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Wyniki wyszukiwania dla: parallel computing
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Review of parallel computing methods and tools for FPGA technology
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Parallel Programming for Modern High Performance Computing Systems
PublikacjaIn view of the growing presence and popularity of multicore and manycore processors, accelerators, and coprocessors, as well as clusters using such computing devices, the development of efficient parallel applications has become a key challenge to be able to exploit the performance of such systems. This book covers the scope of parallel programming for modern high performance computing systems. It first discusses selected and...
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Highly parallel distributed computing systems with optical interconnections
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Highly Parallel Distributed Computing System With Optical Interconnections
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Parallel multithread computing for spectroscopic analysis in optical coherence tomography
PublikacjaSpectroscopic Optical Coherence Tomography (SOCT) is an extension of Optical Coherence Tomography (OCT). It allows gathering spectroscopic information from individual scattering points inside the sample. It is based on time-frequency analysis of interferometric signals. Such analysis requires calculating hundreds of Fourier transforms while performing a single A-scan. Additionally, further processing of acquired spectroscopic information...
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Survey of Methodologies, Approaches, and Challenges in Parallel Programming Using High-Performance Computing Systems
PublikacjaThis paper provides a review of contemporary methodologies and APIs for parallel programming, with representative technologies selected in terms of target system type (shared memory, distributed, and hybrid), communication patterns (one-sided and two-sided), and programming abstraction level. We analyze representatives in terms of many aspects including programming model, languages, supported platforms, license, optimization goals,...
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Teaching High–performance Computing Systems – A Case Study with Parallel Programming APIs: MPI, OpenMP and CUDA
PublikacjaHigh performance computing (HPC) education has become essential in recent years, especially that parallel computing on high performance computing systems enables modern machine learning models to grow in scale. This significant increase in the computational power of modern supercomputers relies on a large number of cores in modern CPUs and GPUs. As a consequence, parallel program development based on parallel thinking has become...
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Efficient parallel implementation of crowd simulation using a hybrid CPU+GPU high performance computing system
PublikacjaIn the paper we present a modern efficient parallel OpenMP+CUDA implementation of crowd simulation for hybrid CPU+GPU systems and demonstrate its higher performance over CPU-only and GPU-only implementations for several problem sizes including 10 000, 50 000, 100 000, 500 000 and 1 000 000 agents. We show how performance varies for various tile sizes and what CPU–GPU load balancing settings shall be preferred for various domain...
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Optimization of hybrid parallel application execution in heterogeneous high performance computing systems considering execution time and power consumption
PublikacjaMany important computational problems require utilization of high performance computing (HPC) systems that consist of multi-level structures combining higher and higher numbers of devices with various characteristics. Utilizing full power of such systems requires programming parallel applications that are hybrid in two meanings: they can utilize parallelism on multiple levels at the same time and combine together programming interfaces...
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Machine Learning in Multi-Agent Systems using Associative Arrays
PublikacjaIn this paper, a new machine learning algorithm for multi-agent systems is introduced. The algorithm is based on associative arrays, thus it becomes less complex and more efficient substitute of artificial neural networks and Bayesian networks, which is confirmed by performance measurements. Implementation of machine learning algorithm in multi-agent system for aided design of selected control systems allowed to improve the performance...
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Drawing maps with advice
PublikacjaRozważamy następujący problem obliczeniowy. Agent zostaje umieszczony w wierzchołku nieznanego mu grafu. Wierzchołki grafu są nierozróżnialne, natomiast krawędzie posiadają numery portów. Zadaniem agenta jest wyznaczenie mapy, tzn. obliczenie izomorficznej kopii grafu, lub obliczenie dowolnego drzewa spinającego grafu. Bez dodatkowej informacji zadań tych nie można wykonać. W artykule wyznaczamy oszacowania na minimalną liczbę...
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General Provisioning Strategy for Local Specialized Cloud Computing Environments
PublikacjaThe well-known management strategies in cloud computing based on SLA requirements are considered. A deterministic parallel provisioning algorithm has been prepared and used to show its behavior for three different requirements: load balancing, consolidation, and fault tolerance. The impact of these strategies on the total execution time of different sets of services is analyzed for randomly chosen sets of data. This makes it possible...
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Dynamic Data Management Among Multiple Databases for Optimization of Parallel Computations in Heterogeneous HPC Systems
PublikacjaRapid development of diverse computer architectures and hardware accelerators caused that designing parallel systems faces new problems resulting from their heterogeneity. Our implementation of a parallel system called KernelHive allows to efficiently run applications in a heterogeneous environment consisting of multiple collections of nodes with different types of computing devices. The execution engine of the system is open for...
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Auto-tuning methodology for configuration and application parameters of hybrid CPU + GPU parallel systems based on expert knowledge
PublikacjaAuto-tuning of configuration and application param- eters allows to achieve significant performance gains in many contemporary compute-intensive applications. Feasible search spaces of parameters tend to become too big to allow for exhaustive search in the auto-tuning process. Expert knowledge about the utilized computing systems becomes useful to prune the search space and new methodologies are needed in the face of emerging heterogeneous...
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MERPSYS: An environment for simulation of parallel application execution on large scale HPC systems
PublikacjaIn this paper we present a new environment called MERPSYS that allows simulation of parallel application execution time on cluster-based systems. The environment offers a modeling application using the Java language extended with methods representing message passing type communication routines. It also offers a graphical interface for building a system model that incorporates various hardware components such as CPUs, GPUs, interconnects...
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Benchmarking Parallel Chess Search in Stockfish on Intel Xeon and Intel Xeon Phi Processors
PublikacjaThe paper presents results from benchmarking the parallel multithreaded Stockfish chess engine on selected multi- and many-core processors. It is shown how the strength of play for an n-thread version compares to 1-thread version on both Intel Xeon and latest Intel Xeon Phi x200 processors. Results such as the number of wins, losses and draws are presented and how these change for growing numbers of threads. Impact of using particular...
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Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
PublikacjaWe report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms...
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Parallel Background Subtraction in Video Streams Using OpenCL on GPU Platforms
PublikacjaImplementation of the background subtraction algorithm using OpenCL platform is presented. The algorithm processes live stream of video frames from the surveillance camera in on-line mode. Processing is performed using a host machine and a parallel computing device. The work focuses on optimizing an OpenCL algorithm implementation for GPU devices by taking into account specific features of the GPU architecture, such as memory access,...
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Recognition of hazardous acoustic events employing parallel processing on a supercomputing cluster . Rozpoznawanie niebezpiecznych zdarzeń dźwiękowych z wykorzystaniem równoległego przetwarzania na klastrze superkomputerowym
PublikacjaA method for automatic recognition of hazardous acoustic events operating on a super computing cluster is introduced. The methods employed for detecting and classifying the acoustic events are outlined. The evaluation of the recognition engine is provided: both on the training set and using real-life signals. The algorithms yield sufficient performance in practical conditions to be employed in security surveillance systems. The...
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Towards an efficient multi-stage Riemann solver for nuclear physics simulations
PublikacjaRelativistic numerical hydrodynamics is an important tool in high energy nuclear science. However, such simulations are extremely demanding in terms of computing power. This paper focuses on improving the speed of solving the Riemann problem with the MUSTA-FORCE algorithm by employing the CUDA parallel programming model. We also propose a new approach to 3D finite difference algorithms, which employ a GPU that uses surface memory....
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Assessment of OpenMP Master–Slave Implementations for Selected Irregular Parallel Applications
PublikacjaThe paper investigates various implementations of a master–slave paradigm using the popular OpenMP API and relative performance of the former using modern multi-core workstation CPUs. It is assumed that a master partitions available input into a batch of predefined number of data chunks which are then processed in parallel by a set of slaves and the procedure is repeated until all input data has been processed. The paper experimentally...
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Performance/energy aware optimization of parallel applications on GPUs under power capping
PublikacjaIn the paper we present an approach and results from application of the modern power capping mechanism available for NVIDIA GPUs to the bench- marks such as NAS Parallel Benchmarks BT, SP and LU as well as cublasgemm- benchmark which are widely used for assessment of high performance computing systems’ performance. Specifically, depending on the benchmarks, various power cap configurations are best for desired trade-off of performance...
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Acceleration of the DGF-FDTD method on GPU using the CUDA technology
PublikacjaWe present a parallel implementation of the discrete Green's function formulation of the finite-difference time-domain (DGF-FDTD) method on a graphics processing unit (GPU). The compute unified device architecture (CUDA) parallel computing platform is applied in the developed implementation. For the sake of example, arrays of Yagi-Uda antennas were simulated with the use of DGF-FDTD on GPU. The efficiency of parallel computations...
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Development and tuning of irregular divide-and-conquer applications in DAMPVM/DAC
PublikacjaThis work presents implementations and tuning experiences with parallel irregular applications developed using the object oriented framework DAM-PVM/DAC. It is implemented on top of DAMPVM and provides automatic partitioning of irregular divide-and-conquer (DAC) applications at runtime and dynamic mapping to processors taking into account their speeds and even loads by other user processes. New implementations of parallel applications...
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublikacjaBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
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Network-aware Data Prefetching Optimization of Computations in a Heterogeneous HPC Framework
PublikacjaRapid development of diverse computer architectures and hardware accelerators caused that designing parallel systems faces new problems resulting from their heterogeneity. Our implementation of a parallel system called KernelHive allows to efficiently run applications in a heterogeneous environment consisting of multiple collections of nodes with different types of computing devices. The execution engine of the system is open for...
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A Parallel MPI I/O Solution Supported by Byte-addressable Non-volatile RAM Distributed Cache
PublikacjaWhile many scientific, large-scale applications are data-intensive, fast and efficient I/O operations have become of key importance for HPC environments. We propose an MPI I/O extension based on in-system distributed cache with data located in Non-volatile Random Access Memory (NVRAM) available in each cluster node. The presented architecture makes effective use of NVRAM properties such as persistence and byte-level access behind...
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Minimizing Distribution and Data Loading Overheads in Parallel Training of DNN Acoustic Models with Frequent Parameter Averaging
PublikacjaIn the paper we investigate the performance of parallel deep neural network training with parameter averaging for acoustic modeling in Kaldi, a popular automatic speech recognition toolkit. We describe experiments based on training a recurrent neural network with 4 layers of 800 LSTM hidden states on a 100-hour corpora of annotated Polish speech data. We propose a MPI-based modification of the training program which minimizes the...
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Performance Analysis of the OpenCL Environment on Mobile Platforms
PublikacjaToday’s smartphones have more and more features that so far were only assigned to personal computers. Every year these devices are composed of better and more efficient components. Everything indicates that modern smartphones are replacing ordinary computers in various activities. High computing power is required for tasks such as image processing, speech recognition and object detection. This paper analyses the performance of...
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Use of ICT infrastructure for teaching HPC
PublikacjaIn this paper we look at modern ICT infrastructure as well as curriculum used for conducting a contemporary course on high performance computing taught over several years at the Faculty of Electronics Telecommunications and Informatics, Gdansk University of Technology, Poland. We describe the infrastructure in the context of teaching parallel programming at the cluster level using MPI, node level using OpenMP and CUDA. We present...
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Three levels of fail-safe mode in MPI I/O NVRAM distributed cache
PublikacjaThe paper presents architecture and design of three versions for fail-safe data storage in a distributed cache using NVRAM in cluster nodes. In the first one, cache consistency is assured through additional buffering write requests. The second one is based on additional write log managers running on different nodes. The third one benefits from synchronization with a Parallel File System (PFS) for saving data into a new file which...
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A Regular Expression Matching Application with Configurable Data Intensity for Testing Heterogeneous HPC Systems
PublikacjaModern High Performance Computing (HPC) systems are becoming increasingly heterogeneous in terms of utilized hardware, as well as software solutions. The problems, that we wish to efficiently solve using those systems have different complexity, not only considering magnitude, but also the type of complexity: computation, data or communication intensity. Developing new mechanisms for dealing with those complexities or choosing an...
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Benchmarking Deep Neural Network Training Using Multi- and Many-Core Processors
PublikacjaIn the paper we provide thorough benchmarking of deep neural network (DNN) training on modern multi- and many-core Intel processors in order to assess performance differences for various deep learning as well as parallel computing parameters. We present performance of DNN training for Alexnet, Googlenet, Googlenet_v2 as well as Resnet_50 for various engines used by the deep learning framework, for various batch sizes. Furthermore,...
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Video Analytics-Based Algorithm for Monitoring Egress from Buildings
PublikacjaA concept and practical implementation of the algorithm for detecting of potentially dangerous situations of crowding in passages is presented. An example of such situation is a crush which may be caused by obstructed pedestrian pathway. Surveillance video camera signal analysis performed on line is employed in order to detect hold-ups near bottlenecks like doorways or staircases. The details of implemented algorithm which uses...
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Tuning matrix-vector multiplication on GPU
PublikacjaA matrix times vector multiplication (matvec) is a cornerstone operation in iterative methods of solving large sparse systems of equations such as the conjugate gradients method (cg), the minimal residual method (minres), the generalized residual method (gmres) and exerts an influence on overall performance of those methods. An implementation of matvec is particularly demanding when one executes computations on a GPU (Graphics...
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Parallel computations in the volunteer based Comcute system
PublikacjaThe paper presents Comcute which is a novel multi-level implemen- tation of the volunteer based computing paradigm. Comcute was designed to let users donate the computing power of their PCs in a simplified manner, requiring only pointing their web browser at a specific web address and clicking a mouse. The server side appoints several servers to be in charge of execution of particular tasks. Thanks to that the system can survive...
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Behavior Analysis and Dynamic Crowd Management in Video Surveillance System
PublikacjaA concept and practical implementation of a crowd management system which acquires input data by the set of monitoring cameras is presented. Two leading threads are considered. First concerns the crowd behavior analysis. Second thread focuses on detection of a hold-ups in the doorway. The optical flow combined with soft computing methods (neural network) is employed to evaluate the type of crowd behavior, and fuzzy logic aids detection...
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Distributed NVRAM Cache – Optimization and Evaluation with Power of Adjacency Matrix
PublikacjaIn this paper we build on our previously proposed MPI I/O NVRAM distributed cache for high performance computing. In each cluster node it incorporates NVRAMs which are used as an intermediate cache layer between an application and a file for fast read/write operations supported through wrappers of MPI I/O functions. In this paper we propose optimizations of the solution including handling of write requests with a synchronous mode,...
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The parallel environment for endoscopic image analysis
PublikacjaThe jPVM-oriented environment to support high performance computing required for the Endoscopy Recommender System (ERS) is defined. SPMD model of image matching is considered and its two implementations are proposed: Lexicographical Searching Algorithm (LSA) and Gradient Serching Algorithm (GSA). Three classes of experiments are considered and the relative degree of similarity and execution time of each algorithm are analysed....
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KernelHive: a new workflow-based framework for multilevel high performance computing using clusters and workstations with CPUs and GPUs
PublikacjaThe paper presents a new open-source framework called KernelHive for multilevel parallelization of computations among various clusters, cluster nodes, and finally, among both CPUs and GPUs for a particular application. An application is modeled as an acyclic directed graph with a possibility to run nodes in parallel and automatic expansion of nodes (called node unrolling) depending on the number of computation units available....
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A new deterministic PSO algorithm for real-time systems implemented on low-power devices
PublikacjaThe paper presents a novel, deterministic particle swarm optimization (PSO) algorithm, facilitating its implementation in low-power application specific integrated circuits (ASIC) realized in CMOS technology. The PSO algorithms are commonly used in a variety of optimization problems. They allow to search for a global extreme in a selected fitness function, which is used for numerical modeling of specific optimized problems. The...
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Acceleration of Electromagnetic Simulations on Reconfigurable FPGA Card
PublikacjaIn this contribution, the hardware acceleration of electromagnetic simulations on the reconfigurable field-programmable-gate-array (FPGA) card is presented. In the developed implementation of scientific computations, the matrix-assembly phase of the method of moments (MoM) is accelerated on the Xilinx Alveo U200 card. The computational method involves discretization of the frequency-domain mixed potential integral equation using...
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Performance and Power-Aware Modeling of MPI Applications for Cluster Computing
PublikacjaThe paper presents modeling of performance and power consumption when running parallel applications on modern cluster-based systems. The model includes basic so-called blocks representing either computations or communication. The latter includes both point-to-point and collective communication. Real measurements were performed using MPI applications and routines run on three different clusters with both Infiniband and Gigabit Ethernet...
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Genetic Positioning of Fire Stations Utilizing Grid-computing Platform
PublikacjaA chapter presents a model for determining near-optimal locations of fire stations based on topography of a given area and location of forests, rivers, lakes and other elements of the site. The model is based on principals of genetic algorithms and utilizes the power of the grid to distribute and execute in parallel most performance-demanding computations involved in the algorithm.
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Simulation of Parallel Applications on Large-scale Distributed Systems
PublikacjaThis chapter has a form of a review article in the field of simulating High-Performance Computing systems. We justify the need for a new versatile simulator considering heterogeneity, energy efficiency and reliability of HPC systems. We sketch the problems that need to be solved by such simulator and rationalize using discrete-event simulation for this purpose. Based on a review of existing discrete-event HPC simulation solutions...
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Online sound restoration system for digital library applications
PublikacjaAudio signal processing algorithms were introduced to the new online non-commercial service for audio restoration intended to enhance the content of digitized audio repositories. Missing or distorted audio samples are predicted using neural networks and a specific implementation of the Jannsen interpolation method based on the autoregressive model (AR) combined with the iterative restoring of missing signal samples. Since the distortion...
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Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublikacjaG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
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An MOR Algorithm Based on the Immittance Zero and Pole Eigenvectors for Fast FEM Simulations of Two-Port Microwave Structures
PublikacjaThe aim of this article is to present a novel model-order reduction (MOR) algorithm for fast finite-element frequency-domain simulations of microwave two-port structures. The projection basis used to construct the reduced-order model (ROM) comprises two sets: singular vectors and regular vectors. The first set is composed of the eigenvectors associated with the poles of the finite-element method (FEM) state-space system, while...
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Wpływ kontekstu na efektywność wykonania interaktywnych aplikacji iteracyjnych w dedykowanej przestrzeni usług
PublikacjaTematyka rozprawy dotyczy aplikacji kontekstowych wykonywanych w środowisku czasu rzeczywistego typu *pervasive computing*. To środowisko nazywane jest przestrzenią inteligentną a aplikacje w niej wykonywane określane są jako Interaktywne Aplikacje Iteracyjne (IAI). IAI analizuje w sposób ciągły sytuacje (wyrażone przez kontekst) zachodzące w przestrzeni i w zależności od bieżącego kontekstu podejmuje określone działania. W skład...
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Online sound restoration system for digital library applications.
PublikacjaAudio signal processing algorithms were introduced to the new online non-commercial service for audio restoration intended to enhance the content of digitized audio repositories. Missing or distorted audio samples are predicted using neural networks and a specific implementation of the Jannsen interpolation method based on the autoregressive model (AR) combined with the iterative restoring of missing signal samples. Since the distortion...