Volume 3(64)

CONTENTS

  1. Abotaleb M. S. A. Establishing the significance of the coefficients of the quasi-linear equation of N-factor autoregression
  2. Gerb A.R., Deviatykh E.E., Omarova G. A. Graph reduction methods in chemical kinetics models
  3. Mischenko E. A., Demin I. Yu. Applying machine learning for segmentation of skeletal muscle ultrasound images
  4. Rybkin A. V., Smirnov R. 0., Kotikhina E. E., Karchkov D. A., Moskalenko V. A., Osipov G. V., Smirnov L. A. Analysis of epicardial electrograms using artificial intelligence
  5. Romanyuta A. A., Kurnosov M. G. Algorithms for MPI All-to-all exchange using shared memory

M.S.A. Abotaleb.

South Ural State University 454080, Chelyabinsk, Russia

ESTABLISHING THE SIGNIFICANCE OF THE COEFFICIENTS OF THE QUASI-LINEAR EQUATION OF N-FACTOR AUTOREGRESSION

DOI: 10.24412/2073-0667-2024-3-5-28
EDN: TIKBLU

This article conducts a thorough analysis of the Generalized Least Deviation Method (GLDM) applied to time series forecasting. The study concentrates on establishing the optimal model order and identifying conditions that lead to zero coefficients. Central to this analysis is the GLDM Estimator, which determines the coefficients {cij}j"^ by minimizing an objective function F(a), expressed as the sum of the arctangents of the absolute deviations from the time series data {yt}f=1 which belongs to R. The adaptability of GLDM to capture complex dataset interactions is examined, highlighting how it adjusts to different model orders. It is shown that the appropriate model order depends not only on the dataset size but also on the inherent data characteristics, which govern the model’s complexity. For example, the data for temperature, with its significant seasonal variations and autocorrelations, requires a fifth-order model, whereas wind speed and COVID-19 death counts in Russia are suitably modeled by a second-order framework. The paper also explores the subtleties of higher-order models and suggests a custom strategy for model selection that enhances the accuracy and interpretability of time series forecasting predictions.

Key words: Time series forecasting, Generalized Least Deviation Method, predictive modeling coefficients.

 
 

Bibliographic reference: Abotaleb M. S. A. Establishing the significance of the coefficients of the quasi-linear equation of N-factor autoregression //journal “Problems of informatics”. 2024, № 3. P.5-28. DOI: 10.24412/2073-0667-2024-3-28. EDN: TIKBLU


A. R. Gerb, E. E. Deviatykh*, G.A. Omarova

Institute of Computational Mathematics and Mathematical Geophysics SB RAS, 630090, Novosibirsk, Russia
* Novosibirsk State University, 630090, Novosibirsk, Russia

GRAPH REDUCTION METHODS IN CHEMICAL KINETICS MODELS

DOI: 10.24412/2073-0667-2024-3-29-46
EDN: DBIOYQ
 
The work is devoted to the study and analysis of graph reduction algorithms in chemical kinetics models. A comparative study of pyMARS based on the supported methods DRG, DRGEP,
PFA is carried out. The “pros” and “cons” of the pyMARS software package are reflected.

The study was carried out within the framework of the scientific program of the National Center for Physics and Mathematics (the project “Mathematical modeling on supercomputers with exa- and zettaflop performance”

Key words: graph, reduction, chemical kinetics model, DRG, DRGEP, PFA, pyMARS.

 

Bibliographic reference: Gerb A.R., Deviatykh E.E., Omarova G. A. Graph reduction methods in chemical kinetics models //journal “Problems of informatics”. 2024, № 3. P.29-46. DOI: 10.24412/2073-0667-2024-3-29-46. EDN: DBIOYQ


E. A. Mischenko, I. Yu. Demin

Lobachevsky State University, 603022, Nizhny Novgorod, Russia

APPLYING MACHINE LEARNING FOR SEGMENTATION OF SKELETAL MUSCLE ULTRASOUND IMAGES

DOI: 10.24412/2073-0667-2024-3-47-57
EDN: LTKQYZ

 

This paper discusses the use of machine learning techniques for segmenting ultrasound images of human skeletal muscles. Ultrasound is a non-invasive diagnostic tool that provides ample information about the structure and condition of organs and tissues. It is widely used in diagnostics, and modern ultrasound machines can produce high-resolution scans. The study’s significance lies in the difficulty and time required to interpret medical materials, as well as the potential for subjectivity and errors. One promising approach to assist clinicians is the use of machine learning models and methods. These techniques are commonly employed for tasks such as data analysis, diagnosis and prognosis, and medical material classification and segmentation. Machine learning models can aid inexperienced practitioners and expedite the provision of high-quality medical care. The aim of the paper is to create an accurate and efficient healthy skeletal muscle segmentation model using machine learning for medical imaging ultrasound method.

Convolutional neural networks were used to build a model for segmentation of ultrasound images of skeletal muscles. U-net network architecture with different number of convolutional layers was used, as well as U-net++ network, which is a modification of the classical U-net. The U-Net architecture is one of the classical CNNs for image segmentation tasks, and it has been actively applied to biomedical images. Among the main advantages of the network is its ability to train well on a small amount of data. The U-Net++ network was proposed as a modification of the U-Net network architecture, which was designed to improve the network performance on medical image segmentation tasks. U-Net++ is based on the idea that the model will be more efficient and faster trained if the feature maps of the encoder and decoder are semantically similar.

To train the neural network, a dataset of ultrasound images of healthy skeletal muscles from open sources was used, because to obtain a high-quality model it is not only necessary to tune the neural network competently, but also to train it on a sufficient, high quality and diverse dataset. The images were annotated manually using binary masks to indicate muscle tissue boundaries. A binary mask was created for each image, replacing the muscle layer boundaries with white pixels and the rest with black pixels. These masks serve as truth labels when training neural networks. The dataset was divided into training and validation samples, and the training data was augmented. To prevent data leakage, augmentation is performed after dividing the data into samples. Increasing the validation sample is not recommended as it will not improve the training accuracy. The final model was tested using a dataset of ultrasound images of skeletal muscles of volunteers obtained using a Verasonics acoustic system.

The results of segmentation using the U-Net network, U-Net++ network, and their variants with increased number of convolution layers were compared. All training processes used the same dataset of skeletal muscle ultrasound images, which was divided into training and validation in the ratio of 8/2. Accuracy and loU were used as metrics for evaluation. Callbacks such as Early Stopping, which stops training when the validation error is unchanged and ReduceLROnPlateau designed to adaptively adjust the learning rate when there is no improvement on the monitored metric were used, both calls track the required parameters for a certain number of epochs. These callbacks were used to prevent overlearning. In the context of this work, where the task was to classify a small number of classes and small size images were used, the three-convolution network did not perform better than the two- convolution network. This is because the more complex features that a three-convolution network can learn were not necessary for the task at hand. Under such conditions, the simpler two convolution network can learn more efficiently because it has fewer parameters and requires less computational resources. In addition, the simpler network is less prone to overlearning, which is an important factor in tasks with small amounts of data.

A neural network model was trained, analyzed and tested, and a model that can segment ultrasound images of skeletal muscles was developed. In this study, it was shown that neural networks of U-Net and U-Net++ architectures can be effectively used for segmentation of ultrasound images of skeletal muscles. The main result of the study is to obtain an effective neural network model and to confirm the potential of its application for segmenting ultrasound images of skeletal muscles. The application of neural networks in medicine has a number of advantages, including improved diagnostic accuracy, reduced labour costs for physicians and increased speed of data processing. Further development of training and testing of neural networks will allow to expand the possibilities of their application in medicine in the future, for example, for diagnosing complex diseases or developing new treatment methods.

 

Key words: machine learning, skeletal muscle, ultrasound images segmentation, convolutional neural network.

The work was carried out with the support of the Ministry of Science and Higher Education of the Russian Federation (state assignment N FSWR-2023-0031).

 

Bibliographic reference: Mischenko E. A., Demin I. Yu. Applying machine learning for segmentation of skeletal muscle ultrasound images //journal “Problems of informatics”. 2024, № 3. P.47-57. DOI: 10.24412/2073-0667-2024-3-47-57. EDN: LTKQYZ


A. V. Rybkin, R. 0. Smirnov, E. E. Kotikhina, D.A. Karchkov, V. A. Moskalenko, G.V. Osipov, L.A. Smirnov

ANALYSIS OF EPICARDIAL ELECTROGRAMS USING ARTIFICIAL INTELLIGENCE

National Research Lobachevsky State University of Nizhny Novgorod, 603022, Nizhny Novgorod, Russia

DOI: 10.24412/2073-0667-2024-3-58-71
EDN: SZYHQZ

One of the most effective electrophysiological methods for studying the myocardium today is the method of using microelectrode arrays, which is characterized by high spatial resolution of recording extracellular potentials. Difficulties in analyzing bioelectric potentials recorded from living objects of study (cell, tissue, organ) by direct methods lie in the instability of the shape, amplitude and frequency of the recorded bioelectric potentials depending on the experimental conditions, as well as in the presence of electrical noise and artifacts. There is a need to constantly monitor the parameters of the signal processing algorithm over multiple short time intervals, followed by careful verification of the result. Taking into account the high recording sampling rates of modern measuring equipment and the impressive volumes of output data, the need to use artificial intelligence algorithms to solve these analytical problems becomes obvious. In addition, the use of artificial intelligence methods has great prospects for identifying predictors of life-threatening arrhythmias in cardiac electrograms during experimental modeling of these conditions. The electrograms involved in the study were obtained by multielectrode mapping with flexible arrays, including 64 recording electrodes, from the epicardial surface of isolated perfused rat hearts. The moments of activation on the electrogram graph mean the points of maximum steepness of the potential decline, which correspond to the moments of the appearance of action potentials on the membranes of cardiomyocytes, that is, tissue excitation. Analysis of the frequency of occurrence of activation moments on one electrode or the sequence of occurrence on several electrodes within the arrays allows one to evaluate such parameters of the heart as its pacemaker activity and electrical conductivity of the myocardium. As part of the study of the bioelectrical activity of the heart, a promising direction is the use of artificial intelligence methods to automate the analysis of electrograms recorded from the surface of the epicardium. The presented work describes the creation of a software package for analyzing electrograms of isolated hearts of small rodents, the main part of which is a segmenting neural network for localizing moments of myocardial activation based on UNet architecture. The choice of this architecture is due to its effectiveness in image segmentation tasks, which is especially important for identifying structures in cardiac electrograms. UNet architecture is characterized by the presence of convolutional layers for feature extraction and a decoder for accurate reconstruction of spatial information. This makes it an excellent choice for medical data segmentation tasks, such as electrograms, where prescision and recall are critical. However, as mentioned earlier: UNet from the original paper is intended for image segmentation, and therefore the neural network

was adapted for the analysis of one-dimensional signals. Due to the small amount of labeled data, cross­validation was carried out to measure the quality of the model; it was evaluated on eight folds. The success of segmentation is measured by Fl metric, which is the harmonic mean between precision and recall. In this context, an Fl value of around 0.77 indicates the model’s ability to accurately identify and localize moments of activation in a heart. The goal of the work is to create software that includes the following functionality: creating a data set for training, validation and testing, training a model; creating and editing markup. Taken together, this will allow automatic localization of activation moments in epicardial electrograms. Thus, the software package we have developed ensures the identification and precise determination of the desired moments of activation, which facilitates further analysis of bioelectrical activity and increases the efficiency of research in the field of cardiology, including due to the possibility of processing big data. In general, the developed software package represents a promising solution for automating the analysis of epicardial electrograms using a segmenting neural network based on UNet architecture and related algorithms.

 

Key words: deep learning, neural networks, UNet, microelectrode mapping, local field potential, myocardial electrograms.

Data collection and preprocessing was carried out with the financial support of the Ministry of Education and Science of the Russian Federation, project N 0729-2021-013. Neural network training was carried out as part of the implementation of the strategic academic leadership program Prioritet 2030.

Bibliographic reference: Rybkin A. V., Smirnov R. 0., Kotikhina E. E., Karchkov D. A., Moskalenko V. A., Osipov G. V., Smirnov L. A. Analysis of epicardial electrograms using artificial intelligence//journal “Problems of informatics”. 2024, № 3. P.58-71. DOI: 10.24412/2073-0667-2024-3-58-71. EDN: SZYHQZ


A. A. Romanyuta, M.G. Kurnosov

ALGORITHMS FOR MPI ALL-TO-ALL EXCHANGE USING SHARED MEMORY

Siberian State University of Telecommunications and Information Science, 630102, Novosibirsk, Russia

DOI: 10.24412/2073-0667-2024-3-72-81
EDN: ZIZPYY
Proposed algorithms for implementing MPI_Alltoall and MPI_Alltoallv collective operations using shared memory of multiprocessor servers and the Linux kernel CMA mechanism.
The algorithms use either a queue system or CMA system calls for message exchange. The software implementation is based on the Open MPI library as a separate component coll/sharm.
In experiments conducted on a server with x86-64 architecture, the MPI_Alltoall operation achieved the greatest time reduction by 1.48 times and MPI_Alltoallv by 1.37 times compared
to implementations in the coll/tuned and coll/ucc components of the Open MPI library. Recommendations for using the algorithms for different message sizes are proposed.
 

Key words: Alltoall, MPI, collective communications, computer systems.

The work was supported by research project N 071-03-2024-008.

References

  1. A Message-Passing Interface Standard Version 4.0. [El. Res.]: http://www.mpi-forum.org/ docs/mpi-4.0/mpi40-report .pdf. (Cited 25 May 2024).
  2. Open Source High Performance Computing. [El. Res.]: http://www.open-mpi.org. (Cited 25 May 2024).
  3. Cross Memory Attach. [El. Res.]: https://lwn.net/Articles/405284/. (Cited 25 May 2024).
  4. Linux Cross-Memory Attach. [EL Res.]: https://github.com/hjelmn/xpmem. (Cited 25 May 2024).
  5. Graham R. L., Shipman G. MPI Support for Multi-core Architectures: Optimized Shared Memory Collectives // Proc, of the 15th European PVM/MPI Users’ Group Meeting, 2008. P. 130-140.
  6. MVAPICH: MPI over InfiniBand, Omni-Path, Ethernet/iWARP, RoCE, and Slingshot. [EL Res.]: https: //mvapich. cse . ohio-state . edu/.
  7. Unified Communication X. [El. Res.]: https ://github. com/openuex/uex. (Cited 25 May 2024).
  8. Unified Collective Communication. [El. Res.]: https://github.com/openucx/ucc. (Cited 25 May 2024).
  9. Romanyuta A. A., Kurnosov M. G. Shared memory based MPI Reduce and Beast algorithms // Numerical Methods and Programming. 24. 339-351. 10.26089/NumMet.v24r424. (Cited: 25 May 2024).
  10. Intel(R) MPI Benchmarks. [EL Res.]: https://github.com/intel/mpi-benchmarks. (Cited 25 May 2024).

 

Bibliographic reference: Romanyuta A. A., Kurnosov M. G. Algorithms for MPI All-to-all exchange using shared memory//journal “Problems of informatics”. 2024, № 3. P.5-40. DOI: 10.24412/2073-0667-2024-3-72-81. EDN: ZIZPYY