Jiří Jaroš

Publications

• 2024

  HUYNH Trung Nam, ZHANG Edward, FRANCIES Olivia, KUKLIŠ Filip, ALLEN Thomas, ZHU Jiaqi, ABEYAKOON Oshaani, LUCKA Felix, BETCKE Marta, JAROŠ Jiří, ARRIDGE Simon, COX Ben T., PLUMB Andrew and BEARD Paul. A fast all-optical 3D photoacoustic scanner for clinical vascular imaging. Nature Biomedical Engineering, vol. 8, no. 10, 2024, pp. 1-18. ISSN 2157-846X.
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  JAROŠ Jiří and DUCHOŇ Radek. Acceleration of Ultrasound Neurostimulation Using Mixed-Precision Arithmetic. In: HPDC '24: Proceedings of the 33rd International Symposium on High-Performance Parallel and Distributed Computing. New York: Association for Computing Machinery, 2024, pp. 370-372. ISBN 979-8-4007-0413-0.
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  JAROŠ Jiří and BAYER David. afft: a C++17 wrapper library for FFT-like computations on various targets. Soláň, 2024.
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  JAROŠ Jiří, JAROŠ Marta and BUCHTA Martin. Estimation of Distributed Ultrasound Simulation Execution Time Using Machine Learning. In: 2024 IEEE Congress on Evolutionary Computation (CEC). Yokohama: Institute of Electrical and Electronics Engineers, 2024, pp. 1-8. ISBN 979-8-3503-0836-5.
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  OLŠÁK Ondřej and JAROŠ Jiří. Investigating the Possibility of Using Pruned FFT in Ultrasound Wave Propagation Simulations. Ostrava, 2024.
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  JAROŠ Marta and JAROŠ Jiří. k-Dispatch: Enabling Cost-Optimized Biomedical Workflow Offloading. In: HPDC '24: Proceedings of the 33rd International Symposium on High-Performance Parallel and Distributed Computing. New York: Association for Computing Machinery, 2024, pp. 358-360. ISBN 979-8-4007-0413-0.
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  JAROŠ Marta and JAROŠ Jiří. k-Dispatch: Enabling Cost-Optimized Biomedical Workflow Offloading. Solan, 2024.
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  JAROŠ Marta, TREEBY Bradley E. and JAROŠ Jiří. k-Plan: From the Hospital to the Cluster and Back. Sydney, 2024.
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  BAYER David and JAROŠ Jiří. MATLAB Interface To The afft Library. Ostrava, 2024.
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  OLŠÁK Ondřej and JAROŠ Jiří. On the usage of the Sparse Fourier Transform in ultrasound propagation simulation. In: ICBRA '23: Proceedings of the 10th International Conference on Bioinformatics Research and Applications. New York: Association for Computing Machinery, 2024, pp. 107-113. ISBN 979-8-4007-0815-2.
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  JAROŠ Marta, OLŠÁK Ondřej and JAROŠ Jiří. System for managing HPC-services and workflow executions. Ostrava, 2024.
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  OLŠÁK Ondřej and JAROŠ Jiří. Techniques for Efficient Fourier Transform Computation in Ultrasound Simulations. In: HPDC '24: Proceedings of the 33nd International Symposium on High-Performance Parallel and Distributed Computing. New York: Association for Computing Machinery, 2024, pp. 361-363. ISBN 979-8-4007-0413-0.
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  OLŠÁK Ondřej and JAROŠ Jiří. Techniques for Efficient Fourier Transform Computation in Ultrasound Simulations. Soláň, 2024.
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• 2023

  BAYER David and JAROŠ Jiří. Acceleration of Heat Diffusion Simulation on Single-Node Systems. Ostrava, 2023.
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  CHLEBÍK Jakub and JAROŠ Jiří. Evolutionary Exploration of a Neural Network for Predicting Ultrasound Propagation. Ostrava, 2023.
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  CHLEBÍK Jakub and JAROŠ Jiří. Evolutionary Optimization of a Focused Ultrasound Propagation Predictor Neural Network. GECCO 2023 Companion - Proceedings of the 2023 Genetic and Evolutionary Computation Conference Companion. Lisbon: Association for Computing Machinery, 2023. ISBN 979-8-4007-0120-7.
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  JAROŠ Marta and JAROŠ Jiří. Optimization of Execution Parameters of Moldable Ultrasound Workflows Under Incomplete Performance Data. In: Job Scheduling Strategies for Parallel Processing. Lecture Notes in Computer Science, LNCS 13592, vol. 13592. Virtual Event: Springer Nature Switzerland AG, 2023, pp. 152-171. ISBN 978-3-031-22697-7.
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  OLŠÁK Ondřej, JAROŠ Marta and JAROŠ Jiří. System for managing HPC-services and workflow executions. Ostrava, 2023.
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• 2022

  AUBRY Jean-Francois, BATES Oscar, BOEHM Christian, PAULY Kim Butts, CHRISTENSEN Douglas, CUETO Carlos, GÉLAT Pierre, GUASCH Lluis, JAROŠ Jiří, JING Yun, JONES Rebecca, LI Ningrui, MARTY Patrick, MONTANARO Hazael, NEUFELD Esra, PICHARDO Samuel, PINTON Gianmarco, PULKKINEN Aki, STANZIOLA Antonio, THIELSCHER Axel, TREEBY Bradley E. and VAN 't Wout Elwin. Benchmark problems for transcranial ultrasound simulation: Intercomparison of compressional wave models. Journal of the Acoustical Society of America, vol. 152, no. 2, 2022, pp. 1003-1019. ISSN 1520-8524.
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  OLŠÁK Ondřej and JAROŠ Jiří. Comparison of SpFFT and FFTW3 library. Soláň, 2022.
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  OLŠÁK Ondřej and JAROŠ Jiří. Evaluation of libraries for the one-dimensional sparse Fourier transform. Ostrava, 2022.
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  JAROŠ Marta and JAROŠ Jiří. k-Dispatch's Performance Modules for Advanced Workflow Submission. Soláň, 2022.
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  JAROŠ Marta, TREEBY Bradley E. and JAROŠ Jiří. k-Plan: from the Hospital to the Cluster and back. Ostrava, 2022.
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  KLEPÁRNÍK Petr, ZEMČÍK Pavel, TREEBY Bradley E. and JAROŠ Jiří. On-the-Fly Calculation of Time-Averaged Acoustic Intensity in Time-Domain Ultrasound Simulations Using a k-Space Pseudospectral Method. IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, vol. 69, no. 10, 2022, pp. 2917-2929. ISSN 1525-8955.
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• 2021

  JAROŠ Marta, TREEBY Bradley E. and JAROŠ Jiří. Adaptive Execution Planning in Biomedical Workflow Management Systems. The Platform for Advanced Scientific Computing (PASC) Conference 2021. Geneva, 2021.
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  PHAM Khoa, NOIMARK Sacha, HUYNH Nam, ZHANG Edward, KUKLIŠ Filip, JAROŠ Jiří, DESJARDINS Adrien, COX Ben T. and BEARD Paul. Broadband all-optical plane-wave ultrasound imaging system based on a Fabry-Perot scanner. IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, vol. 68, no. 4, 2021, pp. 1007-1016. ISSN 1525-8955.
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  CHLEBÍK Jakub and JAROŠ Jiří. Distributed Evolutionary Design of HIFU Treatment Plans. GECCO 2021 Companion - Proceedings of the 2021 Genetic and Evolutionary Computation Conference Companion. Lille: Association for Computing Machinery, 2021. ISBN 978-1-4503-8351-6.
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  CHLEBÍK Jakub and JAROŠ Jiří. Distributed Evolutionary Design of High Intensity Focused Ultrasound Treatment Plans. In: IEEE International Conference on Systems, Man and Cybernetics . Melbourne: IEEE Circuits and Systems Society, 2021, pp. 2203-2208. ISBN 978-1-6654-4207-7.
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  JAROŠ Marta, SASÁK Tomáš, TREEBY Bradley E. and JAROŠ Jiří. Estimation of Execution Parameters for k-Wave Simulations. In: High Performance Computing in Science and Engineering. HPCSE 2019. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Cham: Springer Nature Switzerland AG, 2021, pp. 116-134. ISBN 978-3-030-67076-4.
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  JAROŠ Jiří. Handling C++ Exceptions in MPI Applications. The International Conference for High Performance Computing, Networking, Storage, and Analysis. St. Louis, MO, USA, 2021.
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  JAROŠ Marta and JAROŠ Jiří. k-Dispatch's Performance Modules for Advanced Workflow Submission. 5th Users' Conference of IT4Innovations. Ostrava, 2021.
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  VAVERKA Filip, TREEBY Bradley E. and JAROŠ Jiří. Performance Evaluation of Pseudospectral Ultrasound Simulations on a Cluster of Xeon Phi Accelerators. In: High Performance Computing in Science and Engineering. HPCSE 2019. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Cham: Springer Nature Switzerland AG, 2021, pp. 99-115. ISBN 978-3-030-67076-4.
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  JAROŠ Marta and JAROŠ Jiří. Performance-Cost Optimization of Moldable Scientific Workflows. In: Job Scheduling Strategies for Parallel Processing. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Portland, Oregon USA: Springer International Publishing, 2021, pp. 149-167. ISBN 978-3-030-88223-5. ISSN 0302-9743.
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  WISE Elliott S., JAROŠ Jiří, COX Ben T. and TREEBY Bradley E. Pseudospectral Time-Domain (PSTD) Methods for the Wave Equation: Realizing Boundary Conditions with Discrete Sine and Cosine Transforms. Journal of Theoretical and Computational Acoustics, vol. 29, no. 4, 2021, pp. 2050021-2050021. ISSN 2591-7285.
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• 2020

  KUKLIŠ Filip, JAROŠ Marta and JAROŠ Jiří. Accelerated Design of HIFU Treatment Plans Using Island-Based Evolutionary Strategy. In: Applications of Evolutionary Computation. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 12104. Cham: Springer International Publishing, 2020, pp. 463-478. ISBN 978-3-030-43721-3.
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  MARTIN Eleanor, JAROŠ Jiří and TREEBY Bradley E. Experimental Validation of k-Wave: Nonlinear Wave Propagation in Layered, Absorbing Fluid Media. IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, vol. 67, no. 1, 2020, pp. 81-91. ISSN 1525-8955.
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  JAROŠ Marta, TREEBY Bradley E., GEORGIOU Panayiotis and JAROŠ Jiří. k-Dispatch: A Workflow Management System for the Automated Execution of Biomedical Ultrasound Simulations on Remote Computing Resources. In: Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2020. New York: Association for Computing Machinery, 2020, pp. 1-10. ISBN 978-1-4503-7993-9.
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  TREEBY Bradley E., WISE Elliott S., KUKLIŠ Filip, JAROŠ Jiří and COX Ben T. Nonlinear ultrasound simulation in an axisymmetric coordinate system using a k-space pseudospectral method. Journal of the Acoustical Society of America, vol. 148, no. 4, 2020, pp. 2288-2300. ISSN 1520-8524.
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  JAROŠ Marta, KLUSÁČEK Dalibor and JAROŠ Jiří. Optimizing Biomedical Ultrasound Workflow Scheduling Using Cluster Simulations. In: Job Scheduling Strategies for Parallel Processing. JSSPP 2020. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 12326. New Orleans: Springer Nature Switzerland AG, 2020, pp. 68-84. ISBN 978-3-030-63170-3.
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• 2019

  JAROŠ Marta, TREEBY Bradley E. and JAROŠ Jiří. Adaptive Execution Planning in Biomedical Workflow Management Systems. Ostrava, 2019.
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  JAROŠ Marta, JAROŠ Jiří and TREEBY Bradley E. Adaptive Execution Planning in Workflow Management Systems. Denver, 2019.
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  VAVERKA Filip, TREEBY Bradley E. and JAROŠ Jiří. Advancements in Ultrasound Simulations Enabled by High-bandwidth GPU Interconnects. Denver, 2019.
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  VAVERKA Filip, TREEBY Bradley E. and JAROŠ Jiří. Evaluation of the Suitability of Intel Xeon Phi Clusters for the Simulation of Ultrasound Wave Propagation using Pseudospectral Methods. In: 19th International Conference on Computational Science 2019, Faro, Portugal, June 12-14, 2019. Lecture Notes in Computer Science, vol. 11538. Faro: Springer International Publishing, 2019, pp. 577-590. ISBN 978-3-030-22743-2.
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  TREEBY Bradley E., JAROŠ Jiří, MARTIN Eleanor and COX Ben T. From Biology to Bytes: Predicting the Path of Ultrasound Waves Through the Human Body. Acoustics Today, vol. 15, no. 2, 2019, pp. 36-44. ISSN 1557-0223.
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  BORDOVSKÝ Gabriel and JAROŠ Jiří. On the Complexity of Photoacoustic Tomography: A Trade-off Between Image Quality and Computational Cost. Solaň, 2019.
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  WISE Elliott S., COX Ben T., JAROŠ Jiří and TREEBY Bradley E. Representing arbitrary acoustic source and sensor distributions in Fourier collocation methods. Journal of the Acoustical Society of America, vol. 146, no. 1, 2019, pp. 278-288. ISSN 1520-8524.
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  JAROŠ Marta, TREEBY Bradley E. and JAROŠ Jiří. Scientific workflow management framework. Soláň, 2019.
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• 2018

  ČUDOVÁ Marta, TREEBY Bradley E. and JAROŠ Jiří. Design of HIFU Treatment Plans using Evolutionary Strategy. In: GECCO 2018 Companion - Proceedings of the 2018 Genetic and Evolutionary Computation Conference Companion. Kyoto: Association for Computing Machinery, 2018, pp. 1568-1575. ISBN 978-1-4503-5764-7.
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  JAROŠ Marta, TREEBY Bradley E. and JAROŠ Jiří. Design of HIFU Treatment Plans using an Evolutionary Strategy. Ostrava, 2018.
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  KLEPÁRNÍK Petr, ZEMČÍK Pavel and JAROŠ Jiří. Efficient Lossy Compression of Ultrasound Data. In: 2017 IEEE International Symposium on Signal Processing and Information Technology, ISSPIT 2017. Bilbao: Institute of Electrical and Electronics Engineers, 2018, pp. 232-237. ISBN 978-1-5386-4662-5.
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  KLEPÁRNÍK Petr, BAŘINA David, ZEMČÍK Pavel and JAROŠ Jiří. Efficient Low-Resource Compression of HIFU Data. Information, vol. 9, no. 7, 2018, pp. 1-14. ISSN 2078-2489.
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  KADLUBIAK Kristián, TREEBY Bradley E. and JAROŠ Jiří. Fourth-order Time-stepping Scheme in Simulation of Ultrasound Propagation. Ostrava, 2018.
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  SUOMI Visa, JAROŠ Jiří, TREEBY Bradley E. and CLEVELAND Robin. Full modelling of high-intensity focused ultrasound and thermal heating in the kidney of realistic patient models. IEEE Transactions on Biomedical Engineering, vol. 65, no. 11, 2018, pp. 2660-2670. ISSN 0018-9294.
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  KADLUBIAK Kristián, JAROŠ Jiří and TREEBY Bradley E. GPU-accelerated Simulation of Elastic Wave Propagation. Frankfurt am Main, 2018.
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  KADLUBIAK Kristián, JAROŠ Jiří and TREEBY Bradley E. GPU-accelerated Simulation of Elastic Wave Propagation. In: Proceedings - 2018 International Conference on High Performance Computing and Simulation, HPCS 2018. Orleans: IEEE Computer Society, 2018, pp. 188-195. ISBN 978-1-5386-7878-7.
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  KOZUBEK Tomáš, ČERMÁK Martin, TICHÝ Petr, BLAHETA Radim, ŠÍSTEK Jakub, LUKÁŠ Dalibor and JAROŠ Jiří, ed. HPCSE: 3rd International Conference on High Performance Computing in Science and Engineering. Lecture Notes in Computer Science, vol. 11087. Cham: Springer International Publishing, 2018. ISBN 978-3-319-97135-3.
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  VAVERKA Filip, ŠPEŤKO Matej, TREEBY Bradley E. and JAROŠ Jiří. Optimization of Ultrasound Simulations on Multi-GPU Servers. Dallas, 2018.
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  TREEBY Bradley E., VAVERKA Filip and JAROŠ Jiří. Performance and Accuracy Analysis of Nonlinear k-Wave Simulations Using Local Domain Decomposition with an 8-GPU Server. Proceedings of Meetings on Acoustics, vol. 34, no. 1, 2018, pp. 1-5. ISSN 1939-800X.
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  BORDOVSKÝ Gabriel, COX Ben T. and JAROŠ Jiří. Photoacoustic Tomography Using the k-Wave Toolbox. Ostrava, 2018.
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  TREEBY Bradley E., BUDISKÝ Jakub, WISE Elliott S., JAROŠ Jiří and COX Ben T. Rapid calculation of acoustic fields from arbitrary continuous-wave sources. Journal of the Acoustical Society of America, vol. 143, no. 1, 2018, pp. 529-537. ISSN 1520-8524.
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  VAVERKA Filip, TREEBY Bradley E. and JAROŠ Jiří. Running Large-Scale Ultrasound Simulations on Intel Xeon Phi (KNC) accelerators. Ostrava, 2018.
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  DANTUMA Maura, LUCKA Felix, TREEBY Bradley E., JAROŠ Jiří, COX Ben T. and MANOHAR Srirang. Signal Frequency Content and Appearance of Tumors in Photoacoustic Breast Tomography: A Simulation. Caparica, 2018.
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  SUOMI Visa, TREEBY Bradley E., JAROŠ Jiří, SAUNAVAARA Jani, KIVINIEMI Aida and BLANCO Roberto. The Effect of Tissue Physiological Variability on Transurethral Ultrasound Therapy of the Prostate. In: 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). Honolulu, HI: Institute of Electrical and Electronics Engineers, 2018, pp. 5701-5704. ISBN 978-1-5386-3646-6.
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  SUOMI Visa, TREEBY Bradley E., JAROŠ Jiří, MAKELA Pietari, ANTTINEN Mikael, SAUNAVAARA Jani, SAINIO Teija, KIVINIEMI Aida and BLANCO Roberto. Transurethral ultrasound therapy of the prostate in the presence of calcifications: a simulation study. Medical Physics, vol. 45, no. 11, 2018, pp. 4793-4805. ISSN 0094-2405.
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• 2017

  ROBERTSON James L., COX Ben T., JAROŠ Jiří and TREEBY Bradley E. Accurate simulation of transcranial ultrasound propagation for ultrasonic neuromodulation and stimulation. Journal of the Acoustical Society of America, vol. 141, no. 3, 2017, pp. 1726-1738. ISSN 1520-8524.
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  AHMED Hashim U., SHAH Taimur T., GEORGIOU Panayiotis, JAROŠ Jiří, PAYNE Heather, ALLEN Clare, GIBSON Eli, BARRATT Dean and TREEBY Bradley E. Beam Distortion Due to Gold Fiducial Markers During Salvage High-Intensity Focused Ultrasound in the Prostate. Medical Physics, vol. 44, no. 2, 2017, pp. 679-693. ISSN 0094-2405.
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  JAROŠ Jiří, TREEBY Bradley E. and ROBERTSON James L. Convergence Testing of a k-space Pseudospectral Scheme for Transcranial Time-reversal Focusing. Supercomputing in Science and Engineering. Ostrava: VŠB-Technical University of Ostrava - IT4I, 2017, pp. 195-197. ISBN 978-80-248-4037-6.
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  ČUDOVÁ Marta and JAROŠ Jiří. Framework for Planning, Executing and Monitoring Cooperating Computations. Ostrava, 2017.
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  JAROŠ Jiří. High Performance Computing in Ultrasound Cancer Treatment. Brno, 2017.
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  JAROŠ Jiří, TREEBY Bradley E. and GEORGIOU Panayiotis. Modelling Beam Distortion during Focused Ultrasound Surgery in the Prostate using k-Wave. Supercomputing in Science and Engineering. Ostrava: VŠB-Technical University of Ostrava - IT4I, 2017, pp. 205-207. ISBN 978-80-248-4037-6.
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  BORDOVSKÝ Gabriel and JAROŠ Jiří. Optimization of Fracture Tests Simulation in Civil Engineering. Ostrava, 2017.
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  VAVERKA Filip, TREEBY Bradley E. and JAROŠ Jiří. Running Large-Scale Ultrasound Simulations on 256 Salomon Nodes. Ostrava, 2017.
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  VAVERKA Filip, TREEBY Bradley E. and JAROŠ Jiří. Running Large-Scale Ultrasound Simulations on Piz Daint with 512 Pascal GPUs. Denver, 2017.
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  TREEBY Bradley E., BUDISKÝ Jakub, WISE Elliott S., JAROŠ Jiří and COX Ben T. Single-step Calculation of the Acoustic Field from Arbitrary Continuous-wave Sources. Ostrava, 2017.
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  NIKL Vojtěch, HRADECKÝ Michal, JAROŠ Jiří and KELEČÉNI Jakub. The investigation of the ARMv7 and Intel Haswell architectures suitability for performance and energy-aware computing. In: High Performance Computing. Lecture Notes in Computer Science, vol. 10266. Cham: Springer International Publishing, 2017, pp. 377-393. ISBN 978-3-319-58666-3.
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• 2016

  VAVERKA Filip, TREEBY Bradley E. and JAROŠ Jiří. Acceleration of Ultrasound Wave Propagation using a Cluster of GPUs. Frankfurt am Main, 2016.
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  TREEBY Bradley E., JAROŠ Jiří and COX Ben T. Advanced photoacoustic image reconstruction using the k-Wave toolbox. In: Progress in Biomedical Optics and Imaging - Proceedings of SPIE. Progress in Biomedical Optics and Imaging - Proceedings of SPIE, vol. 9708. San Francisco: SPIE - the international society for optics and photonics, 2016, pp. 1-14. ISBN 978-1-62841-942-9.
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  BROWN Michael D., JAROŠ Jiří, COX Ben T. and TREEBY Bradley E. Control of Broadband Optically Generated Ultrasound Pulses Using Binary Amplitude Holograms. Journal of the Acoustical Society of America, vol. 139, no. 4, 2016, pp. 1637-1647. ISSN 1520-8524.
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  JAROŠ Jiří, RENDELL Alistair P. and TREEBY Bradley E. Full-wave nonlinear ultrasound simulation on distributed clusters with applications in high-intensity focused ultrasound. International Journal of High Performance Computing Applications, vol. 30, no. 2, 2016, pp. 137-155. ISSN 1741-2846.
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  BREITENBACHER Dominik, HOMOLIAK Ivan, JAROŠ Jiří and HANÁČEK Petr. Impact of Optimization and Parallelism on Factorization Speed of SIQS. In: Proceedings of The 20th World Multi-Conference on Systemics, Cybernetics and Informatics. WMSCI 2016 - 20th World Multi-Conference on Systemics, Cybernetics and Informatics, Proceedings, vol. 1. Orlando: The International Institute of Informatics and Systemics, 2016, pp. 55-62. ISBN 978-1-941763-47-6. ISSN 1690-4524.
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  BREITENBACHER Dominik, HOMOLIAK Ivan, JAROŠ Jiří and HANÁČEK Petr. Impact of Optimization and Parallelism on Factorization Speed of SIQS. Journal on Systemics, Cybernetics and Informatics, vol. 14, no. 3, 2016, pp. 51-58. ISSN 1690-4524.
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  MERTA Michal, ZAPLETAL Jan and JAROŠ Jiří. Many Core Acceleration of the Boundary Element Method. In: Proceedings of High Performance Computing in Science and Engineering. Lecture Notes in Computer Science, vol. 9611. Basel: Springer International Publishing, 2016, pp. 116-125. ISBN 978-3-319-40360-1.
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  SUOMI Visa, JAROŠ Jiří, TREEBY Bradley E. and CLEVELAND Robin. Nonlinear 3-D simulation of high-intensity focused ultrasound therapy in the kidney. In: 38th Annual International Conference of the IEEE-Engineering-in-Medicine-and-Biology-Society (EMBC). Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS. Orlando: Institute of Electrical and Electronics Engineers, 2016, pp. 5648-5651. ISBN 978-1-4577-0220-4.
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  JAROŠ Jiří, VAVERKA Filip and TREEBY Bradley E. Spectral Domain Decomposition Using Local Fourier Basis: Application to Ultrasound Simulation on a Cluster of GPUs. Supercomputing Frontiers and Innovations, vol. 3, no. 3, 2016, pp. 40-55. ISSN 2313-8734.
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  JAROŠ Jiří, VAVERKA Filip and TREEBY Bradley E. Spectral Domain Decomposition Using Local Fourier Basis: Application to Ultrasound Simulation on a Cluster of GPUs. Salt Lake City, 2016.
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• 2015

  JAROŠ Jiří, NIKL Vojtěch and TREEBY Bradley E. Large-scale Ultrasound Simulations Using the Hybrid OpenMP/MPI Decomposition. In: Proceedings of the 3rd International Conference on Exascale Applications and Software. Edinburgh: Association for Computing Machinery, 2015, pp. 115-119. ISBN 978-0-9926615-1-9.
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  JAROŠ Jiří, DOHNAL Matěj and TREEBY Bradley E. Large-scale Ultrasound Simulations with Local Fourier Basis Decomposition. The International Conference for High Performance Computing, Networking, Storage Analysis, SC15. Austin, 2015.
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  JAROŠ Jiří, MAREK Jan and MENŠÍK Pavel. Optimisation of Water Management Systems Using a GPU-Accelerated Differential Evolution. In: Proceedings - 2015 IEEE Symposium Series on Computational Intelligence, SSCI 2015. Cape Town: IEEE Computer Society, 2015, pp. 1727-1734. ISBN 978-1-4799-7560-0.
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  GROEN Derek, CHACRA David A., NASH Rupert W., JAROŠ Jiří, BERNABEU Miguel O. and COVENEY Peter V. Weighted decomposition in high-performance lattice-Boltzmann simulations: are some lattice sites more equal than others?. In: Solving Software Challengesfor Exascale. Lecture Notes in Computer Science, vol. 8759. Stockholm: Springer Verlag, 2015, pp. 28-38. ISBN 978-3-319-15975-1.
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• 2014

  JAROŠ Jiří and TYRALA Radek. GPU-accelerated Evolutionary Design of the Complete Exchange Communication on Wormhole Networks. In: GECCO 2014 - Proceedings of the 2014 Genetic and Evolutionary Computation Conference. New York, NY: Association for Computing Machinery, 2014, pp. 1023-1030. ISBN 978-1-4503-2662-9.
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  TREEBY Bradley E., JAROŠ Jiří, ROHRBACH Daniel and COX Ben T. Modelling Elastic Wave Propagation Using the k-Wave MATLAB Toolbox. In: IEEE International Ultrasonics Symposium, IUS. Chicago, IL: Institute of Electrical and Electronics Engineers, 2014, pp. 146-149. ISBN 978-1-4799-7049-0.
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  NIKL Vojtěch and JAROŠ Jiří. Parallelisation of the 3D Fast Fourier Transform Using the Hybrid OpenMP/MPI Decomposition. In: Mathematical and Engineering Methods in Computer Science. Lecture Notes in Computer Science, vol. 8934. Heidelberg: Springer International Publishing, 2014, pp. 100-112. ISBN 978-3-319-14895-3.
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  ZÁŇ Drahoslav and JAROŠ Jiří. Solving Multidimensional Knapsack Problem using CUDA Accelerated PSO. In: Proceedings of the 2014 IEEE Congress on Evolutionary Computation, CEC 2014. Beijing: IEEE Computational Intelligence Society, 2014, pp. 2933-2939. ISBN 978-1-4799-1488-3.
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• 2013

  BASERMANN Achim, MATURA Gregor, CHEN Fang, FLATKEN Markus, GERNDT Andreas, HETHERINGTON James, KRÜGER Tim, JAROŠ Jiří and NASH Rupert W. Exascale Pre and Post Processing. Barcelona, 2013.
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• 2012

  JAROŠ Jiří and POSPÍCHAL Petr. A Fair Comparison of Modern CPUs and GPUs Running the Genetic Algorithm under the Knapsack Benchmark. Lecture Notes in Computer Science, vol. 2012, no. 7248, pp. 426-435. ISSN 0302-9743.
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  NANDAPALAN Nimalan, JAROŠ Jiří, TREEBY Bradley E. and RENDELL Alistair P. Implementation of 3D FFTs Across Multiple GPUs in Shared Memory Environments. In: Parallel and Distributed Computing, Applications and Technologies, PDCAT Proceedings. Beijing, 2012, pp. 167-172. ISBN 978-0-7695-4879-1.
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  TREEBY Bradley E., JAROŠ Jiří, RENDELL Alistair P. and COX Ben T. Modeling Nonlinear Ultrasound Propagation in Heterogeneous Media with Power Law Absorption using a k-space Pseudospectral Method. Journal of the Acoustical Society of America, vol. 131, no. 6, 2012, pp. 4324-4336. ISSN 1520-8524.
  Detail

  WANG Kejia, TEOH Emily, JAROŠ Jiří and TREEBY Bradley E. Modelling Nonlinear Ultrasound Propagation in Absorbing Media using the k-Wave Toolbox: Experimental Validation. In: IEEE International Ultrasonics Symposium, IUS. Dresden: Institute of Electrical and Electronics Engineers, 2012, pp. 523-526. ISBN 978-1-4673-4561-3.
  Detail

  JAROŠ Jiří. Multi-GPU Island-Based Genetic Algorithm Solving the Knapsack Problem. In: 2012 IEEE Congress on Evolutionary Computation, CEC 2012. CA: Institute of Electrical and Electronics Engineers, 2012, pp. 217-224. ISBN 978-1-4673-1508-1.
  Detail

  JAROŠ Jiří, TREEBY Bradley E. and RENDELL Alistair P. Use of Multiple GPUs on Shared Memory Multiprocessors for Ultrasound Propagation Simulations. In: Australasian Symposium on Parallel and Distributed Computing (AusPDC 2012). Melbourne, 2012, pp. 43-52. ISBN 978-1-921770-08-1.
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• 2011

  DVOŘÁK Václav and JAROŠ Jiří. A Programmable Interconnection Network for Multiple Communication Patterns. In: Proceedings of the Sixth International Conference on Systems, ICONS 2011. St. Maarten: International Academy, Research, and Industry Association, 2011, pp. 6-11. ISBN 978-1-61208-002-4.
  Detail

  POSPÍCHAL Petr, JAROŠ Jiří and SCHWARZ Josef. Acceleration of Grammatical Evolution Using Graphics Processing Units. 7th Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Brno: Brno University of Technology, 2011. ISBN 978-80-214-4305-1.
  Detail

  POSPÍCHAL Petr, SCHWARZ Josef and JAROŠ Jiří. Acceleration of grammatical evolution using graphics processing units: computational intelligence on consumer games and graphics hardware. In: Genetic and Evolutionary Computation Conference, GECCO'11 - Companion Publication. New York: Association for Computing Machinery, 2011, pp. 431-438. ISBN 978-1-4503-0690-4.
  Detail

  JAROŠ Jiří and DVOŘÁK Václav. Evolutionary Design of Collective Communications on Wormhole NoCs. Autonomic Networking-On-Chip: Bio-Inspired Specification, Development, and Verification. Embedded Multi-Core Systems. London: CRC Press LLC, 2011, pp. 60-94. ISBN 978-1-4398-2911-0.
  Detail

  JAROŠ Jiří and DVOŘÁK Václav. Optimizing Collective Communications on the K-port Spidergon Network. In: Proceedings of the Sixth International Conference on Systems, ICONS 2011. St. Maarten: International Academy, Research, and Industry Association, 2011, pp. 24-29. ISBN 978-1-61208-002-4.
  Detail

• 2010

  JAROŠ Jiří. Evolutionary Design of Collective Communications on Wormhole Networks. Brno: Publishing house of Brno University of Technology VUTIUM, 2010. ISBN 978-80-214-4208-5.
  Detail

  JAROŠ Jiří and DVOŘÁK Václav. Evolutionary-Based Conflict-Free Scheduling of Collective Communications on Spidergon NoCs. In: Proceedings of the 12th Annual Genetic and Evolutionary Computation Conference, GECCO '10. New York: Association for Computing Machinery, 2010, pp. 1171-1178. ISBN 978-1-4503-0072-8.
  Detail

  DVOŘÁK Václav and JAROŠ Jiří. Optimizing Collective Communications on 2D-Mesh and Fat Tree NoC. In: 9th International Conference on Networks, ICN 2010. Piscataway, NJ: IEEE Computer Society, 2010, pp. 22-27. ISBN 978-0-7695-3979-9.
  Detail

  POSPÍCHAL Petr, JAROŠ Jiří and SCHWARZ Josef. Parallel Genetic Algorithm on the CUDA Architecture. In: Applications of Evolutionary Computation. Lecture Notes in Computer Science, vol. 6024. Berlin Heidelberg: Springer Verlag, 2010, pp. 442-451. ISBN 978-3-642-12238-5.
  Detail

  POSPÍCHAL Petr, JAROŠ Jiří and SCHWARZ Josef. Parallel Genetic Algorithm on the CUDA Architecture. In: 6th Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Brno: Masaryk University, 2010, pp. 210-2011. ISBN 978-80-87342-10-7.
  Detail

  POSPÍCHAL Petr, SCHWARZ Josef and JAROŠ Jiří. Parallel Genetic Algorithm Solving 0/1 Knapsack Problem Running on the GPU. In: 16th International Conference on Soft Computing MENDEL 2010. Brno: Brno University of Technology, 2010, pp. 64-70. ISBN 978-80-214-4120-0.
  Detail

  KOTÁSEK Zdeněk, BIDLO Michal and JAROŠ Jiří, ed. Počítačové architektury a diagnostika. Brno: Faculty of Information Technology BUT, 2010. ISBN 978-80-214-4140-8.
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• 2009

  SEKANINA Lukáš, VAŠÍČEK Zdeněk, RŮŽIČKA Richard, BIDLO Michal, JAROŠ Jiří and ŠVENDA Petr. Evoluční hardware: Od automatického generování patentovatelných invencí k sebemodifikujícím se strojům. Edice Gerstner. Praha: Academia, 2009. ISBN 978-80-200-1729-1.
  Detail

  JAROŠ Jiří. Evolutionary Optimization of Multistage Interconnection Networks Performance. In: Proceeding of Genetic and Evolutionary Computation Conference, GECCO 2009. New York: Association for Computing Machinery, 2009, pp. 1537-1544. ISBN 978-1-60558-325-9.
  Detail

  JAROŠ Jiří and SCHWARZ Josef. Parallel BMDA with an Aggregation of Probability Models. In: Proceeding of 2009 IEEE Congress on Evolutionary Computation. Trondheim: IEEE Computational Intelligence Society, 2009, pp. 1683-1690. ISBN 978-1-4244-2959-2.
  Detail

• 2008

  JAROŠ Jiří and DVOŘÁK Václav. An Evolutionary Design Technique for Collective Communications on Optimal Diameter-Degree Networks. In: 2008 Genetic and Evolutionary Computational Conference GECCO. New York: Association for Computing Machinery, 2008, pp. 1539-1546. ISBN 978-1-60558-131-6.
  Detail

  JAROŠ Jiří. Evolutionary Design of Fault Tolerant Collective Communications. In: Evolvable Systems: From Biology to Hardware. Lecture Notes in Computer Science, vol. 5216. Berlin: Springer Verlag, 2008, pp. 261-272. ISBN 978-3-540-85856-0.
  Detail

  JAROŠ Jiří and SCHWARZ Josef. Evolutionary Design of Wormhole Switched Collective Communications. In: Proceedings of Junior Scientist Conference 2008. Vienna: Technical University Wien, 2008, p. 2. ISBN 978-3-200-01612-5.
  Detail

  SCHWARZ Josef and JAROŠ Jiří. Parallel Bivariate Marginal Distribution Algorithm with Probability Model Migration. Linkage in Evolutionary Computation. LNSC, Studies in Computational Intelligence Vol. 157. Berlin / Heidelberg: Springer Verlag, 2008, pp. 3-23. ISBN 978-3-540-85067-0.
  Detail

• 2007

  JAROŠ Jiří, OHLÍDAL Miloš and DVOŘÁK Václav. An Evolutionary Approach to Collective Communication Scheduling. In: 2007 Genetic and Evolutionary Computation Conference. Volume II. New York: Association for Computing Machinery, 2007, pp. 2037-2044. ISBN 978-1-59593-697-4.
  Detail

  SCHWARZ Josef, JAROŠ Jiří and OČENÁŠEK Jiří. Migration of Probabilistic Models for Island-Based Bivariate EDA Algorithm. In: 2007 Genetic and Evolutionary Computational Conference. Volume I. New York: Association for Computing Machinery, 2007, pp. 631-631. ISBN 978-1-59593-697-4.
  Detail

  JAROŠ Jiří. Optimalizace kolektivních komunikací na wormhole propojovacích sítích. In: Sborník příspěvků semináře Počítačové architektury a diagnostika pro studenty doktorského studia. Plzeň: University of West Bohemia in Pilsen, 2007, p. 6. ISBN 987-80-7043-605-9.
  Detail

  DVOŘÁK Václav, JAROŠ Jiří and OHLÍDAL Miloš. Optimum Topology-Aware Scheduling of Collective Communications. In: Proceedings of The Sixth International Conference on Networking. New York: IEEE Computer Society, 2007, pp. 1-6. ISBN 0-7695-2805-8.
  Detail

  JAROŠ Jiří and SCHWARZ Josef. Parallel BMDA with Probability Model Migration. In: Proceeding of 2007 IEEE Congress on Evolutionary Computation. Singapore: IEEE Computer Society, 2007, pp. 1059-1066. ISBN 1-4244-1340-0.
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• 2006

  JAROŠ Jiří, OHLÍDAL Miloš and DVOŘÁK Václav. Complexity of Collective Communications on NoCs. In: Proc. of 5th International Symposium on Parallel Computing in Electrical Engineering. Los Alamitos, CA 90720-1314: IEEE Computer Society, 2006, pp. 127-132. ISBN 0-7695-2554-7.
  Detail

  JAROŠ Jiří. Evoluční optimalizace skupinových komunikačních vzorů. In: Zborník príspevkouv pracovného semináre Počítačové architektúry a diagnostika pre studenty doktorského štúdia. Bratislava: Institute of Informatics, Slovak Academy of Sciences, 2006, pp. 31-36. ISBN 80-969202-2-7.
  Detail

  OHLÍDAL Miloš, JAROŠ Jiří, DVOŘÁK Václav and SCHWARZ Josef. Evolutionary Design of OAB and AAB Communication Schedules for Interconnection Networks. In: EvoStar 2006. Lecture Notes in Computer Science, vol. 3907. Berlin: Springer Verlag, 2006, pp. 267-278. ISBN 978-3-540-33237-4.
  Detail

  JAROŠ Jiří and DVOŘÁK Václav. Evolutionary Design of OAB and AAB Communication Schedules for Networking Systems on Chips. In: Proc. of 2006 IEEE Design and Diagnostics of Electronic Circuits and Systems Workshop. Praha: IEEE Computer Society, 2006, pp. 222-223. ISBN 1-4244-0184-4.
  Detail

  JAROŠ Jiří and DVOŘÁK Václav. Evolutionary Design of OAB and AAB Communication Schedules for Networking Systems on Chips. In: MEMICS 2006 Second Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Mikulov: Masaryk University, 2006, pp. 63-68. ISBN 80-214-3287-X.
  Detail

  OHLÍDAL Miloš, JAROŠ Jiří and DVOŘÁK Václav. Performance of Collective Communications on Interconnection Networks with Fat Nodes and Edges. In: Proceedings of the Fifth International Conference on Networking ICN 2006. Los Alamitos: IEEE Computer Society, 2006, pp. 619-624. ISBN 0-7695-2570-9.
  Detail

• 2005

  JAROŠ Jiří, OHLÍDAL Miloš and DVOŘÁK Václav. Evolutionary Design of Group Communication Schedules for Interconnection Networks. In: Proceedings of the 20th International Symposium Computer and Information Sciences - ISCIS 2005. Lecture Notes in Computer Science, vol. 3733. Berlin: Springer Verlag, 2005, pp. 472-481. ISBN 978-3-540-29414-6.
  Detail

  JAROŠ Jiří. Hledání optimálních plánů skupinové komunikace OAB. In: Sborník příspěvků ze semináře Počítačové Architektury a Diagnostika. Karlovo náměstí 13, Praha: Czech Technical University, 2005, pp. 67-72. ISBN 80-01-03298-1.
  Detail

  JAROŠ Jiří and DVOŘÁK Václav. Speeding-up OAS and AAS Communication in Networking System on Chips. In: Proc. of 8th IEEE Workshop on Design and Diagnostic of Electronic Circuits and Systems. Sopron: University of West Hungary, 2005, p. 4. ISBN 9639364487.
  Detail

• 2004

  SCHWARZ Josef and JAROŠ Jiří. A PROBLEM KNOWLEDGE BASED BAYESIAN OPTIMIZATION ALGORITHM APPLIED IN MULTIPROCESSOR SCHEDULING. In: Mendel Conference on Soft Computing. Brno: Faculty of Mechanical Engineering BUT, 2004, pp. 83-88. ISBN 80-214-2676-4.
  Detail

  SCHWARZ Josef, OČENÁŠEK Jiří and JAROŠ Jiří. Advanced Bayesian Optimization Algorithms Applied in Decomposition Problems. In: Proceedings of ECBS 2004. Los Alamitos: IEEE Computer Society, 2004, pp. 102-111. ISBN 0-7695-2125-8.
  Detail

  JAROŠ Jiří and SCHWARZ Josef. Development tools for rapid prototyping of evolutionary algorithms. In: Proceedings of 38th International conference MOSIS'04. Rožnov pod Radhoštěm, 2004, pp. 97-104. ISBN 80-85988-98-4.
  Detail

  JAROŠ Jiří. Úloha plánování procesů na paralelním multiprocesorovém systému pomocí bayesovských optimalizačních algoritmů. In: Zborník príspevkov ze seminara Počítačové Architektury a Diagnostika. Bratislava: Slovak University of Technology in Bratislava, 2004, pp. 60-65. ISBN 80-969202-0-0.
  Detail

  JAROŠ Jiří. Vývojové prostředky pro rychlé prototypování genetických algoritmů. Brno: Czech Science Foundation, 2004.
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