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Wielgosz M.,AGH University of Science and Technology | Wielgosz M.,Academic Computer Center | Pietron M.,AGH University of Science and Technology | Pietron M.,Academic Computer Center
Neurocomputing | Year: 2017

This paper examines the performance of a Spatial Pooler (SP) of a Hierarchical Temporal Memory (HTM) in the task of noisy object recognition. To address this challenge, a dedicated custom-designed system based on the SP, histogram calculation module and SVM classifier was implemented. In addition to implementing their own version of HTM, the authors also designed a profiler which is capable of tracing all of the key parameters of the system. This was necessary, since an analysis and monitoring of the system performance turned out to be extremely difficult using conventional testing and debugging tools. The system was initially trained on artificially prepared videos without noise and then tested with a set of noisy video streams. This approach was intended to mimic a real life scenario where an agent or a system trained to deal with ideal objects faces a task of classifying distorted and noisy ones in its regular working conditions. The authors conducted a series of experiments for various macro parameters of HTM SP, as well as for different levels of video reduction ratios. The experiments allowed them to evaluate the performance of two different system setups (i.e. ‘Multiple HTMs’ and ‘Single HTM’) under various noise conditions with 32-frame video files. Results of all the tests were compared to SVM baseline setup. It was determined that the system featuring SP is capable of achieving approximately 12 times the noise reduction for a video signal with distorted bits accounting for 13% of the total. Furthermore, the system featuring SP performed better also in the experiments without a noise component and achieved a max F1 score of 0.96. The experiments also revealed that a rise of column and synapse number of SP has a substantial impact on the performance of the system. Consequently, the highest F1 score values were obtained for 256 and 4096 synapses and columns, respectively. It is worth noting that ‘Multiple HTMs’ setup outperforms the ‘Single HTM’ one. Nevertheless, this is achieved at the expense of increased computational demands. © 2017 Elsevier B.V.


Malawski M.,Institute of Computer Science | Bartynski T.,Academic Computer Center | Bubak M.,Institute of Computer Science | Bubak M.,University of Amsterdam
Future Generation Computer Systems | Year: 2010

In this paper we address the complexity of building and running modern scientific applications on various Grid systems with heterogeneous middleware. As a solution we have proposed the Grid Operation Invoker (GOI) which offers an object-oriented method invocation semantics for interacting with diverse computational services. GOI forms the core of the ViroLab virtual laboratory and it is used to invoke operations from within in-silico experiments described using a scripting notation. We describe the details of GOI (including architecture, technology adapters and asynchronous invocations) focusing on a mechanism which allows adding high-level support for batch job processing middleware, e.g. EGEE LCG/gLite. As an example, we present the NAMD molecular dynamics program, deployed on EGEE infrastructure. The main achievement is the creation of the Grid Object abstraction, which can be used to represent and access such diverse technologies as Web Services, distributed components and job processing systems. Such an application model, based on high-level scripting, is an interesting alternative to graphical workflow-based tools. © 2009 Elsevier B.V. All rights reserved.


Romanczyk P.P.,Cracow University of Technology | Rotko G.,Cracow University of Technology | Noga K.,Jagiellonian University | Noga K.,Academic Computer Center | And 4 more authors.
Electrochimica Acta | Year: 2014

A tungsten alkoxy scorpionate shows activity in the electrocatalytic reductive dehalogenation of pentachloroethane and trichloroethylene owing to the formation of hydrogen and halogen bonded adducts with the substrates, which is further reinforced by dispersive interactions. The ensuing proximity between the substrate molecule and the metal centre promotes dechlorination in a concerted process. Two-electron reduction of pentachloroethane yields trichloroethylene that undergoes further, non-catalysed, reactions that ultimately give acetylenes. Interestingly, pentachloroethane proved to be a highly efficient proton donor for the transient anions, in extremely exothermic and rapid proton transfer concerted with chloride anion abstraction, which yields perchloroethylene. The total process and the mechanism thereof were verified based on DFT and coupled cluster (CC) calculations. The calculations evaluated feasibility of various pathways in the mechanism. Standard redox potentials for the environmentally relevant species, participating in the studied reactions, were accurately computed employing the explicitly correlated CCSD(T)-F12 method that provides an improved C-Cl bond energy, of essential importance to the dissociative potentials. © 2014 Elsevier Ltd.


Wyrwa A.,AGH University of Science and Technology | Wyrwa A.,Academic Computer Center
Environmental Modelling and Software | Year: 2015

The article demonstrates the features and applicability of the πESA platform designed for optimization of the Poland's power sector considering air pollution and health effects. πESA is comprised of: a bottom-up energy-economic model TIMES-PL, an air quality modelling system Polyphemus and a module for assessment of environmental and health impacts MAEH. It has been designed as a web application employing computational resources of the ZEUS cluster of the PL-Grid infrastructure. The results show, that the impact of carbon prices on the fuel and technological power generation structure is much stronger as compared to impact of fuel prices. Future PM emissions from the centralized power and heat generation sector do not differ much irrespective of energy scenario considered. For analysed cases, the statistical life expectancy in Poland due to long-term exposure to PM2.5 air pollution is reduced on average by approx. 183 days. That gives over 12 million years lost for all cohorts included in the analysis. © 2015 Elsevier Ltd.


Romanczyk P.P.,Cracow University of Technology | Noga K.,Jagiellonian University | Noga K.,Academic Computer Center | Radon M.,Jagiellonian University | And 3 more authors.
Electrochimica Acta | Year: 2013

Two cases of mediated electron transfer are presented: chloroform reduction catalysed by MoII/I alkoxy scorpionates and debromination of hexabromocyclododecane (HBCD) in the presence of free-base tetraphenylporphyrin (H2TPP). Although H2TPP should act as a typical outer-sphere mediator, it is not active towards analogous dehalogenation of 1,2-dibromocyclododecane. The observed phenomena can be rationalised by considering the catalytically relevant transient adducts formed owing to noncovalent interactions (CH hydrogen bonds and dispersive Chalogenâ̄ π interactions or directional halogen bonding), which warrants the close and prolonged contact between the catalyst and its substrate, thus increases the probability of electron transfer, and decisively accelerates the reaction. Crucial for this action is thermodynamic stability of the adducts, which can only be explained if dispersive van der Waals interactions are properly accounted for, e.g., as by dispersion-corrected density functional theory (DFT-D) calculations. The structures involving strong and anisotropic interactions, like the surprisingly short CHâ̄Oalkoxide H-bonding in the MoI-chloroform adduct, may be reasonably well described by standard DFT calculations and the energy needs only be corrected for dispersion without the need for structure re-optimisation at the DFT-D level. The latter is, however, a method of choice for the prediction of supramolecular structures chiefly controlled by weak non-directional van der Waals forces.© 2013 Elsevier Ltd. All rights reserved.


Balis B.,AGH University of Science and Technology | Kowalewski B.,Academic Computer Center | Bubak M.,AGH University of Science and Technology | Bubak M.,Academic Computer Center
Future Generation Computer Systems | Year: 2011

Monitoring systems in Grid infrastructures typically collect and aggregate data originating in distributed agents and store it in global, periodically refreshed repositories. However, in some scenarios access to real-time streams of monitoring information, rather than persistent data sets, would be beneficial. In this paper, we evaluate the Complex Event Processing (CEP) approach applied to real-time Grid monitoring and argue that CEP enables us to achieve two goals, otherwise difficult to combine: real-time access to monitoring data and advanced query capabilities. Monitoring for the purpose of dynamic allocation of Grid resources serves as a case study to demonstrate powerful real-time query capabilities provided by CEP. In addition, we show how to employ CEP for data reduction. For practical verification of our solution, a CEP-based Grid monitoring infrastructure, GEMINI2, has been developed. We have measured the overhead due to CEP-based monitoring and conclude that real-time Grid monitoring is possible without excessive intrusiveness for resources and network. © 2011 Elsevier B.V. All rights reserved.


Romanczyk P.P.,Cracow University of Technology | Radon M.,Jagiellonian University | Radon M.,Academic Computer Center | Noga K.,Jagiellonian University | And 2 more authors.
Physical Chemistry Chemical Physics | Year: 2013

A combined action of the C-H⋯Oalkoxide hydrogen bonding and Cl⋯πpyrazolyl dispersive interactions facilitates intramolecular electron transfer (ET) in the transient {MoI(NO) (TpMe2)(Oalkoxide)}-⋯HCCl3 adduct ([TpMe2]- = κ3-hydrotris(3,5- dimethylpyrazol-1-yl)borate), setting off a radical autocatalytic process, eventually leading to chloroform degradation. In the voltammetric curve, this astonishingly fast process is seen as an almost vertical drop-down. The potential at which it occurs is favorably shifted by ca. 1 V in comparison with uncatalyzed reduction. As predicted by DFT calculations, crucial in the initial step is a close and prolonged contact between the electron donor (MoI 4d-based SOMO) and acceptor (-based LUMO). This occurs owing to the exceptionally short (dH⋯O = 1.82 Å) and nearly linear C-H⋯Oalkoxide bonding, which is reflected by a large ΔνC-H red-shift of 380 cm-1 and a noticeable reorganization of electronic density along the H-bond axis. The advantageous noncovalent interactions inside the cavity formed by two pyrazolyl (pz) rings are strengthened during the C-Cl bond elongation coupled with the ET, giving rise to possible transition state stabilization. After the initial period, the reaction proceeds as a series of consecutive alternating direct or Mo II/I-mediated electron and proton transfers. Alcohols inhibit the electrocatalysis by binding with the {MoI-Oalkoxide} - active site, and olefins by trapping transient radicals. The proximity and stabilization effects, and competitive inhibition in the studied system may be viewed as analogous to those operating in enzymatic catalysis. © 2013 the Owner Societies.


Balis B.,Institute of Computer Science | Balis B.,Academic Computer Center | Kowalewski B.,Academic Computer Center | Bubak M.,Institute of Computer Science | Bubak M.,Academic Computer Center
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2010

Currently existing monitoring services for Grid infrastructures typically collect information from local agents and store it as data sets in global repositories. However, for some scenarios querying real-time streams of monitoring information would be extremely useful. In this paper, we evaluate Complex Event Processing technologies applied to real-time Grid monitoring. We present a monitoring system which uses CEP technologies to expose monitoring information as queryable data streams. We study an example use case - monitoring for job rescheduling. We also employ CEP technologies for data reduction, measure the overhead of monitoring, and conclude that real-time Grid monitoring is possible without excessive intrusiveness for resources and network. © 2010 Springer-Verlag Berlin Heidelberg.


Rycerz K.,Institute of Computer Science | Bubak M.,Institute of Computer Science | Bubak M.,Academic Computer Center
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2016

In this work we investigate possibilities given by the modern technologies as Akka actor platform and Docker toolkit for managing execution of multiscale applications. We present fine-grained (i.e. iteration) level approach to this problem which is rather difficult to address in standard HPC environments with coarse-grained queuing systems. We propose the solution that uses Docker containers as wrappers for computational modules that are components of multiscale applications. This apprach allows for a fine-grained assignment of resources to such modules. We also investigate possibilities of Akka actor framework for building distributed steering systems for such applications with the REST protocol offered by the Spray toolkit. Results of an experiment validation shows that thanks to Docker features, sheduling application on a fine graned iteration level is possible. They also show that using Akka dispatcher as a scheduler for computational tasks (iterations) is a promising approach; moreover the Akka and Spray toolkits do not introduce a significant overhead. © Springer International Publishing Switzerland 2016.


Stelmach M.,Institute of Computer Science AGH UST | Kryza B.,Institute of Computer Science AGH UST | Kryza B.,Academic Computer Center | Slota R.,Institute of Computer Science AGH UST | And 2 more authors.
Procedia Computer Science | Year: 2011

Nowadays, with the broadening usage of distributed systems and Grid, the need for cooperation between many different heterogeneous organizations occurs. Such cooperation usually requires sharing of access to data, service and other tangible or intangible resources. To accomplish such cooperative efforts between organizations, an idea of the Virtual Organization (VO) emerged. It allows the organizations to share resources between the partners, while enforcing proper quality of service and security. In order to enable creation of such Virtual Organization, it is necessary to allow the participants of the VO to negotiation an agreement concerning the rules of cooperation, which will be encoded in a machine processable format. In this paper we present the application of the ESB integration architecture in the specialized distributed contract negotiation service - the FiVO DCNS, which is responsible for distributing contract negotiation events and queries between components of FiVO deployed in different organizations. © 2011 Published by Elsevier Ltd.

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