation can help to nevertheless measure the true synchronization and avoid such pitfalls
Geovisualization offers powerful tools, techniques, and strategies to present, explore, analyze, and manage geoinformation. Interactive geovirtual environments such as virtual 3D maps or virtual 3D city models, however, raise the question how to control geodata usage and distribution. We present a concept for embedding digital rights in geovisualizations. It is based on geo-documents, an object-oriented scheme to specify a wide range of geo visualizations. Geo-documents are assembled by building blocks categorized into presentation, structure, interaction, animation, and Digital Rights Management (DRM) classes. DRM objects allow for defining permissions and constraints for all objects contained in geo-documents. In this way, authors of geo visualizations can control how their geo-documents are used, personalized, and redistributed by users. The strengths of the presented concept include the ability to integrate heterogeneous 2D and 3D geodata within a compact design scheme and the ability to cope with privacy, security, and copyright issues. Embedded digital rights in geovisualizations can be applied to improve the usability of geodata user interfaces, to implement publisher-subscriber communication systems for geodata, and to establish business models for geodata trading systems
Reiter's default logic is one of the best known and most studied of the approaches to nonmonotonic reasoning. Several variants of default logic have subsequently been proposed to give systems with properties differing from the original. In this paper, we examine the relationship between default logic and its major variants. We accomplish this by translating a default theory under a variant interpretation into a second default theory, under the original Reiter semantics, wherein the variant interpretation is respected. That is, in each case we show that, given an extension of a translated theory, one may extract an extension of the original variant default logic theory. We show how constrained, rational, justified, and cumulative default logic can be expressed in Reiter's default logic. As well, we show how Reiter's default logic can be expressed in rational default logic. From this, we suggest that any such variant can be similarly treated. Consequently, we provide a unification of default logics, showing how the original formulation of default logic may express its variants. Moreover, the translations clearly express the relationships between alternative approaches to default logic. The translations themselves are shown to generally have good properties. Thus, in at least a theoretical sense, we show that these variants are in a sense superfluous, in that for any of these variants of default logic, we can exactly mimic the behaviour of a variant in standard default logic. As well, the translations lend insight into means of classifying the expressive power of default logic variants; specifically we suggest that the property of semi-monotonicity represents a division with respect to expressibility, whereas regularity and cumulativity do not
In this paper we prove Chaitin's "heuristic principle," the theorems of a finitely-specified theory cannot be significantly more complex than the theory itself, for an appropriate measure of complexity. We show that the measure is invariant under the change of the Godel numbering. For this measure, the theorems of a finitely-specified, sound, consistent theory strong enough to formalize arithmetic which is arithmetically sound (like Zermelo-Fraenkel set theory with choice or Peano Arithmetic) have bounded complexity, hence every sentence of the theory which is significantly more complex than the theory is unprovable. Previous results showing that incompleteness is not accidental, but ubiquitous are here reinforced in probabilistic terms: the probability that a true sentence of length n is provable in the theory tends to zero when n tends to infinity, while the probability that a sentence of length n is true is strictly positive. (c) 2004 Elsevier Inc. All rights reserved
We study a novel representation of semiautomata, which is motivated by the method of trace-assertion specifications of software modules. Each state of the semiautomaton is represented by an arbitrary word leading to that state, the canonical word. The transitions of the semiautomaton give rise to a right congruence, the state-equivalence, on the set of input words of the semiautomaton: two words are state-equivalent if and only if they lead to the same state. We present a simple algorithm for finding a set of generators for state-equivalence. Directly from this set of generators, we construct a confluent prefix-rewriting system which permits us to transform any word to its canonical representative. In general, the rewriting system may allow infinite derivations. To address this issue, we impose the condition of prefix-continuity on the set of canonical words. A set is prefix-continuous if, whenever a word w and a prefix u of w axe in the set, then all the prefixes of w longer than u are also in the set. Prefix-continuous sets include prefix-free and prefix-closed sets as special cases. We prove that the rewriting system is Noetherian if and only if the set of canonical words is prefix-continuous. Furthermore, if the set of canonical words is prefix- continuous, then the set of rewriting rules is irredundant. We show that each prefix-continuous canonical set corresponds to a spanning forest of the semiautomaton
E-Government requires technical and organizational innovation. Research has already shown that the respective innovation process is complex and contingent upon specific organizational structures. Managing such innovation processes successfully is difficult. Drawing on assumptions of micropolitical behavior, a framework of innovation arenas is proposed. It supports the analysis of ongoing E-Government projects as well as the ex post investigation of successful or failed projects. Testing this framework in case studies already demonstrates its usefulness for individual actors making strategic choices about change management. Furthermore, the results indicate that many commonly held assumptions about successful change management have to be reconsidered
We investigate the operation problem for linear and deterministic context-free languages: Fix an operation on formal languages. Given linear (deterministic, respectively) context-free languages, is the application of this operation to the given languages still a linear (deterministic, respectively) context-free language? Besides the classical operations, for which the linear and deterministic context-free languages are not closed, we also consider the recently introduced root and power operation. We show non-semidecidability, to be more precise, we show completeness for the second level of the arithmetic hierarchy for all of the aforementioned operations, except for the power operation, if the underlying alphabet contains at least two letters. The result for the power opera, tion solves an open problem stated in Theoret. Comput. Sci. 314 (2004) 445-449
It is proved that the number of components in context-free cooperating distributed (CD) grammar systems can be reduced to 3 when they are working in the so-called sf-mode of derivation, which is the cooperation protocol which has been considered first for CD grammar systems. In this derivation mode, a component continues the derivation until and unless there is a nonterminal in the sentential form which cannot be rewritten according to that component. Moreover, it is shown that CD grammar systems in sf-mode with only one component can generate only the context-free languages but they can generate non-context-free languages if two components are used. The sf-mode of derivation is compared with other well-known cooperation protocols with respect to the hierarchies induced by the number of components. (C) 2004 Elsevier B.V. All rights reserved
Computational methods for the design of effective therapies against drug resistant HIV strains
(2005)
The development of drug resistance is a major obstacle to successful treatment of HIV infection. The extraordinary replication dynamics of HIV facilitates its escape from selective pressure exerted by the human immune system and by combination drug therapy. We have developed several computational methods whose combined use can support the design of optimal antiretroviral therapies based on viral genomic data
This paper analyses data privacy issues as they arise from different deployment scenarios for networks that use embedded sensor devices. Maintaining data privacy in pervasive environments requires the management and implementation of privacy protection measures close to the data source. We propose a set of atomic privacy parameters that is generic enough to form specific privacy classes and might be applied directly at the embedded sensor device.