Analyzing large-scale DNA Sequences on Multi-core Architectures

Rapid analysis of DNA sequences is important in preventing the evolution of different viruses and bacteria during an early phase, early diagnosis of genetic predispositions to certain diseases (cancer, cardiovascular diseases), and in DNA forensics. However, real-world DNA sequences may comprise several Gigabytes and the process of DNA analysis demands adequate computational resources to be completed within a reasonable time. In this paper we present a scalable approach for parallel DNA analysis that is based on Finite Automata, and which is suitable for analyzing very large DNA segments. We evaluate our approach for real-world DNA segments of mouse (2.7GB), cat (2.4GB), dog (2.4GB), chicken (1GB), human (3.2GB) and turkey (0.2GB). Experimental results on a dual-socket shared-memory system with 24 physical cores show speed-ups of up to 17.6x. Our approach is up to 3x faster than a pattern-based parallel approach that uses the RE2 library.Comment: The 18th IEEE International Conference on Computational Science and Engineering (CSE 2015), Porto, Portugal, 20 - 23 October 201

Genomics, Molecular Imaging, Bioinformatics, and Bio-Nano-Info Integration are Synergistic Components of Translational Medicine and Personalized Healthcare Research

Supported by National Science Foundation (NSF), International Society of Intelligent Biological Medicine (ISIBM), International Journal of Computational Biology and Drug Design and International Journal of Functional Informatics and Personalized Medicine, IEEE 7th Bioinformatics and Bioengineering attracted more than 600 papers and 500 researchers and medical doctors. It was the only synergistic inter/multidisciplinary IEEE conference with 24 Keynote Lectures, 7 Tutorials, 5 Cutting-Edge Research Workshops and 32 Scientific Sessions including 11 Special Research Interest Sessions that were designed dynamically at Harvard in response to the current research trends and advances. The committee was very grateful for the IEEE Plenary Keynote Lectures given by: Dr. A. Keith Dunker (Indiana), Dr. Jun Liu (Harvard), Dr. Brian Athey (Michigan), Dr. Mark Borodovsky (Georgia Tech and President of ISIBM), Dr. Hamid Arabnia (Georgia and Vice-President of ISIBM), Dr. Ruzena Bajcsy (Berkeley and Member of United States National Academy of Engineering and Member of United States Institute of Medicine of the National Academies), Dr. Mary Yang (United States National Institutes of Health and Oak Ridge, DOE), Dr. Chih-Ming Ho (UCLA and Member of United States National Academy of Engineering and Academician of Academia Sinica), Dr. Andy Baxevanis (United States National Institutes of Health), Dr. Arif Ghafoor (Purdue), Dr. John Quackenbush (Harvard), Dr. Eric Jakobsson (UIUC), Dr. Vladimir Uversky (Indiana), Dr. Laura Elnitski (United States National Institutes of Health) and other world-class scientific leaders. The Harvard meeting was a large academic event 100% full-sponsored by IEEE financially and academically. After a rigorous peer-review process, the committee selected 27 high-quality research papers from 600 submissions. The committee is grateful for contributions from keynote speakers Dr. Russ Altman (IEEE BIBM conference keynote lecturer on combining simulation and machine learning to recognize function in 4D), Dr. Mary Qu Yang (IEEE BIBM workshop keynote lecturer on new initiatives of detecting microscopic disease using machine learning and molecular biology, http://ieeexplore.ieee.org/servlet/opac? punumber=4425386) and Dr. Jack Y.Yang (IEEE BIBM workshop keynote lecturer on data mining and knowledge discovery in translational medicine) from the first IEEE Computer Society BioInformatics and BioMedicine (IEEE BIBM) international conference and workshops, November 2- 4, 2007, Silicon Valley, California, USA

HSTREAM: A directive-based language extension for heterogeneous stream computing

Big data streaming applications require utilization of heterogeneous parallel computing systems, which may comprise multiple multi-core CPUs and many-core accelerating devices such as NVIDIA GPUs and Intel Xeon Phis. Programming such systems require advanced knowledge of several hardware architectures and device-specific programming models, including OpenMP and CUDA. In this paper, we present HSTREAM, a compiler directive-based language extension to support programming stream computing applications for heterogeneous parallel computing systems. HSTREAM source-to-source compiler aims to increase the programming productivity by enabling programmers to annotate the parallel regions for heterogeneous execution and generate target specific code. The HSTREAM runtime automatically distributes the workload across CPUs and accelerating devices. We demonstrate the usefulness of HSTREAM language extension with various applications from the STREAM benchmark. Experimental evaluation results show that HSTREAM can keep the same programming simplicity as OpenMP, and the generated code can deliver performance beyond what CPUs-only and GPUs-only executions can deliver.Comment: Preprint, 21st IEEE International Conference on Computational Science and Engineering (CSE 2018

A Failure Adapted, Load-balanced Distributed Routing for Wireless Ad-hoc Sensor Networks

part of 12th IEEE International Conference on Computational Science and Engineering - CSE 2009International audiencethis paper proposes a distributed routing protocol for ad hoc sensor networks which uses Fuzzy Logic. Each sensor uses a Fuzzy decision making process to find the best Cluster Head. Simulation shows that this protocol is able to dynamically adapt to sensors' mobility and failure. By a new load balancing method, it provides also stable clusters and so a cluster head have greater lifetime, which results minimum message exchange and so minimum energy consumption

High performance lattice reduction on heterogeneous computing platform

The final publication is available at Springer via http://dx.doi.org/10.1007/s11227-014-1201-2The lattice reduction (LR) technique has become very important in many engineering fields. However, its high complexity makes difficult its use in real-time applications, especially in applications that deal with large matrices. As a solution, the modified block LLL (MB-LLL) algorithm was introduced, where several levels of parallelism were exploited: (a) fine-grained parallelism was achieved through the cost-reduced all-swap LLL (CR-AS-LLL) algorithm introduced together with the MB-LLL by Jzsa et al. (Proceedings of the tenth international symposium on wireless communication systems, 2013) and (b) coarse-grained parallelism was achieved by applying the block-reduction concept presented by Wetzel (Algorithmic number theory. Springer, New York, pp 323-337, 1998). In this paper, we present the cost-reduced MB-LLL (CR-MB-LLL) algorithm, which allows to significantly reduce the computational complexity of the MB-LLL by allowing the relaxation of the first LLL condition while executing the LR of submatrices, resulting in the delay of the Gram-Schmidt coefficients update and by using less costly procedures during the boundary checks. The effects of complexity reduction and implementation details are analyzed and discussed for several architectures. A mapping of the CR-MB-LLL on a heterogeneous platform is proposed and it is compared with implementations running on a dynamic parallelism enabled GPU and a multi-core CPU. The mapping on the architecture proposed allows a dynamic scheduling of kernels where the overhead introduced is hidden by the use of several CUDA streams. Results show that the execution time of the CR-MB-LLL algorithm on the heterogeneous platform outperforms the multi-core CPU and it is more efficient than the CR-AS-LLL algorithm in case of large matrices.Financial support for this study was provided by grants TAMOP-4.2.1./B-11/2/KMR-2011-0002, TAMOP-4.2.2/B-10/1-2010-0014 from the Pazmany Peter Catholic University, European Union ERDF, Spanish Government through TEC2012-38142-C04-01 project and Generalitat Valenciana through PROMETEO/2009/013 project.Jozsa, CM.; Domene Oltra, F.; Vidal Maciá, AM.; Piñero Sipán, MG.; González Salvador, A. (2014). High performance lattice reduction on heterogeneous computing platform. Journal of Supercomputing. 70(2):772-785. https://doi.org/10.1007/s11227-014-1201-2S772785702Józsa CM, Domene F, Piñero G, González A, Vidal AM (2013) Efficient GPU implementation of lattice-reduction-aided multiuser precoding. In: Proceedings of the tenth international symposium on wireless communication systems (ISWCS 2013)Wetzel S (1998) An efficient parallel block-reduction algorithm. In: Buhler JP (ed) Algorithmic number theory. Lecture notes in computer science, vol 1423. Springer, Berlin, Heidelberg, pp 323–337Wubben D, Seethaler D, Jaldén J, Matz G (2011) Lattice reduction. Signal Process Mag IEEE 28(3):70–91Lenstra AK, Lenstra HW, Lovász L (1982) Factoring polynomials with rational coefficients. Math Ann 261(4):515–534Bremner MR (2012) Lattice basis reduction: an introduction to the LLL algorithm and its applications. CRC Press, USAWu D, Eilert J, Liu D (2008) A programmable lattice-reduction aided detector for MIMO-OFDMA. In: 4th IEEE international conference on circuits and systems for communications (ICCSC 2008), pp 293–297Barbero LG, Milliner DL, Ratnarajah T, Barry JR, Cowan C (2009) Rapid prototyping of Clarkson’s lattice reduction for MIMO detection. In: IEEE international conference on communications (ICC’09), pp 1–5Gestner B, Zhang W, Ma X, Anderson D (2011) Lattice reduction for MIMO detection: from theoretical analysis to hardware realization. IEEE Trans Circ Syst I Regul Pap 58(4):813–826Shabany M, Youssef A, Gulak G (2013) High-throughput 0.13- \upmu μ m CMOS lattice reduction core supporting 880 Mb/s detection. IEEE Trans Very Large Scale Integr (VLSI) Syst 21(5):848–861Luo Y, Qiao S (2011) A parallel LLL algorithm. In: Proceedings of the fourth international C* conference on computer science and software engineering, pp 93–101Backes W, Wetzel S (2011) Parallel lattice basis reduction—the road to many-core. In: IEEE 13th international conference on high performance computing and communications (HPCC)Ahmad U, Amin A, Li M, Pollin S, Van der Perre L, Catthoor F (2011) Scalable block-based parallel lattice reduction algorithm for an SDR baseband processor. In: 2011 IEEE international conference on communications (ICC)Villard G (1992) Parallel lattice basis reduction. In: Papers from the international symposium on symbolic and algebraic computation (ISSAC’92). ACM, New YorkDomene F, Józsa CM, Vidal AM, Piñero G, Gonzalez A (2013) Performance analysis of a parallel lattice reduction algorithm on many-core architectures. In: Proceedings of the 13th international conference on computational and mathematical methods in science and engineeringGestner B, Zhang W, Ma X, Anderson DV (2008) VLSI implementation of a lattice reduction algorithm for low-complexity equalization. In: 4th IEEE international conference on circuits and systems for communications (ICCSC 2008), pp 643–647Burg A, Seethaler D, Matz G (2007) VLSI implementation of a lattice-reduction algorithm for multi-antenna broadcast precoding. In: IEEE international symposium on circuits and systems (ISCAS 2007), pp 673–676Bruderer L, Studer C, Wenk M, Seethaler D, Burg A (2010) VLSI implementation of a low-complexity LLL lattice reduction algorithm for MIMO detection. In: Proceedings of 2010 IEEE international symposium on circuits and systems (ISCAS

Real-time agreement and fulfilment of SLAs in Cloud Computing environments

A Cloud Computing system must readjust its resources by taking into account the demand for its services. This raises the need for designing protocols that provide the individual components of the Cloud architecture with the ability to self-adapt and to reach agreements in order to deal with changes in the services demand. Furthermore, if the Cloud provider has signed a Service Level Agreement (SLA) with the clients of the services that it offers, the appropriate agreement mechanism has to ensure the provision of the service contracted within a specified time. This paper introduces real-time mechanisms for the agreement and fulfilment of SLAs in Cloud Computing environments. On the one hand, it presents a negotiation protocol inspired by the standard WSAgreement used in web services to manage the interactions between the client and the Cloud provider to agree the terms of the SLA of a service. On the other hand, it proposes the application of a real-time argumentation framework for redistributing resources and ensuring the fulfilment of these SLAs during peaks in the service demand.This work is supported by the Spanish government Grants CONSOLIDER-INGENIO 2010 CSD2007-00022, TIN2011-27652-C03-01, TIN2012-36586-C03-01 and TIN2012-36586-C03-03.De La Prieta, F.; Heras Barberá, SM.; Palanca Cámara, J.; Rodríguez, S.; Bajo, J.; Julian Inglada, VJ. (2014). Real-time agreement and fulfilment of SLAs in Cloud Computing environments. AI Communications. 1-24. doi:10.3233/AIC-140626S124[1]V. Aleven and K.D. Ashley, Teaching case-based argumentation through a model and examples, empirical evaluation of an intelligent learning environment, in: Artificial Intelligence in Education, AIED-97, Frontiers in Artificial Intelligence and Applications, Vol. 39, IOS Press, 1997, pp. 87–94.[2]M. Alhamad, W. Perth, T. Dillon and E. Chang, Conceptual SLA framework for cloud computing, in: 4th IEEE International Conference on Digital Ecosystems and Technologies (DEST), IEEE Press, 2010, pp. 606–610.Armbrust, M., Stoica, I., Zaharia, M., Fox, A., Griffith, R., Joseph, A. D., … Rabkin, A. (2010). A view of cloud computing. Communications of the ACM, 53(4), 50. doi:10.1145/1721654.1721672Ashley, K. D. (1991). Reasoning with cases and hypotheticals in HYPO. International Journal of Man-Machine Studies, 34(6), 753-796. doi:10.1016/0020-7373(91)90011-u[6]P. Barham, B. Dragovic, K. Fraser, S. Hand, T. Harris, A. Ho, R. Neugebauer, I. Pratt and A. Warfield, Xen and the art of virtualization, in: 9th ACM Symposium on Operating Systems Principles (SOSP-03), ACM Press, 2003, pp. 164–177.Beloglazov, A., Abawajy, J., & Buyya, R. (2012). Energy-aware resource allocation heuristics for efficient management of data centers for Cloud computing. Future Generation Computer Systems, 28(5), 755-768. doi:10.1016/j.future.2011.04.017[8]A. Beloglazov and R. Buyya, Energy efficient allocation of virtual machines in cloud data centers, in: 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing, IEEE Computer Society, 2010, pp. 577–578.[9]A. Beloglazov and R. Buyya, Energy efficient resource management in virtualized cloud data centers, in: 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing, IEEE Computer Society, 2010, pp. 826–831.Bench-Capon, T., & Sartor, G. (2003). A model of legal reasoning with cases incorporating theories and values. Artificial Intelligence, 150(1-2), 97-143. doi:10.1016/s0004-3702(03)00108-5[11]T.J. Bench-Capon, Specification and implementation of Toulmin dialogue game, in: International Conferences on Legal Knowledge and Information Systems, JURIX-98, Frontiers of Artificial Intelligence and Applications, IOS Press, 1998, pp. 5–20.[12]R. Buyya, R. Ranjan and R.N. Calheiros, Intercloud: Utility-oriented federation of cloud computing environments for scaling of application services, in: 10th International Conference on Algorithms and Architectures for Parallel Processing – Volume Part I, ICA3PP’10, Springer-Verlag, 2010, pp. 13–31.[13]R. Buyya, C.S. Yeo and S. Venugopal, Market-oriented cloud computing: Vision, hype, and reality for delivering it services as computing utilities, in: High Performance Computing and Communications, 2008. HPCC’08. 10th IEEE International Conference, September 2008, IEEE, 2008, pp. 5–13.Chen, C., Li, S. S., Chen, B., & Wen, D. (2011). Agent Recommendation for Agent-Based Urban-Transportation Systems. IEEE Intelligent Systems, 26(6), 77-81. doi:10.1109/mis.2011.94[15]Y.Y. Cheng, M. Low, S. Zhou, W. Cai and C.S. Choo, Evolving agent-based simulations in the clouds, in: 3rd International Workshop on Advanced Computational Intelligence (IWACI), 2010, pp. 244–249.[16]F. Dignum and H. Weigand, Communication and Deontic Logic, in: Information Systems – Correctness and Reusability. Selected Papers from the IS-CORE Workshop, R. Wieringa and R. Feenstra, eds, World Scientific Publishing Co., 1995, pp. 242–260.Erdogmus, H. (2009). Cloud Computing: Does Nirvana Hide behind the Nebula? IEEE Software, 26(2), 4-6. doi:10.1109/ms.2009.31[19]J.O. Fitó, I. Goiri and J. Guitart, SLA-driven elastic cloud hosting provider, in: 18th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP), IEEE Computer Society, 2010, pp. 111–118.Fuentes-Fernández, R., Hassan, S., Pavón, J., Galán, J. M., & López-Paredes, A. (2012). Metamodels for role-driven agent-based modelling. Computational and Mathematical Organization Theory, 18(1), 91-112. doi:10.1007/s10588-012-9110-5Heras, S., Botti, V., & Julián, V. (2009). Challenges for a CBR framework for argumentation in open MAS. The Knowledge Engineering Review, 24(4), 327-352. doi:10.1017/s0269888909990178Heras, S., Jordán, J., Botti, V., & Julián, V. (2013). Argue to agree: A case-based argumentation approach. International Journal of Approximate Reasoning, 54(1), 82-108. doi:10.1016/j.ijar.2012.06.005[24]M. Jensen, J. Schwenk, N. Gruschka and L. Iacono, On technical security issues in cloud computing, in: IEEE International Conference on Cloud Computing, IEEE Press, 2009, pp. 109–116.Kakas, A., Maudet, N., & Moraitis, P. (2005). Modular Representation of Agent Interaction Rules through Argumentation. Autonomous Agents and Multi-Agent Systems, 11(2), 189-206. doi:10.1007/s10458-005-2176-4[26]M.J. Kim, H.G. Yoon and H.K. Lee, MAV: An intelligent Multi-agent model based on Cloud computing for resource virtualization, in: Computers, Networks, Systems, and Industrial Engineering, Studies in Computational Intelligence, Vol. 365, Springer, 2011, pp. 99–111.Kraus, S., Sycara, K., & Evenchik, A. (1998). Reaching agreements through argumentation: a logical model and implementation. Artificial Intelligence, 104(1-2), 1-69. doi:10.1016/s0004-3702(98)00078-2[28]W.-Y. Lin, G.-Y. Lin and H.-Y. Wei, Dynamic auction mechanism for cloud resource allocation, in: 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing, CCGRID’10, IEEE Computer Society, Washington, DC, USA, 2010, pp. 591–592.[29]S. Liu, G. Quan and S. Ren, On-line scheduling of real-time services for cloud computing, in: 6th World Congress on Services, SERVICES’10, IEEE Computer Society, 2010, pp. 459–464.Navarro, M., Heras, S., Botti, V., & Julián, V. (2013). Towards real-time agreements. Expert Systems with Applications, 40(10), 3906-3917. doi:10.1016/j.eswa.2012.12.087Ontañón, S., & Plaza, E. (2011). An argumentation framework for learning, information exchange, and joint-deliberation in multi-agent systems1. Multiagent and Grid Systems, 7(2-3), 95-108. doi:10.3233/mgs-2011-0169Palanca, J., Navarro, M., García-Fornes, A., & Julian, V. (2013). Deadline prediction scheduling based on benefits. Future Generation Computer Systems, 29(1), 61-73. doi:10.1016/j.future.2012.05.007[33]C. Pautasso, O. Zimmermann and F. Leymann, Restful web services vs. “big”’ web services: making the right architectural decision, in: Proceedings of the 17th International Conference on World Wide Web, WWW’08, ACM, New York, NY, USA, 2008, pp. 805–814.[34]J. Peng, X. Zhang, Z. Lei, B. Zhang, W. Zhang and Q. Li, Comparison of several cloud computing platforms, in: 2nd International Symposium on Information Science and Engineering, ISISE’09, IEEE Computer Society, 2009, pp. 23–27.Prakken, H., & Sartor, G. (1998). Artificial Intelligence and Law, 6(2/4), 231-287. doi:10.1023/a:1008278309945[36]I. Rahwan and G. Simari, eds, Argumentation in Artificial Intelligence, Springer, 2009.Ross, J. W., & Westerman, G. (2004). Preparing for utility computing: The role of IT architecture and relationship management. IBM Systems Journal, 43(1), 5-19. doi:10.1147/sj.431.0005Schaffer, H. E. (2009). X as a Service, Cloud Computing, and the Need for Good Judgment. IT Professional, 11(5), 4-5. doi:10.1109/mitp.2009.112[39]K.M. Sim, Agent-based cloud commerce, in: IEEE International Conference on Industrial Engineering and Engineering Management, IEEE Press, 2009, pp. 717–721.Soh, L.-K., & Tsatsoulis, C. (2005). A Real-Time Negotiation Model and A Multi-Agent Sensor Network Implementation. Autonomous Agents and Multi-Agent Systems, 11(3), 215-271. doi:10.1007/s10458-005-0539-5Talia, D. (2012). Clouds Meet Agents: Toward Intelligent Cloud Services. IEEE Internet Computing, 16(2), 78-81. doi:10.1109/mic.2012.28Tolchinsky, P., Modgil, S., Atkinson, K., McBurney, P., & Cortés, U. (2011). Deliberation dialogues for reasoning about safety critical actions. Autonomous Agents and Multi-Agent Systems, 25(2), 209-259. doi:10.1007/s10458-011-9174-5[44]A. Toniolo, T. Norman and K. Sycara, An empirical study of argumentation schemes in deliberative dialogue, in: 20th European Conference on Artificial Intelligence, ECAI-12, Frontiers in Artificial Intelligence and Applications, Vol. 242, IOS Press, 2012, pp. 756–761.[45]W.-T. Tsai, Q. Shao, X. Sun and J. Elston, Real-time service-oriented cloud computing, in: IEEE 6th World Congress on Services, SERVICES’10, IEEE Press, 2010, pp. 473–478.[46]D. Walton, C. Reed and F. Macagno, Argumentation Schemes, Cambridge University Press, 2008.[47]L. Wang, J. Tao, M. Kunze, A. Castellanos, D. Kramer and W. Karl, Scientific cloud computing: Early definition and experience, in: 10th IEEE International Conference on High Performance Computing and Communications (HPCC-08), IEEE Press, 2008, pp. 825–830.[48]Y.O. Yazir, C. Matthews, R. Farahbod, S. Neville, A. Guitouni, S. Ganti and Y. Coady, Dynamic resource allocation in computing clouds using distributed multiple criteria decision analysis, in: IEEE 3rd International Conference on Cloud Computing (CLOUD), IEEE Computer Society, 2010, pp. 91–98.[49]Y. Yu, S. Ren, N. Chen and X. Wang, Profit and penalty aware (pp-aware) scheduling for tasks with variable task execution time, in: ACM Symposium on Applied Computing, SAC’10, ACM, 2010, pp. 334–339

Multi-level Autonomic Business Process Management

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-642-38484-4_14Nowadays, business processes are becoming increasingly complex and heterogeneous. Autonomic Computing principles can reduce this complexity by autonomously managing the software systems and the running processes, their states and evolution. Business Processes that are able to be self-managed are referred to as Autonomic Business Processes (ABP). However, a key challenge is to keep the models of such ABP understandable and expressive in increasingly complex scenarios. This paper discusses the design aspects of an autonomic business process management system able to self-manage processes based on operational adaptation. The goal is to minimize human intervention during the process definition and execution phases. This novel approach, named MABUP, provides four well-defined levels of abstraction to express business and operational knowledge and to guide the management activity; namely, Organizational Level, Technological Level, Operational Level and Service Level. A real example is used to illustrate our proposal.Research supported by CAPES, CNPQ and Spanish Ministry of Science and Innovation.Oliveira, K.; Castro, J.; España Cubillo, S.; Pastor López, O. (2013). Multi-level Autonomic Business Process Management. En Enterprise, Business-Process and Information Systems Modeling. Springer. 184-198. doi:10.1007/978-3-642-38484-4_14S184198España, S., González, A., Pastor, Ó.: Communication Analysis: A Requirements Engineering Method for Information Systems. In: van Eck, P., Gordijn, J., Wieringa, R. (eds.) CAiSE 2009. LNCS, vol. 5565, pp. 530–545. Springer, Heidelberg (2009)Ganek, A.G., Corbi, T.A.: The dawning of the autonomic computing era. IBM Systems Journal 42(1), 5–18 (2003)Gonzalez, A., et al.: Unity criteria for Business Process Modelling. In: Third International Conference on Research Challenges in Information Science, RCIS 2009, pp. 155–164 (2009)Greenwood, D., Rimassa, G.: Autonomic Goal-Oriented Business Process Management. Management, 43 (2007)Haupt, T., et al.: Autonomic execution of computational workflows. In: 2011 Federated Conference on Computer Science and Information Systems, FedCSIS, pp. 965–972 (2011)Kephart, J.O., Chess, D.M.: The vision of autonomic computing. IEEE (2003)Lee, K., et al.: Workflow adaptation as an autonomic computing problem. In: Proceedings of the 2nd Workshop on Workflows in Support of Large-Scale Science, New York, NY, USA, pp. 29–34 (2007)Mosincat, A., Binder, W.: Transparent Runtime Adaptability for BPEL Processes. In: Bouguettaya, A., Krueger, I., Margaria, T. (eds.) ICSOC 2008. LNCS, vol. 5364, pp. 241–255. Springer, Heidelberg (2008)Oliveira, K., et al.: Towards Autonomic Business Process Models. In: International Conference on Software Engineering and Knowledge, SEKE 2012, San Francisco, California, USA (2012)Rahman, M., et al.: A taxonomy and survey on autonomic management of applications in grid computing environments. Concurr. Comput.: Pract. Exper. 23(16), 1990–2019 (2011)Reijers, H.A., Mendling, J.: Modularity in process models: Review and effects. In: Dumas, M., Reichert, M., Shan, M.-C. (eds.) BPM 2008. LNCS, vol. 5240, pp. 20–35. Springer, Heidelberg (2008)Rodrigues Nt., J.A., Monteiro Jr., P.C.L., de O. Sampaio, J., de Souza, J.M., Zimbrão, G.: Autonomic Business Processes Scalable Architecture. In: ter Hofstede, A.H.M., Benatallah, B., Paik, H.-Y. (eds.) BPM Workshops 2007. LNCS, vol. 4928, pp. 78–83. Springer, Heidelberg (2008)Strohmaier, M., Yu, E.: Towards autonomic workflow management systems. ACM Press (2006)Terres, L.D., et al.: Selection of Business Process for Autonomic Automation. In: 2010 14th IEEE International Enterprise Distributed Object Computing Conference, pp. 237–246 (October 2010)Tretola, G., Zimeo, E.: Autonomic internet-scale workflows. In: Proceedings of the 3rd International Workshop on Monitoring, Adaptation and Beyond, New York, NY, USA, pp. 48–56 (2010)Vedam, H., Venkatasubramanian, V.: A wavelet theory-based adaptive trend analysis system for process monitoring and diagnosis. In: Proceedings of the 1997 American Control Conference, vol. 1, pp. 309–313 (June 1997)Wang, Y., Mylopoulos, J.: Self-Repair through Reconfiguration: A Requirements Engineering Approach. In: 2009 IEEE/ACM International Conference on Automated Software Engineering, pp. 257–268 (November 2009)Yu, T., Lin, K.: Adaptive algorithms for finding replacement services in autonomic distributed business processes. In: Proceedings Autonomous Decentralized Systems, ISADS 2005, pp. 427–434 (2005

Parallel SUMIS Soft Detector for Large MIMO Systems on Multicore and GPU

[EN] The number of transmit and receiver antennas is an important factor that affects the performance and complexity of a MIMO system. A MIMO system with very large number of antennas is a promising candidate technology for next generations of wireless systems. However, the vast majority of the methods proposed for conventional MIMO system are not suitable for large dimensions. In this context, the use of high-performance computing systems, such us multicore CPUs and graphics processing units has become attractive for efficient implementation of parallel signal processing algorithms with high computational requirements. In the present work, two practical parallel approaches of the Subspace Marginalization with Interference Suppression detector for large MIMO systems have been proposed. Both approaches have been evaluated and compared in terms of performance and complexity with other detectors for different system parameters.This work has been partially supported by the Spanish MINECO Grant RACHEL TEC2013-47141-C4-4-R, the PROMETEO FASE II 2014/003 Project and FPU AP-2012/71274Ramiro Sánchez, C.; Simarro, MA.; Gonzalez, A.; Vidal Maciá, AM. (2019). Parallel SUMIS Soft Detector for Large MIMO Systems on Multicore and GPU. The Journal of Supercomputing. 75(3):1256-1267. https://doi.org/10.1007/s11227-018-2403-9S12561267753Rusek F, Persson D, Lau BK, Larsson EG, Marzetta TL, Edfors O, Tufvesson F (2013) Scaling up MIMO: opportunities and challenges with very large arrays. IEEE Signal Proc Mag 30(1):40–60Studer C, Burg A, Bölcskei H (2008) Soft-output sphere decoding: algorithms and VLSI implementation. IEEE J Sel Areas Commun 26(2):290–300Wang R, Giannakis GB (2004) Approaching MIMO channel capacity with reduced-complexity soft sphere decoding. In: Wireless Communications and Networking Conference, 2004. WCNC. 2004 IEEE vol 3, pp 1620–1625Persson D, Larsson EG (2011) Partial marginalization soft MIMO detection with higher order constellations. IEEE Trans Signal Procces 59(1):453–458Cîrkić M, Larsson EG (2014) SUMIS: near-optimal soft-in soft-out MIMO detection with low and fixed complexity. IEEE Trans Signal Process 62(12):3084–3097Alberto Gonzalez C, Ramiro, M, Ángeles Simarro, Antonio M Vidal (2017) Parallel SUMIS soft detector for MIMO systems on multicore. In: Proceedings of the 17th International Conference on Computational and Mathematical Methods in Science and Engineering, pp 1729–1736Hochwald BM, ten Brink S (2003) Achieving near-capacity on a multiple-antenna channel. IEEE Trans Commun 51:389–399Kaipeng L, Bei Y, Michael W, Joseph RC, Christoph S (2015) Accelerating massive MIMO uplink detection on GPU for SDR systems. In: 2015 IEEE dallas circuits and systems conference (DCAS), pp 1–4Di W, Eilert J, Liu D (2011) Implementation of a high-speed MIMO soft-output symbol detector for software defined radio. J Signal Process Syst 63(1):27–37Anderson E, Bai Z, Bischof C, Blackford LS, Demmel J, Dongarra J, Du Croz J, Greenbaum A, Hammarling S, McKenney A, Sorensen D (1999) LAPACK users’ guide. SIAM, LondonIntel MKL Reference Manual (2015) https://software.intel.com/en-us/articles/mkl-reference-manualcuBLAS Documentation (2015) http://docs.nvidia.com/cuda/cublasDagum L, Enon R (1998) OpenMP: an industry standard API for shared-memory programming. IEEE Comput Sci Eng 5(1):46–55CUDA Toolkit Documentation, Version 7.5 (2015) https://developer.nvidia.com/cuda-toolkitRoger S, Ramiro C, Gonzalez A, Almenar V, Vidal AM (2012) Fully parallel GPU implementation of a fixed-complexity soft-output MIMO detector. IEEE Trans Veh Technol 61(8):3796–3800Senst M, Ascheid G, Lüders H (2010) Performance evaluation of the markov chain monte carlo MIMO detector based on mutual information. 2010 IEEE International Conference on Communications (ICC), pp 1–

Application of mutual information-based sequential feature selection to ISBSG mixed data

[EN] There is still little research work focused on feature selection (FS) techniques including both categorical and continuous features in Software Development Effort Estimation (SDEE) literature. This paper addresses the problem of selecting the most relevant features from ISBSG (International Software Benchmarking Standards Group) dataset to be used in SDEE. The aim is to show the usefulness of splitting the ranked list of features provided by a mutual information-based sequential FS approach in two, regarding categorical and continuous features. These lists are later recombined according to the accuracy of a case-based reasoning model. Thus, four FS algorithms are compared using a complete dataset with 621 projects and 12 features from ISBSG. On the one hand, two algorithms just consider the relevance, while the remaining two follow the criterion of maximizing relevance and also minimizing redundancy between any independent feature and the already selected features. On the other hand, the algorithms that do not discriminate between continuous and categorical features consider just one list, whereas those that differentiate them use two lists that are later combined. As a result, the algorithms that use two lists present better performance than those algorithms that use one list. Thus, it is meaningful to consider two different lists of features so that the categorical features may be selected more frequently. We also suggest promoting the usage of Application Group, Project Elapsed Time, and First Data Base System features with preference over the more frequently used Development Type, Language Type, and Development Platform.Fernández-Diego, M.; González-Ladrón-De-Guevara, F. (2018). Application of mutual information-based sequential feature selection to ISBSG mixed data. Software Quality Journal. 26(4):1299-1325. https://doi.org/10.1007/s11219-017-9391-5S12991325264Angelis, L., & Stamelos, I. (2000). A simulation tool for efficient analogy based cost estimation. Empirical Software Engineering, 5(1), 35–68. https://doi.org/10.1023/A:1009897800559 .Auer, M., Trendowicz, A., Graser, B., Haunschmid, E., & Biffl, S. (2006). Optimal project feature weights in analogy-based cost estimation: improvement and limitations. Software Engineering, IEEE Transactions on, 32(2), 83–92.Awada, W., Khoshgoftaar, T. M., Dittman, D., Wald, R., Napolitano, A. (2012). A review of the stability of feature selection techniques for bioinformatics data. In 2012 I.E. 13th International Conference on Information Reuse and Integration (IRI) (pp. 356–363). Presented at the 2012 I.E. 13th International Conference on Information Reuse and Integration (IRI). https://doi.org/10.1109/IRI.2012.6303031 .Battiti, R. (1994). Using mutual information for selecting features in supervised neural net learning. Neural Networks, IEEE Transactions, 5(4), 537–550.Bennasar, M., Hicks, Y., & Setchi, R. (2015). Feature selection using joint mutual information maximisation. Expert Systems with Applications, 42(22), 8520–8532. https://doi.org/10.1016/j.eswa.2015.07.007 .Bibi, S., Tsoumakas, G., Stamelos, I., & Vlahavas, I. (2008). Regression via classification applied on software defect estimation. Expert Systems with Applications, 34(3), 2091–2101. https://doi.org/10.1016/j.eswa.2007.02.012 .Chandrashekar, G., & Sahin, F. (2014). A survey on feature selection methods. Computers & Electrical Engineering, 40(1), 16–28.Chatzipetrou, P., Papatheocharous, E., Angelis, L., Andreou, A. S. (2012). An investigation of software effort phase distribution using compositional data analysis. In 2012 38th EUROMICRO Conference on Software Engineering and Advanced Applications (SEAA) (pp. 367–375). Presented at the 2012 38th EUROMICRO Conference on Software Engineering and Advanced Applications (SEAA). https://doi.org/10.1109/SEAA.2012.50 .Chen, Z., Menzies, T., Port, D., & Boehm, B. (2005). Feature subset selection can improve software cost estimation accuracy. In Proceedings of the 2005 workshop on predictor models in software engineering (pp. 1–6). New York: ACM. https://doi.org/10.1145/1082983.1083171 .Chiu, N.-H., & Huang, S.-J. (2007). The adjusted analogy-based software effort estimation based on similarity distances. Journal of Systems and Software, 80(4), 628–640.Dash, M., & Liu, H. (2003). Consistency-based search in feature selection. Artificial Intelligence, 151(1), 155–176.Dejaeger, K., Verbeke, W., Martens, D., & Baesens, B. (2012). Data mining techniques for software effort estimation: a comparative study. Software Engineering, IEEE Transactions on, 38(2), 375–397. https://doi.org/10.1109/TSE.2011.55 .Deng, K., & MacDonell, S. G. (2008). Maximising data retention from the ISBSG repository. In Proceedings of the 12th international conference on evaluation and assessment in software engineering (pp. 21–30). Swinton: British Computer Society http://dl.acm.org/citation.cfm?id=2227115.2227118 . Accessed 21 Jan 2014.Doquire, G., & Verleysen, M. (2011). An hybrid approach to feature selection for mixed categorical and continuous data. In International Conference on Knowledge Discovery and Information Retrieval. http://hdl.handle.net/2078.1/90765 . Accessed 2 Nov 2015.Dudani, S. A. (1976). The distance-weighted k-nearest-neighbor rule. IEEE Transactions on Systems, Man and Cybernetics, SMC, 6(4), 325–327. https://doi.org/10.1109/TSMC.1976.5408784 .Estévez, P. A., Tesmer, M., Perez, C. A., & Zurada, J. M. (2009). Normalized mutual information feature selection. IEEE Transactions on Neural Networks, 20(2), 189–201. https://doi.org/10.1109/TNN.2008.2005601 .Fayyad, U.M., & Irani, K.B. (1993). Multi-Interval Discretization of Continuous-Valued Attributes for Classification Learning. In Proceedings of the International Joint Conference on Uncertainty in AI (pp. 1022–1027). Presented at the International Joint Conference on Uncertainty in AI. https://www.researchgate.net/publication/220815890_Multi-Interval_Discretization_of_Continuous-Valued_Attributes_for_Classification_Learning . Accessed 22 June 2016.Fernández-Diego, M., & González-Ladrón-de-Guevara, F. (2014). Potential and limitations of the ISBSG dataset in enhancing software engineering research: a mapping review. Information and Software Technology, 56(6), 527–544. https://doi.org/10.1016/j.infsof.2014.01.003 .Ferreira, A., & Figueiredo, M. (2011). Unsupervised joint feature discretization and selection. In J. Vitrià, J. M. Sanches, & M. Hernández (Eds.), Pattern recognition and image analysis (Vol. 6669, pp. 200–207). Berlin, Heidelberg: Springer Berlin Heidelberg http://link.springer.com/10.1007/978-3-642-21257-4_25 . Accessed 4 Mar 2016.Fleuret, F. (2004). Fast binary feature selection with conditional mutual information. Journal of Machine Learning Research, 5, 1531–1555.González-Ladrón-de-Guevara, F., Fernández-Diego, M., & Lokan, C. (2016). The usage of ISBSG data fields in software effort estimation: a systematic mapping study. Journal of Systems and Software, 113, 188–215. https://doi.org/10.1016/j.jss.2015.11.040 .Gupta, P., Jain, S., & Jain, A. (2014). A review of fast clustering-based feature subset selection algorithm. International Journal of Scientific & Technology Research, 3(11), 86–91.Guyon, I., & Elisseeff, A. (2003). An introduction to variable and feature selection. The Journal of Machine Learning Research, 3, 1157–1182.Hall, M. A., & Holmes, G. (2003). Benchmarking attribute selection techniques for discrete class data mining. IEEE Transactions on Knowledge and Data Engineering, 15(6), 1437–1447. https://doi.org/10.1109/TKDE.2003.1245283 .Hausser, J., & Strimmer, K. (2009). Entropy inference and the James-Stein estimator, with application to nonlinear gene association networks. Journal of Machine Learning Research, 10(Jul), 1469–1484.Hill, P. (2010). Practical software project estimation: a toolkit for estimating software development effort & duration. McGraw Hill Professional.Hsu, H.-H., Hsieh, C.-W., & Lu, M.-D. (2011). Hybrid feature selection by combining filters and wrappers. Expert Systems with Applications, 38(7), 8144–8150.Huang, S.-J., & Chiu, N.-H. (2006). Optimization of analogy weights by genetic algorithm for software effort estimation. Information and Software Technology, 48(11), 1034–1045. https://doi.org/10.1016/j.infsof.2005.12.020 .Huang, S.-J., Chiu, N.-H., & Liu, Y.-J. (2008). A comparative evaluation on the accuracies of software effort estimates from clustered data. Information and Software Technology, 50(9–10), 879–888. https://doi.org/10.1016/j.infsof.2008.02.005 .Huang, J., Li, Y.-F., & Xie, M. (2015). An empirical analysis of data preprocessing for machine learning-based software cost estimation. Information and Software Technology, 67, 108–127. https://doi.org/10.1016/j.infsof.2015.07.004 .ISBSG. (2013a). ISBSG Dataset Release 12. ISBSG. http://isbsg.org/ . Accessed 1 Mar 2016.ISBSG. (2013b). ISBSG Guidelines Release 12.ISBSG. (2013c). ISBSG Data Demographics Release 12.Jeffery, R., Ruhe, M., Wieczorek, I. (2001). Using public domain metrics to estimate software development effort. In Software Metrics Symposium, 2001. METRICS 2001. Proceedings. Seventh International (pp. 16–27). https://doi.org/10.1109/METRIC.2001.915512 .Jiang, Z., & Comstock, C. (2007). The factors significant to software development productivity. In C. Ardil (Ed.), Proceedings of World Academy of Science, Engineering and Technology, Vol 19 (Vol. 19, pp. 160–164). Presented at the Conference of the World-Academy-of-Science-Engineering-and-Technology, Bangkok: World Acad Sci, Eng & Tech-Waset.Jørgensen, M., Indahl, U., & Sjøberg, D. (2003). Software effort estimation by analogy and ‘regression toward the mean’. Journal of Systems and Software, 68(3), 253–262. https://doi.org/10.1016/S0164-1212(03)00066-9 .Kabir, M. M., Shahjahan, M., & Murase, K. (2011). A new local search based hybrid genetic algorithm for feature selection. Neurocomputing, 74(17), 2914–2928.Kadoda, G., Cartwright, M., Chen, L., Shepperd, M. (2000). Experiences using case-based reasoning to predict software project effort. In EASE 2000 (pp. 2–3). Presented at the EASE 2000, Staffordshire, UK.Keung, J., Kocaguneli, E., & Menzies, T. (2012). Finding conclusion stability for selecting the best effort predictor in software effort estimation. Automated Software Engineering, 20(4), 543–567. https://doi.org/10.1007/s10515-012-0108-5 .Kirsopp, C., Shepperd, M. J., Hart, J. (2002). Search heuristics, case-based reasoning and software project effort prediction. In Proceedings of the Genetic and Evolutionary Computation Conference (pp. 9–13). New York, USA. http://v-scheiner.brunel.ac.uk/handle/2438/1554 . Accessed 27 Jan 2016.Kohavi, R., & John, G. H. (1997). Wrappers for feature subset selection. Artificial Intelligence, 97(1–2), 273–324. https://doi.org/10.1016/S0004-3702(97)00043-X .Kwak, N., & Choi, C.-H. (2002). Input feature selection for classification problems. IEEE Transactions on Neural Networks, 13(1), 143–159. https://doi.org/10.1109/72.977291 .Langdon, W. B., Dolado, J., Sarro, F., & Harman, M. (2016). Exact mean absolute error of baseline predictor, MARP0. Information and Software Technology, 73, 16–18. https://doi.org/10.1016/j.infsof.2016.01.003 .Li, Y. F., Xie, M., & Goh, T. N. (2009). A study of mutual information based feature selection for case based reasoning in software cost estimation. Expert Systems with Applications, 36(3), 5921–5931.Liu, H., & Motoda, H. (2012). Feature selection for knowledge discovery and data mining (Vol. 454). Springer Science & Business Media. https://books.google.es/books?hl=en&lr=&id=aaDbBwAAQBAJ&oi=fnd&pg=PP10&dq=Feature+selection+for+knowledge+discovery+and+data+mining&ots=iuMhcWZGcf&sig=KlmNEIcsBdDVs-m1HUuICfpYZiM . Accessed 25 Jan 2016.Liu, H., & Yu, L. (2005). Toward integrating feature selection algorithms for classification and clustering. IEEE Transactions on Knowledge and Data Engineering, 17(4), 491–502. https://doi.org/10.1109/TKDE.2005.66 .Liu, H., Wei, R., & Jiang, G. (2013). A hybrid feature selection scheme for mixed attributes data. Computational and Applied Mathematics, 32(1), 145–161. https://doi.org/10.1007/s40314-013-0019-5 .Liu, Q., Wang, J., Xiao, J., Zhu, H. (2014). Mutual information based feature selection for symbolic interval data. In International Conference on Software Intelligence Technologies and Applications International Conference on Frontiers of Internet of Things 2014 (pp. 62–69). Presented at the International Conference on Software Intelligence Technologies and Applications International Conference on Frontiers of Internet of Things 2014. https://doi.org/10.1049/cp.2014.1537 .Lokan, C. (2005). What should you optimize when building an estimation model? In Software Metrics, 2005. 11th IEEE International Symposium (pp. 1–10). https://doi.org/10.1109/METRICS.2005.55 .Lokan, C., & Mendes, E. (2009a). Investigating the use of chronological split for software effort estimation. Software, IET, 3(5), 422–434. https://doi.org/10.1049/iet-sen.2008.0107 .Lokan, C., & Mendes, E. (2009b). Applying moving windows to software effort estimation. In Proceedings of the 2009 3rd international symposium on empirical software engineering and measurement (pp. 111–122). Washington, DC: IEEE Computer Society. https://doi.org/10.1109/ESEM.2009.5316019 .Lokan, C., & Mendes, E. (2012). Investigating the use of duration-based moving windows to improve software effort prediction. 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Feature selection based on mutual information criteria of max-dependency, max-relevance, and min-redundancy. IEEE Transactions on Pattern Analysis and Machine Intelligence, 27(8), 1226–1238. https://doi.org/10.1109/TPAMI.2005.159 .R Core Team. (2015). R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing https://www.R-project.org/ .Romanski, P., & Kotthoff, L. (2014). FSelector: Selecting attributes. R package version 0.20. https://CRAN.R-project.org/package=FSelector .Shannon, C. E. (1949). The mathematical theory of communication. Urbana: University of Illinois Press.Shepperd, M., & MacDonell, S. (2012). Evaluating prediction systems in software project estimation. Information and Software Technology, 54(8), 820–827.Shepperd, M., & Schofield, C. (1997). Estimating software project effort using analogies. Software Engineering, IEEE Transactions on, 23(11), 736–743.Somol, P., Pudil, P., & Kittler, J. (2004). 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New prioritized value iteration for Markov decision processes

The problem of solving large Markov decision processes accurately and quickly is challenging. Since the computational effort incurred is considerable, current research focuses on finding superior acceleration techniques. For instance, the convergence properties of current solution methods depend, to a great extent, on the order of backup operations. On one hand, algorithms such as topological sorting are able to find good orderings but their overhead is usually high. On the other hand, shortest path methods, such as Dijkstra's algorithm which is based on priority queues, have been applied successfully to the solution of deterministic shortest-path Markov decision processes. Here, we propose an improved value iteration algorithm based on Dijkstra's algorithm for solving shortest path Markov decision processes. The experimental results on a stochastic shortest-path problem show the feasibility of our approach. © Springer Science+Business Media B.V. 2011.García Hernández, MDG.; Ruiz Pinales, J.; Onaindia De La Rivaherrera, E.; Aviña Cervantes, JG.; Ledesma Orozco, S.; Alvarado Mendez, E.; Reyes Ballesteros, A. (2012). New prioritized value iteration for Markov decision processes. Artificial Intelligence Review. 37(2):157-167. doi:10.1007/s10462-011-9224-zS157167372Agrawal S, Roth D (2002) Learning a sparse representation for object detection. In: Proceedings of the 7th European conference on computer vision. Copenhagen, Denmark, pp 1–15Bellman RE (1954) The theory of dynamic programming. Bull Amer Math Soc 60: 503–516Bellman RE (1957) Dynamic programming. Princeton University Press, New JerseyBertsekas DP (1995) Dynamic programming and optimal control. Athena Scientific, MassachusettsBhuma K, Goldsmith J (2003) Bidirectional LAO* algorithm. 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