Publications

• 2025

  OLŠÁK, O.; BAYER, D.; JAROŠ, J. Accelerating Two-dimensional Wave Propagation Simulations Using Pruned Fast Fourier Transform. 2025 IEEE International Parallel and Distributed Processing Symposium (IPDPS). 2025. p. 0-0.
  

• 2024

  JAROŠ, J.; DUCHOŇ, R. Acceleration of Ultrasound Neurostimulation Using Mixed-Precision Arithmetic. HPDC '24: Proceedings of the 33rd International Symposium on High-Performance Parallel and Distributed Computing. New York: Association for Computing Machinery, 2024. p. 370-372. ISBN: 979-8-4007-0413-0.
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  JAROŠ, J.; TREEBY, B.; JAROŠ, M. k-Plan: From the Hospital to the Cluster and Back. Sydney: 2024. p. 0-0.
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  OLŠÁK, O.; JAROŠ, J. Techniques for Efficient Fourier Transform Computation in Ultrasound Simulations. HPDC '24: Proceedings of the 33nd International Symposium on High-Performance Parallel and Distributed Computing. New York: Association for Computing Machinery, 2024. p. 361-363. ISBN: 979-8-4007-0413-0.
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  OLŠÁK, O.; JAROŠ, J. 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. p. 107-113. ISBN: 979-8-4007-0815-2.
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  JAROŠ, M.; OLŠÁK, O.; JAROŠ, J. System for managing HPC-services and workflow executions. Ostrava: 2024. p. 0-0.
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  OLŠÁK, O.; JAROŠ, J. Techniques for Efficient Fourier Transform Computation in Ultrasound Simulations. Soláň: 2024. p. 0-0.
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  JAROŠ, M.; JAROŠ, J. k-Dispatch: Enabling Cost-Optimized Biomedical Workflow Offloading. HPDC '24: Proceedings of the 33rd International Symposium on High-Performance Parallel and Distributed Computing. New York: Association for Computing Machinery, 2024. p. 358-360. ISBN: 979-8-4007-0413-0.
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  JAROŠ, J.; JAROŠ, M.; BUCHTA, M. 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. p. 1-8. ISBN: 979-8-3503-0836-5.
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• 2023

  BAYER, D.; JAROŠ, J. Acceleration of Heat Diffusion Simulation on Single-Node Systems. Ostrava: 2023. p. 0-0.
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  JAROŠ, M.; JAROŠ, J. Optimization of Execution Parameters of Moldable Ultrasound Workflows Under Incomplete Performance Data. In Job Scheduling Strategies for Parallel Processing. JSSPP 2022. Lecture Notes in Computer Science, LNCS 13592. Virtual Event: Springer Nature Switzerland AG, 2023. p. 152-171. ISBN: 978-3-031-22697-7.
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  OLŠÁK, O.; JAROŠ, M.; JAROŠ, J. System for managing HPC-services and workflow executions. Ostrava: 2023. p. 0-0.
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  CHLEBÍK, J.; JAROŠ, J. 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. p. 635-638. ISBN: 979-8-4007-0120-7.
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• 2022

  OLŠÁK, O.; JAROŠ, J. Evaluation of libraries for the one-dimensional sparse Fourier transform. Ostrava: 2022. p. 0-0.
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  OLŠÁK, O.; JAROŠ, J. Comparison of SpFFT and FFTW3 library. Soláň: 2022. p. 0-0.
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  JAROŠ, M.; JAROŠ, J. k-Dispatch's Performance Modules for Advanced Workflow Submission. Soláň: 2022. p. 0-0.
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  JAROŠ, M.; TREEBY, B.; JAROŠ, J. k-Plan: from the Hospital to the Cluster and back. Ostrava: 2022. p. 0-0.
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  AUBRY, J.; BATES, O.; BOEHM, C.; PAULY, K.; CHRISTENSEN, D.; CUETO, C.; GÉLAT, P.; GUASCH, L.; JAROŠ, J.; JING, Y.; JONES, R.; LI, N.; MARTY, P.; MONTANARO, H.; NEUFELD, E.; PICHARDO, S.; PINTON, G.; PULKKINEN, A.; STANZIOLA, A.; THIELSCHER, A.; TREEBY, B.; VAN 'T WOUT, E. Benchmark problems for transcranial ultrasound simulation: Intercomparison of compressional wave models. Journal of the Acoustical Society of America, 2022, vol. 152, no. 2, p. 1003-1019. ISSN: 1520-8524.
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  KLEPÁRNÍK, P.; ZEMČÍK, P.; TREEBY, B.; JAROŠ, J. 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, 2022, vol. 69, no. 10, p. 2917-2929. ISSN: 1525-8955.
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• 2021

  JAROŠ, M.; SASÁK, T.; TREEBY, B.; JAROŠ, J. 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. p. 116-134. ISBN: 978-3-030-67076-4.
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  WISE, E.; JAROŠ, J.; COX, B.; TREEBY, B. Pseudospectral Time-Domain (PSTD) Methods for the Wave Equation: Realizing Boundary Conditions with Discrete Sine and Cosine Transforms. Journal of Theoretical and Computational Acoustics, 2021, vol. 29, no. 4, p. 2050021-2050021. ISSN: 2591-7285.
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  VAVERKA, F.; TREEBY, B.; JAROŠ, J. 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. p. 99-115. ISBN: 978-3-030-67076-4.
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  JAROŠ, M.; TREEBY, B.; JAROŠ, J. Adaptive Execution Planning in Biomedical Workflow Management Systems. The Platform for Advanced Scientific Computing (PASC) Conference 2021. Geneva: 2021. p. 0-0.
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  JAROŠ, J. Handling C++ Exceptions in MPI Applications. The International Conference for High Performance Computing, Networking, Storage, and Analysis. St. Louis, MO, USA: 2021. p. 0-0.
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  JAROŠ, M.; JAROŠ, J. k-Dispatch's Performance Modules for Advanced Workflow Submission. 5th Users' Conference of IT4Innovations. Ostrava: 2021. p. 0-0.
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  CHLEBÍK, J.; JAROŠ, J. 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. p. 2203-2208. ISBN: 978-1-6654-4207-7.
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  CHLEBÍK, J.; JAROŠ, J. 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. p. 297-298. ISBN: 978-1-4503-8351-6.
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  JAROŠ, M.; JAROŠ, J. Performance-Cost Optimization of Moldable Scientific Workflows. In Job Scheduling Strategies for Parallel Processing. Lecture Notes in Computer Science. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Portland, Oregon USA: Springer International Publishing, 2021. p. 149-167. ISBN: 978-3-030-88223-5. ISSN: 0302-9743.
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  PHAM, K.; NOIMARK, S.; HUYNH, N.; ZHANG, E.; KUKLIŠ, F.; JAROŠ, J.; DESJARDINS, A.; COX, B.; BEARD, P. Broadband all-optical plane-wave ultrasound imaging system based on a Fabry-Perot scanner. IEEE TRANSACTIONS ON ULTRASONICS FERROELECTRICS AND FREQUENCY CONTROL, 2021, vol. 68, no. 4, p. 1007-1016. ISSN: 1525-8955.
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• 2020

  KADLUBIAK, K.; JAROŠ, J. Distributed Multiresolution Pseudospectral Methods for Wave Propagation Simulation. 2020. p. 0-0.
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  MARTIN, E.; JAROŠ, J.; TREEBY, B. Experimental Validation of k-Wave: Nonlinear Wave Propagation in Layered, Absorbing Fluid Media. IEEE TRANSACTIONS ON ULTRASONICS FERROELECTRICS AND FREQUENCY CONTROL, 2020, vol. 67, no. 1, p. 81-91. ISSN: 1525-8955.
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  JAROŠ, M.; TREEBY, B.; GEORGIOU, P.; JAROŠ, J. 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. p. 1-10. ISBN: 978-1-4503-7993-9.
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  TREEBY, B.; WISE, E.; KUKLIŠ, F.; JAROŠ, J.; COX, B. Nonlinear ultrasound simulation in an axisymmetric coordinate system using a k-space pseudospectral method. Journal of the Acoustical Society of America, 2020, vol. 148, no. 4, p. 2288-2300. ISSN: 1520-8524.
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  KUKLIŠ, F.; JAROŠ, M.; JAROŠ, J. 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). Cham: Springer International Publishing, 2020. p. 463-478. ISBN: 978-3-030-43721-3.
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  JAROŠ, M.; KLUSÁČEK, D.; JAROŠ, J. 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). New Orleans: Springer Nature Switzerland AG, 2020. p. 68-84. ISBN: 978-3-030-63170-3.
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• 2019

  WISE, E.; COX, B.; JAROŠ, J.; TREEBY, B. Representing arbitrary acoustic source and sensor distributions in Fourier collocation methods. Journal of the Acoustical Society of America, 2019, vol. 146, no. 1, p. 278-288. ISSN: 1520-8524.
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  TREEBY, B.; JAROŠ, J.; MARTIN, E.; COX, B. From Biology to Bytes: Predicting the Path of Ultrasound Waves Through the Human Body. Acoustics Today, 2019, vol. 15, no. 2, p. 36-44. ISSN: 1557-0223.
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  JAROŠ, M.; TREEBY, B.; JAROŠ, J. Scientific workflow management framework. Soláň: 2019. p. 1 (1 s.).
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  BORDOVSKÝ, G.; JAROŠ, J. On the Complexity of Photoacoustic Tomography: A Trade-off Between Image Quality and Computational Cost. Solaň: 2019. p. 1 (1 s.).
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  JAROŠ, M.; TREEBY, B.; JAROŠ, J. Adaptive Execution Planning in Biomedical Workflow Management Systems. Ostrava: 2019. p. 0-0.
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  VAVERKA, F.; TREEBY, B.; JAROŠ, J. 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. Faro: Springer International Publishing, 2019. p. 577-590. ISBN: 978-3-030-22743-2.
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  VAVERKA, F.; TREEBY, B.; JAROŠ, J. Advancements in Ultrasound Simulations Enabled by High-bandwidth GPU Interconnects. Denver: 2019. p. 0-0.
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  JAROŠ, M.; JAROŠ, J.; TREEBY, B. Adaptive Execution Planning in Workflow Management Systems. Denver: 2019. p. 0-0.
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• 2018

  SUOMI, V.; JAROŠ, J.; TREEBY, B.; CLEVELAND, R. Full modelling of high-intensity focused ultrasound and thermal heating in the kidney of realistic patient models. IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING, 2018, vol. 65, no. 11, p. 2660-2670. ISSN: 0018-9294.
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  TREEBY, B.; BUDISKÝ, J.; WISE, E.; JAROŠ, J.; COX, B. Rapid calculation of acoustic fields from arbitrary continuous-wave sources. Journal of the Acoustical Society of America, 2018, vol. 143, no. 1, p. 529-537. ISSN: 1520-8524.
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  VAVERKA, F.; ŠPEŤKO, M.; TREEBY, B.; JAROŠ, J. Optimization of Ultrasound Simulations on Multi-GPU Servers. Dallas: 2018. p. 1-2.
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  DANTUMA, M.; LUCKA, F.; TREEBY, B.; JAROŠ, J.; COX, B.; MANOHAR, S. Signal Frequency Content and Appearance of Tumors in Photoacoustic Breast Tomography: A Simulation. Caparica: 2018. p. 1 (1 s.).
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  BORDOVSKÝ, G.; COX, B.; JAROŠ, J. Photoacoustic Tomography Using the k-Wave Toolbox. Ostrava: 2018. p. 1 (1 s.).
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  VAVERKA, F.; TREEBY, B.; JAROŠ, J. Running Large-Scale Ultrasound Simulations on Intel Xeon Phi (KNC) accelerators. Ostrava: 2018. p. 1 (1 s.).
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  KADLUBIAK, K.; TREEBY, B.; JAROŠ, J. Fourth-order Time-stepping Scheme in Simulation of Ultrasound Propagation. Ostrava: 2018. p. 1 (1 s.).
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  JAROŠ, M.; TREEBY, B.; JAROŠ, J. Design of HIFU Treatment Plans using an Evolutionary Strategy. Ostrava: 2018. p. 1 (1 s.).
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  KADLUBIAK, K.; JAROŠ, J.; TREEBY, B. GPU-accelerated Simulation of Elastic Wave Propagation. Frankfurt am Main: 2018. p. 0 (1 s.).
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  KLEPÁRNÍK, P.; ZEMČÍK, P.; JAROŠ, J. 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. p. 232-237. ISBN: 978-1-5386-4662-5.
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  KADLUBIAK, K.; JAROŠ, J.; TREEBY, B. 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. p. 188-195. ISBN: 978-1-5386-7878-7.
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  SUOMI, V.; TREEBY, B.; JAROŠ, J.; SAUNAVAARA, J.; KIVINIEMI, A.; BLANCO, R. 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. p. 5701-5704. ISBN: 978-1-5386-3646-6.
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  KLEPÁRNÍK, P.; BAŘINA, D.; ZEMČÍK, P.; JAROŠ, J. Efficient Low-Resource Compression of HIFU Data. Information (Switzerland), 2018, vol. 9, no. 7, p. 1-14. ISSN: 2078-2489.
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  JAROŠ, M.; TREEBY, B.; JAROŠ, J. 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. p. 1568-1575. ISBN: 978-1-4503-5764-7.
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  SUOMI, V.; TREEBY, B.; JAROŠ, J.; MAKELA, P.; ANTTINEN, M.; SAUNAVAARA, J.; SAINIO, T.; KIVINIEMI, A.; BLANCO, R. Transurethral ultrasound therapy of the prostate in the presence of calcifications: a simulation study. MEDICAL PHYSICS, 2018, vol. 45, no. 11, p. 4793-4805. ISSN: 0094-2405.
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  TREEBY, B.; VAVERKA, F.; JAROŠ, J. Performance and Accuracy Analysis of Nonlinear k-Wave Simulations Using Local Domain Decomposition with an 8-GPU Server. Proceedings of Meetings on Acoustics, 2018, vol. 34, no. 1, p. 1-5. ISSN: 1939-800X.
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  KOZUBEK, T.; ČERMÁK, M.; TICHÝ, P.; BLAHETA, R.; ŠÍSTEK, J.; LUKÁŠ, D.; JAROŠ, J. HPCSE: 3rd International Conference on High Performance Computing in Science and Engineering. Lecture Notes in Computer Science. Cham: Springer International Publishing, 2018. p. 0-0. ISBN: 978-3-319-97135-3.
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• 2017

  AHMED, H.; SHAH, T.; GEORGIOU, P.; JAROŠ, J.; PAYNE, H.; ALLEN, C.; GIBSON, E.; BARRATT, D.; TREEBY, B. Beam Distortion Due to Gold Fiducial Markers During Salvage High-Intensity Focused Ultrasound in the Prostate. MEDICAL PHYSICS, 2017, vol. 44, no. 2, p. 679-693. ISSN: 0094-2405.
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  ROBERTSON, J.; COX, B.; JAROŠ, J.; TREEBY, B. Accurate simulation of transcranial ultrasound propagation for ultrasonic neuromodulation and stimulation. Journal of the Acoustical Society of America, 2017, vol. 141, no. 3, p. 1726-1738. ISSN: 1520-8524.
  Detail | WWW | Full text in the Digital Library

  NIKL, V.; HRADECKÝ, M.; JAROŠ, J.; KELEČÉNI, J. 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. Cham: Springer International Publishing, 2017. p. 377-393. ISBN: 978-3-319-58666-3.
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  VAVERKA, F.; TREEBY, B.; JAROŠ, J. Running Large-Scale Ultrasound Simulations on Piz Daint with 512 Pascal GPUs. Denver: 2017. p. 1 (1 s.).
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  VAVERKA, F.; TREEBY, B.; JAROŠ, J. Running Large-Scale Ultrasound Simulations on 256 Salomon Nodes. Ostrava: 2017. p. 1 (1 s.).
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  JAROŠ, J. High Performance Computing in Ultrasound Cancer Treatment. Brno: 2017. p. 0-0.
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  TREEBY, B.; BUDISKÝ, J.; WISE, E.; JAROŠ, J.; COX, B. Single-step Calculation of the Acoustic Field from Arbitrary Continuous-wave Sources. Ostrava: 2017. p. 1 (1 s.).
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  JAROŠ, M.; JAROŠ, J. Framework for Planning, Executing and Monitoring Cooperating Computations. Ostrava: 2017. p. 0-0.
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  KADLUBIAK, K.; TREEBY, B.; JAROŠ, J. Simulation of Ultrasound Propagation in Bone. Ostrava: 2017. p. 1 (1 s.).
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  JAROŠ, J.; TREEBY, B.; ROBERTSON, J. Convergence Testing of a k-space Pseudospectral Scheme for Transcranial Time-reversal Focusing. In Supercomputing in Science and Engineering. Ostrava: VŠB-Technical University of Ostrava - IT4I, 2017. p. 195-197. ISBN: 978-80-248-4037-6.
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  JAROŠ, J.; TREEBY, B.; GEORGIOU, P. Modelling Beam Distortion during Focused Ultrasound Surgery in the Prostate using k-Wave. In Supercomputing in Science and Engineering. Ostrava: VŠB-Technical University of Ostrava - IT4I, 2017. p. 205-207. ISBN: 978-80-248-4037-6.
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  BORDOVSKÝ, G.; JAROŠ, J. Optimization of Fracture Tests Simulation in Civil Engineering. Ostrava: 2017. p. 1 (1 s.).
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• 2016

  JAROŠ, J.; RENDELL, A.; TREEBY, B. Full-wave nonlinear ultrasound simulation on distributed clusters with applications in high-intensity focused ultrasound. International Journal of High Performance Computing Applications, 2016, vol. 30, no. 2, p. 137-155. ISSN: 1741-2846.
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  MERTA, M.; ZAPLETAL, J.; JAROŠ, J. Many Core Acceleration of the Boundary Element Method. In Proceedings of High Performance Computing in Science and Engineering. Lecture Notes in Computer Science. Basel: Springer International Publishing, 2016. p. 116-125. ISBN: 978-3-319-40360-1.
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  BREITENBACHER, D.; HOMOLIAK, I.; JAROŠ, J.; HANÁČEK, P. Impact of Optimization and Parallelism on Factorization Speed of SIQS. In Proceedings of The 20th World Multi-Conference on Systemics, Cybernetics and Informatics. Journal on Systemics, Cybernetics and Informatics. WMSCI 2016 - 20th World Multi-Conference on Systemics, Cybernetics and Informatics, Proceedings. Orlando: The International Institute of Informatics and Systemics, 2016. p. 55-62. ISBN: 978-1-941763-47-6. ISSN: 1690-4524.
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  BROWN, M.; JAROŠ, J.; COX, B.; TREEBY, B. Control of Broadband Optically Generated Ultrasound Pulses Using Binary Amplitude Holograms. Journal of the Acoustical Society of America, 2016, vol. 139, no. 4, p. 1637-1647. ISSN: 1520-8524.
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  JAROŠ, J.; VAVERKA, F.; TREEBY, B. Spectral Domain Decomposition Using Local Fourier Basis: Application to Ultrasound Simulation on a Cluster of GPUs. Salt Lake City: 2016. p. 1 (1 s.).
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  JAROŠ, J.; VAVERKA, F.; TREEBY, B. Spectral Domain Decomposition Using Local Fourier Basis: Application to Ultrasound Simulation on a Cluster of GPUs. International Journal of Supercomputing Frontiers and Innovations, 2016, vol. 3, no. 3, p. 40-55. ISSN: 2313-8734.
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  BREITENBACHER, D.; HOMOLIAK, I.; JAROŠ, J.; HANÁČEK, P. Impact of Optimization and Parallelism on Factorization Speed of SIQS. Journal on Systemics, Cybernetics and Informatics, 2016, vol. 14, no. 3, p. 51-58. ISSN: 1690-4524.
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  SUOMI, V.; JAROŠ, J.; TREEBY, B.; CLEVELAND, R. 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. p. 5648-5651. ISBN: 978-1-4577-0220-4.
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  VAVERKA, F.; TREEBY, B.; JAROŠ, J. Acceleration of Ultrasound Wave Propagation using a Cluster of GPUs. Frankfurt am Main: 2016. p. 1 (1 s.).
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  TREEBY, B.; JAROŠ, J.; COX, B. 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. San Francisco: SPIE - the international society for optics and photonics, 2016. p. 1-14. ISBN: 978-1-62841-942-9.
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• 2015

  GROEN, D.; CHACRA, D.; NASH, R.; JAROŠ, J.; BERNABEU, M.; COVENEY, P. 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. Stockholm: Springer Verlag, 2015. p. 28-38. ISBN: 978-3-319-15975-1.
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  JAROŠ, J.; DOHNAL, M.; TREEBY, B. Large-scale Ultrasound Simulations with Local Fourier Basis Decomposition. The International Conference for High Performance Computing, Networking, Storage Analysis, SC15. Austin: 2015. p. 0-0.
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  JAROŠ, J.; MAREK, J.; MENŠÍK, P. 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. p. 1727-1734. ISBN: 978-1-4799-7560-0.
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  JAROŠ, J.; NIKL, V.; TREEBY, B. Large-scale Ultrasound Simulations Using the Hybrid OpenMP/MPI Decomposition. Proceedings of the 3rd International Conference on Exascale Applications and Software. Edinburgh: Association for Computing Machinery, 2015. p. 115-119. ISBN: 978-0-9926615-1-9.
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• 2014

  ZÁŇ, D.; JAROŠ, J. 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. p. 2933-2939. ISBN: 978-1-4799-1488-3.
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  NIKL, V.; JAROŠ, J. 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. Heidelberg: Springer International Publishing, 2014. p. 100-112. ISBN: 978-3-319-14895-3.
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  TREEBY, B.; JAROŠ, J.; ROHRBACH, D.; COX, B. 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. p. 146-149. ISBN: 978-1-4799-7049-0.
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  JAROŠ, J.; TYRALA, R. 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. p. 1023-1030. ISBN: 978-1-4503-2662-9.
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• 2012

  JAROŠ, J. 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. p. 217-224. ISBN: 978-1-4673-1508-1.
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  JAROŠ, J.; POSPÍCHAL, P. A Fair Comparison of Modern CPUs and GPUs Running the Genetic Algorithm under the Knapsack Benchmark. Lecture Notes in Computer Science, 2012, vol. 2012, no. 7248, p. 426-435. ISSN: 0302-9743.
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• 2011

  DVOŘÁK, V.; JAROŠ, J. A Programmable Interconnection Network for Multiple Communication Patterns. Proceedings of the Sixth International Conference on Systems, ICONS 2011. St. Maarten: International Academy, Research, and Industry Association, 2011. p. 6-11. ISBN: 978-1-61208-002-4.
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  JAROŠ, J.; DVOŘÁK, V. Evolutionary Design of Collective Communications on Wormhole NoCs. In Autonomic Networking-On-Chip: Bio-Inspired Specification, Development, and Verification. Embedded Multi-Core Systems. London: CRC Press LLC, 2011. p. 60-94. ISBN: 978-1-4398-2911-0.
  Detail

  POSPÍCHAL, P.; SCHWARZ, J.; JAROŠ, J. 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. p. 431-438. ISBN: 978-1-4503-0690-4.
  Detail

  JAROŠ, J.; DVOŘÁK, V. Optimizing Collective Communications on the K-port Spidergon Network. Proceedings of the Sixth International Conference on Systems, ICONS 2011. St. Maarten: International Academy, Research, and Industry Association, 2011. p. 24-29. ISBN: 978-1-61208-002-4.
  Detail | WWW

• 2010

  POSPÍCHAL, P.; JAROŠ, J.; SCHWARZ, J. Parallel Genetic Algorithm on the CUDA Architecture. In Applications of Evolutionary Computation. Lecture Notes in Computer Science. Berlin Heidelberg: Springer Verlag, 2010. p. 442-451. ISBN: 978-3-642-12238-5.
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  POSPÍCHAL, P.; SCHWARZ, J.; JAROŠ, J. 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. p. 64-70. ISBN: 978-80-214-4120-0.
  Detail | WWW

  JAROŠ, J. Evolutionary Design of Collective Communications on Wormhole Networks. Brno: Publishing house of Brno University of Technology VUTIUM, 2010. 183 p. ISBN: 978-80-214-4208-5.
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  JAROŠ, J.; DVOŘÁK, V. 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. p. 1171-1178. ISBN: 978-1-4503-0072-8.
  Detail | WWW

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

• 2009

  JAROŠ, J.; SCHWARZ, J. Parallel BMDA with an Aggregation of Probability Models. In Proceeding of 2009 IEEE Congress on Evolutionary Computation. Trondheim: IEEE Computational Intelligence Society, 2009. p. 1683-1690. ISBN: 978-1-4244-2959-2.
  Detail | WWW

  SEKANINA, L.; VAŠÍČEK, Z.; RŮŽIČKA, R.; BIDLO, M.; JAROŠ, J.; ŠVENDA, P. Evoluční hardware: Od automatického generování patentovatelných invencí k sebemodifikujícím se strojům. Edice Gerstner. Edice Gerstner. Praha: Nakladatelství Academia, 2009. 328 p. ISBN: 978-80-200-1729-1.
  Detail

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

• 2008

  JAROŠ, J.; DVOŘÁK, V. 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. p. 1539-1546. ISBN: 978-1-60558-131-6.
  Detail | WWW

  SCHWARZ, J.; JAROŠ, J. Parallel Bivariate Marginal Distribution Algorithm with Probability Model Migration. In Linkage in Evolutionary Computation. LNSC, Studies in Computational Intelligence Vol. 157. Berlin / Heidelberg: Springer Verlag, 2008. p. 3-23. ISBN: 978-3-540-85067-0.
  Detail | WWW

  JAROŠ, J.; SCHWARZ, J. Evoluční návrh wormhole kolektivních komunikací. Proceedings of Junior Scientist Conference 2008. Vienna: Technische Universität Wien, 2008. p. 111-112. ISBN: 978-3-200-01612-5.
  Detail

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

• 2007

  JAROŠ, J. Optimalizace kolektivních komunikací na wormhole propojovacích sítích. Sborník příspěvků semináře Počítačové architektury a diagnostika pro studenty doktorského studia. Plzeň: Západočeská univerzita v Plzni, 2007. p. 93-98. ISBN: 987-80-7043-605-9.
  Detail | WWW

  DVOŘÁK, V.; JAROŠ, J.; OHLÍDAL, M. Optimum Topology-Aware Scheduling of Collective Communications. In Proceedings of The Sixth International Conference on Networking. New York: IEEE Computer Society, 2007. p. 1-6. ISBN: 0-7695-2805-8.
  Detail | WWW

  JAROŠ, J.; SCHWARZ, J. Parallel BMDA with Probability Model Migration. In Proceeding of 2007 IEEE Congress on Evolutionary Computation. Singapore: IEEE Computer Society, 2007. p. 1059-1066. ISBN: 1-4244-1340-0.
  Detail | WWW

  SCHWARZ, J.; JAROŠ, J.; OČENÁŠEK, J. 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. p. 631-631. ISBN: 978-1-59593-697-4.
  Detail | WWW

  JAROŠ, J.; OHLÍDAL, M.; DVOŘÁK, V. An Evolutionary Approach to Collective Communication Scheduling. In 2007 Genetic and Evolutionary Computation Conference. Volume II. New York: Association for Computing Machinery, 2007. p. 2037-2044. ISBN: 978-1-59593-697-4.
  Detail | WWW

• 2006

  OHLÍDAL, M.; JAROŠ, J.; DVOŘÁK, V. 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. p. 619-624. ISBN: 0-7695-2570-9.
  Detail

  JAROŠ, J.; OHLÍDAL, M.; DVOŘÁK, V. 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. p. 127-132. ISBN: 0-7695-2554-7.
  Detail | WWW

  OHLÍDAL, M.; JAROŠ, J.; DVOŘÁK, V.; SCHWARZ, J. Evolutionary Design of OAB and AAB Communication Schedules for Interconnection Networks. In EvoStar 2006. Lecture Notes in Computer Science. Berlin: Springer Verlag, 2006. p. 267-278. ISBN: 978-3-540-33237-4.
  Detail | WWW

  JAROŠ, J.; DVOŘÁK, V. 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. p. 222-223. ISBN: 1-4244-0184-4.
  Detail | WWW

  JAROŠ, J. Evoluční optimalizace skupinových komunikačních vzorů. Zborník príspevkouv pracovného semináre Počítačové architektúry a diagnostika pre studenty doktorského štúdia. Bratislava: Ústav informatiky Slovenskej akadémie vied, 2006. p. 31-36. ISBN: 80-969202-2-7.
  Detail | WWW

  JAROŠ, J.; DVOŘÁK, V. 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. p. 63-68. ISBN: 80-214-3287-X.
  Detail | WWW

• 2005

  JAROŠ, J. Hledání optimálních plánů skupinové komunikace OAB. Sborník příspěvků ze semináře Počítačové Architektury a Diagnostika. Karlovo náměstí 13, Praha: České vysoké učení technické, 2005. p. 67-72. ISBN: 80-01-03298-1.
  Detail

  JAROŠ, J.; OHLÍDAL, M.; DVOŘÁK, V. 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. Berlin: Springer Verlag, 2005. p. 472-481. ISBN: 978-3-540-29414-6.
  Detail

  JAROŠ, J.; DVOŘÁK, V. Speeding-up OAS and AAS Communication in Networking System on Chips. Proc. of 8th IEEE Workshop on Design and Diagnostic of Electronic Circuits and Systems. Sopron: University of West Hungary, 2005. p. 206-209. ISBN: 9639364487.
  Detail

• 2004

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

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

  JAROŠ, J. Vývojové prostředky pro rychlé prototypování genetických algoritmů. Brno: Grantová agentura České republiky, 2004. p. 0-0.
  Detail

  JAROŠ, J. Úloha plánování procesů na paralelním multiprocesorovém systému pomocí bayesovských optimalizačních algoritmů. Zborník príspevkov ze seminara Počítačové Architektury a Diagnostika. Bratislava: Slovenská technická univerzita v Bratislavě, 2004. p. 60-65. ISBN: 80-969202-0-0.
  Detail

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

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