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[nazev] => Analyses of viral genomes for G-quadruplex forming sequences reveal their correlation with the type of infection
[nazev_orig] => Analyses of viral genomes for G-quadruplex forming sequences reveal their correlation with the type of infection
[duvernost_udaju_id] => S
[popis] => G-quadruplexes contribute to the regulation of key molecular processes. Their utilization for antiviral therapy is an emerging field of contemporary research. Here we present comprehensive analyses of the presence and localization of putative G-quadruplex forming sequences (PQS) in all viral genomes currently available in the NCBI database (including subviral agents). The G4Hunter algorithm was applied to a pool of 11,000 accessible viral genomes representing 350 Mbp in total. PQS frequencies differ across evolutionary groups of viruses, and are enriched in repeats, replication origins, 5′UTRs and 3′UTRs. Importantly, PQS presence and localization is connected to viral lifecycles and corresponds to the type of viral infection rather than to nucleic acid type; while viruses routinely causing persistent infections in Metazoa hosts are enriched for PQS, viruses causing acute infections are significantly depleted for PQS. The unique localization of PQS identifies the importance of G-quadruplex-based regulation of viral replication and life cycle, providing a tool for potential therapeutic targeting.
[popis_orig] => G-quadruplexes contribute to the regulation of key molecular processes. Their utilization for antiviral therapy is an emerging field of contemporary research. Here we present comprehensive analyses of the presence and localization of putative G-quadruplex forming sequences (PQS) in all viral genomes currently available in the NCBI database (including subviral agents). The G4Hunter algorithm was applied to a pool of 11,000 accessible viral genomes representing 350 Mbp in total. PQS frequencies differ across evolutionary groups of viruses, and are enriched in repeats, replication origins, 5′UTRs and 3′UTRs. Importantly, PQS presence and localization is connected to viral lifecycles and corresponds to the type of viral infection rather than to nucleic acid type; while viruses routinely causing persistent infections in Metazoa hosts are enriched for PQS, viruses causing acute infections are significantly depleted for PQS. The unique localization of PQS identifies the importance of G-quadruplex-based regulation of viral replication and life cycle, providing a tool for potential therapeutic targeting.
[klicova_slova] => Acute infection; Bioinformatics; G-quadruplex; G4Hunter; Persistent infection; Viral genome
[klicova_slova_orig] => Acute infection; Bioinformatics; G-quadruplex; G4Hunter; Persistent infection; Viral genome
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author="Natália {Bohálová} and Alessio {Cantara} and Martin {Bartas} and Patrik {Kaura} and Jiří {Šťastný} and Petr {Pečinka} and Miroslav {Fojta} and Jean-Louis {Mergny} and Václav {Brázda}",
title="Analyses of viral genomes for G-quadruplex forming sequences reveal their correlation with the type of infection",
journal="Biochimie",
year="2021",
volume="186",
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doi="10.1016/j.biochi.2021.03.017",
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[nazev_en] => Analyses of viral genomes for G-quadruplex forming sequences reveal their correlation with the type of infection
[popis_en] => G-quadruplexes contribute to the regulation of key molecular processes. Their utilization for antiviral therapy is an emerging field of contemporary research. Here we present comprehensive analyses of the presence and localization of putative G-quadruplex forming sequences (PQS) in all viral genomes currently available in the NCBI database (including subviral agents). The G4Hunter algorithm was applied to a pool of 11,000 accessible viral genomes representing 350 Mbp in total. PQS frequencies differ across evolutionary groups of viruses, and are enriched in repeats, replication origins, 5′UTRs and 3′UTRs. Importantly, PQS presence and localization is connected to viral lifecycles and corresponds to the type of viral infection rather than to nucleic acid type; while viruses routinely causing persistent infections in Metazoa hosts are enriched for PQS, viruses causing acute infections are significantly depleted for PQS. The unique localization of PQS identifies the importance of G-quadruplex-based regulation of viral replication and life cycle, providing a tool for potential therapeutic targeting.
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[nazev] => Algorithm 1017: fuzzyreg: An R Package for Fitting Fuzzy Regression Models
[nazev_orig] => Algorithm 1017: fuzzyreg: An R Package for Fitting Fuzzy Regression Models
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[popis] => Fuzzy regression provides an alternative to statistical regression when the model is indefinite, the relationships between model parameters are vague, the sample size is low, or the data are hierarchically structured. Such cases allow to consider the choice of a regression model based on the fuzzy set theory. In fuzzyreg, we implement fuzzy linear regression methods that differ in the expectations of observational data types, outlier handling, and parameter estimation method. We provide a wrapper function that prepares data for fitting fuzzy linear models with the respective methods from a syntax established in R for fitting regression models. The function fuzzylm thus provides a novel functionality for R through standardized operations with fuzzy numbers. Additional functions allow for conversion of real-value variables to be fuzzy numbers, printing, summarizing, model plotting, and calculation of model predictions from new data using supporting functions that perform arithmetic operations with triangular fuzzy numbers. Goodness of fit and total error of the fit measures allow model comparisons. The package contains a dataset named bats with measurements of temperatures of hibernating bats and the mean annual surface temperature reflecting the climate at the sampling sites. The predictions from fuzzy linear models fitted to this dataset correspond well to the observed biological phenomenon. Fuzzy linear regression has great potential in predictive modeling where the data structure prevents statistical analysis and the modeled process exhibits inherent fuzziness.
[popis_orig] => Fuzzy regression provides an alternative to statistical regression when the model is indefinite, the relationships between model parameters are vague, the sample size is low, or the data are hierarchically structured. Such cases allow to consider the choice of a regression model based on the fuzzy set theory. In fuzzyreg, we implement fuzzy linear regression methods that differ in the expectations of observational data types, outlier handling, and parameter estimation method. We provide a wrapper function that prepares data for fitting fuzzy linear models with the respective methods from a syntax established in R for fitting regression models. The function fuzzylm thus provides a novel functionality for R through standardized operations with fuzzy numbers. Additional functions allow for conversion of real-value variables to be fuzzy numbers, printing, summarizing, model plotting, and calculation of model predictions from new data using supporting functions that perform arithmetic operations with triangular fuzzy numbers. Goodness of fit and total error of the fit measures allow model comparisons. The package contains a dataset named bats with measurements of temperatures of hibernating bats and the mean annual surface temperature reflecting the climate at the sampling sites. The predictions from fuzzy linear models fitted to this dataset correspond well to the observed biological phenomenon. Fuzzy linear regression has great potential in predictive modeling where the data structure prevents statistical analysis and the modeled process exhibits inherent fuzziness.
[klicova_slova] => Fuzzy regression; fuzzy set; possibilistic-based fuzzy regression; statistics-based fuzzy regression; R
[klicova_slova_orig] => Fuzzy regression; fuzzy set; possibilistic-based fuzzy regression; statistics-based fuzzy regression; R
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[citace_rtf] =>
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author="Pavel {Škrabánek} and Natália {Martínková}",
title="Algorithm 1017: fuzzyreg: An R Package for Fitting Fuzzy Regression Models",
journal="ACM TRANSACTIONS ON MATHEMATICAL SOFTWARE",
year="2021",
volume="47",
number="3",
pages="1--18",
doi="10.1145/3451389",
issn="0098-3500",
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[nazev_en] => Algorithm 1017: fuzzyreg: An R Package for Fitting Fuzzy Regression Models
[popis_en] => Fuzzy regression provides an alternative to statistical regression when the model is indefinite, the relationships between model parameters are vague, the sample size is low, or the data are hierarchically structured. Such cases allow to consider the choice of a regression model based on the fuzzy set theory. In fuzzyreg, we implement fuzzy linear regression methods that differ in the expectations of observational data types, outlier handling, and parameter estimation method. We provide a wrapper function that prepares data for fitting fuzzy linear models with the respective methods from a syntax established in R for fitting regression models. The function fuzzylm thus provides a novel functionality for R through standardized operations with fuzzy numbers. Additional functions allow for conversion of real-value variables to be fuzzy numbers, printing, summarizing, model plotting, and calculation of model predictions from new data using supporting functions that perform arithmetic operations with triangular fuzzy numbers. Goodness of fit and total error of the fit measures allow model comparisons. The package contains a dataset named bats with measurements of temperatures of hibernating bats and the mean annual surface temperature reflecting the climate at the sampling sites. The predictions from fuzzy linear models fitted to this dataset correspond well to the observed biological phenomenon. Fuzzy linear regression has great potential in predictive modeling where the data structure prevents statistical analysis and the modeled process exhibits inherent fuzziness.
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[nazev] => Mixed-integer programming model for ranking universities: Letting universities choose the weights
[nazev_orig] => Mixed-integer programming model for ranking universities: Letting universities choose the weights
[duvernost_udaju_id] => S
[popis] => Regardless of the shortcomings and criticisms of world university rankings, these metrics are still widely used by students and parents to select universities and by universities to attract talented students and researchers, as well as funding. This paper proposes a new mixed-integer programming model for ranking universities. The new approach alleviates one of the criticisms – the issue of the “arbitrari-ness” of the weights used for aggregation of the individual criteria (or indicators) utilized in the contemporary rankings. Instead, the proposed model uses intervals of different sizes for the weights and lets the universities themselves “choose” the weights to optimize their position in the rankings. A numerical evaluation of the proposed ranking, based on the indicator values and weights from the Times Higher Education World University Ranking, is presented.
[popis_orig] => Regardless of the shortcomings and criticisms of world university rankings, these metrics are still widely used by students and parents to select universities and by universities to attract talented students and researchers, as well as funding. This paper proposes a new mixed-integer programming model for ranking universities. The new approach alleviates one of the criticisms – the issue of the “arbitrari-ness” of the weights used for aggregation of the individual criteria (or indicators) utilized in the contemporary rankings. Instead, the proposed model uses intervals of different sizes for the weights and lets the universities themselves “choose” the weights to optimize their position in the rankings. A numerical evaluation of the proposed ranking, based on the indicator values and weights from the Times Higher Education World University Ranking, is presented.
[klicova_slova] => Mixed integer programming; Multiple-criteria decision-making; Ranking; University ranking
[klicova_slova_orig] => Mixed integer programming; Multiple-criteria decision-making; Ranking; University ranking
[url] => https://mendel-journal.org/index.php/mendel/article/view/133
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[citace_text] => KŮDELA, J. Mixed-integer programming model for ranking universities: Letting universities choose the weights. Mendel Journal series, 2021, vol. 27, no. 1, p. 41-48. ISSN: 1803-3814.
[citace_html] => KŮDELA, J. Mixed-integer programming model for ranking universities: Letting universities choose the weights. Mendel Journal series, 2021, vol. 27, no. 1, p. 41-48. ISSN: 1803-3814.
[citace_rtf] =>
[citace_bibtex] => @article{BUT172124,
author="Jakub {Kůdela}",
title="Mixed-integer programming model for ranking universities: Letting universities choose the weights",
journal="Mendel Journal series",
year="2021",
volume="27",
number="1",
pages="41--48",
doi="10.13164/mendel.2021.1.041",
issn="1803-3814",
url="https://mendel-journal.org/index.php/mendel/article/view/133"
}
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[nazev_en] => Mixed-integer programming model for ranking universities: Letting universities choose the weights
[popis_en] => Regardless of the shortcomings and criticisms of world university rankings, these metrics are still widely used by students and parents to select universities and by universities to attract talented students and researchers, as well as funding. This paper proposes a new mixed-integer programming model for ranking universities. The new approach alleviates one of the criticisms – the issue of the “arbitrari-ness” of the weights used for aggregation of the individual criteria (or indicators) utilized in the contemporary rankings. Instead, the proposed model uses intervals of different sizes for the weights and lets the universities themselves “choose” the weights to optimize their position in the rankings. A numerical evaluation of the proposed ranking, based on the indicator values and weights from the Times Higher Education World University Ranking, is presented.
[klicova_slova_en] => Mixed integer programming; Multiple-criteria decision-making; Ranking; University ranking
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[nazev] => Stabilization of Higher Periodic Orbits of the Lozi and Hénon Maps using Meta-evolutionary Approaches
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[duvernost_udaju_id] => S
[popis] => This paper deals with an advanced adjustment of stabilization sequences for selected discrete chaotic systems by means of meta-evolutionary approaches. As the representative models of deterministic chaotic systems, a two dimensional Lozi map and two dimensional Hénon map were used. The novelty of the approach is in an effective use of a new type of objective function, which is essential for the whole optimization process of higher periodic orbits as well as an effective use of advanced metaheuristic optimization methods. Although the task of stabilizing the Lozi and Hénon chaotic systems is known, its solution presented for periodic orbit four is not trivial. The task of stabilizing the Lozi chaotic systems for period four is a new approach. Furthermore, modern meta-heuristics were used for own design of the external disturbance sequences. The used optimization methods are a naive grid-based algorithm (NG), a grid-based Nelder-Mead Algorithm (NM), a Genetic Algorithm (GA) as well as Genetic Programming (GP). A connection of GP and second level optimization using GA displays significantly better results than the given stand-alone meta-heuristic techniques.
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[klicova_slova] => Chaos control, Evolutionary computation, Lozi map, Henon map, Optimization
[klicova_slova_orig] => Chaos control, Evolutionary computation, Lozi map, Henon map, Optimization
[url] => https://ieeexplore.ieee.org/document/9504798
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[citace_text] => MATOUŠEK, R.; LOZI, R.; HŮLKA, T. Stabilization of Higher Periodic Orbits of the Lozi and Hénon Maps using Meta-evolutionary Approaches. In 2021 IEEE Congress on Evolutionary Computation (CEC). IEEE Congress on Evolutionary Computation (CEC). Kraków, Poland: IEEE, 2021. p. 572-579. ISBN: 978-1-7281-8393-0.
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booktitle="2021 IEEE Congress on Evolutionary Computation (CEC)",
year="2021",
series="IEEE Congress on Evolutionary Computation (CEC)",
number="1",
pages="572--579",
publisher="IEEE",
address="Kraków, Poland",
doi="10.1109/CEC45853.2021.9504798",
isbn="978-1-7281-8393-0",
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[nazev_en] => Stabilization of Higher Periodic Orbits of the Lozi and Hénon Maps using Meta-evolutionary Approaches
[popis_en] => This paper deals with an advanced adjustment of stabilization sequences for selected discrete chaotic systems by means of meta-evolutionary approaches. As the representative models of deterministic chaotic systems, a two dimensional Lozi map and two dimensional Hénon map were used. The novelty of the approach is in an effective use of a new type of objective function, which is essential for the whole optimization process of higher periodic orbits as well as an effective use of advanced metaheuristic optimization methods. Although the task of stabilizing the Lozi and Hénon chaotic systems is known, its solution presented for periodic orbit four is not trivial. The task of stabilizing the Lozi chaotic systems for period four is a new approach. Furthermore, modern meta-heuristics were used for own design of the external disturbance sequences. The used optimization methods are a naive grid-based algorithm (NG), a grid-based Nelder-Mead Algorithm (NM), a Genetic Algorithm (GA) as well as Genetic Programming (GP). A connection of GP and second level optimization using GA displays significantly better results than the given stand-alone meta-heuristic techniques.
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[nazev] => Machining of B1914 nickel-based superalloy using wire electrical discharge machining
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[popis] => The unconventional technology of wire electrical discharge machining is a key engineering technology, designed primarily for machining of conventionally difficult machine materials. One of them is nickel alloys, which are majorly used in the aerospace and energy industries. The subject of research in this study was specifically the B1914 nickel-based superalloy, which was subjected to many analyses leading to an overall optimization of its machining using wire electrical discharge machining. In order to determine the effect of machine parameters setup (pulse off time, gap voltage, discharge current, pulse on time and wire feed) on cutting speed, topography, morphology, surface and subsurface layer quality, an extensive Box-Behnken design experiment consisting of 46 rounds was carried out. The analyses of the condition of the surface and subsurface layers were performed, including their chemical composition and changes caused by wire electrical discharge machining. It was found out that the factors like pulse off time, discharge current and pulse on time have the greatest effect on the cutting speed, although from the point of view of surface topography the parameter pulse off time is not significant. The remaining two parameters cause the cutting speed to act against the surface topography i.e. with the increasing cutting speed, the surface topography gets worse and vice versa.
[popis_orig] => The unconventional technology of wire electrical discharge machining is a key engineering technology, designed primarily for machining of conventionally difficult machine materials. One of them is nickel alloys, which are majorly used in the aerospace and energy industries. The subject of research in this study was specifically the B1914 nickel-based superalloy, which was subjected to many analyses leading to an overall optimization of its machining using wire electrical discharge machining. In order to determine the effect of machine parameters setup (pulse off time, gap voltage, discharge current, pulse on time and wire feed) on cutting speed, topography, morphology, surface and subsurface layer quality, an extensive Box-Behnken design experiment consisting of 46 rounds was carried out. The analyses of the condition of the surface and subsurface layers were performed, including their chemical composition and changes caused by wire electrical discharge machining. It was found out that the factors like pulse off time, discharge current and pulse on time have the greatest effect on the cutting speed, although from the point of view of surface topography the parameter pulse off time is not significant. The remaining two parameters cause the cutting speed to act against the surface topography i.e. with the increasing cutting speed, the surface topography gets worse and vice versa.
[klicova_slova] => Wire electrical discharge machining; nickel alloy; B1914; design of experiment; machining parameters
[klicova_slova_orig] => Wire electrical discharge machining; nickel alloy; B1914; design of experiment; machining parameters
[url] => https://journals.sagepub.com/doi/abs/10.1177/09544089211031746
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author="Kateřina {Mouralová} and Aleš {Polzer} and Libor {Beneš} and Josef {Bednář} and Radim {Zahradníček} and Tomáš {Prokeš} and Zdeněk {Fiala} and Jiří {Fries}",
title="Machining of B1914 nickel-based superalloy using wire electrical discharge machining",
journal="Proceedings of the Institution of Mechanical Engineers. Part E, Journal of process mechanical engineering",
year="2021",
volume="235",
number="6",
pages="2141--2153",
doi="10.1177/09544089211031746",
issn="0954-4089",
url="https://journals.sagepub.com/doi/abs/10.1177/09544089211031746"
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[nazev_en] => Machining of B1914 nickel-based superalloy using wire electrical discharge machining
[popis_en] => The unconventional technology of wire electrical discharge machining is a key engineering technology, designed primarily for machining of conventionally difficult machine materials. One of them is nickel alloys, which are majorly used in the aerospace and energy industries. The subject of research in this study was specifically the B1914 nickel-based superalloy, which was subjected to many analyses leading to an overall optimization of its machining using wire electrical discharge machining. In order to determine the effect of machine parameters setup (pulse off time, gap voltage, discharge current, pulse on time and wire feed) on cutting speed, topography, morphology, surface and subsurface layer quality, an extensive Box-Behnken design experiment consisting of 46 rounds was carried out. The analyses of the condition of the surface and subsurface layers were performed, including their chemical composition and changes caused by wire electrical discharge machining. It was found out that the factors like pulse off time, discharge current and pulse on time have the greatest effect on the cutting speed, although from the point of view of surface topography the parameter pulse off time is not significant. The remaining two parameters cause the cutting speed to act against the surface topography i.e. with the increasing cutting speed, the surface topography gets worse and vice versa.
[klicova_slova_en] => Wire electrical discharge machining; nickel alloy; B1914; design of experiment; machining parameters
[vysledek_datum] => 2021-11-24T00:00:00+01:00
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[nazev] => Novel Approaches for Transport Infrastructure Reduction to Effective Optimisation of Flow Tasks
[nazev_orig] => Novel Approaches for Transport Infrastructure Reduction to Effective Optimisation of Flow Tasks
[duvernost_udaju_id] => S
[popis] => Nowadays, increasing complexity of solved optimisation problems leads to necessity of dealing with computation time demand. In the case of network flow tasks, computation time is highly dependent on detail of transport infrastructure. The presented paper is concerned with developing novel approaches for transport infrastructure reduction using clustering analysis. According to the required outputs of the task, it is possible to variably change the detail of the network in individual territorial units to ensure the solvability of the task, but without significant distortion of the results. The main idea and novelty of the presented research is to have a finer construction only in the vicinity of the monitored subject. With a greater distance, it is possible to reduce the level of detail in the transport network. The principle of reduction technique is based on transformation of geographic coordinates with subsequent cluster analysis. K-means and hierarchical clustering are introduced and results of developed approach are shown on municipalities in Czech Republic. Consistency within clusters of both methods is evaluated using silhouettes. The presented methodology allows to solve optimisation of case studies more efficiently with greater detail in monitored region, which leads to more accurate solutions.
[popis_orig] => Nowadays, increasing complexity of solved optimisation problems leads to necessity of dealing with computation time demand. In the case of network flow tasks, computation time is highly dependent on detail of transport infrastructure. The presented paper is concerned with developing novel approaches for transport infrastructure reduction using clustering analysis. According to the required outputs of the task, it is possible to variably change the detail of the network in individual territorial units to ensure the solvability of the task, but without significant distortion of the results. The main idea and novelty of the presented research is to have a finer construction only in the vicinity of the monitored subject. With a greater distance, it is possible to reduce the level of detail in the transport network. The principle of reduction technique is based on transformation of geographic coordinates with subsequent cluster analysis. K-means and hierarchical clustering are introduced and results of developed approach are shown on municipalities in Czech Republic. Consistency within clusters of both methods is evaluated using silhouettes. The presented methodology allows to solve optimisation of case studies more efficiently with greater detail in monitored region, which leads to more accurate solutions.
[klicova_slova] => Model-size reduction techniques, Cluster analysis, Infrastructure transformation
[klicova_slova_orig] => Model-size reduction techniques, Cluster analysis, Infrastructure transformation
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[citace_text] => PLUSKAL, J.; ŠOMPLÁK, R.; KŮDELA, J. Novel Approaches for Transport Infrastructure Reduction to Effective Optimisation of Flow Tasks. Chemical Engineering transactions, 2021, vol. 88, no. 1, p. 463-468. ISSN: 2283-9216.
[citace_html] => PLUSKAL, J.; ŠOMPLÁK, R.; KŮDELA, J. Novel Approaches for Transport Infrastructure Reduction to Effective Optimisation of Flow Tasks. Chemical Engineering transactions, 2021, vol. 88, no. 1, p. 463-468. ISSN: 2283-9216.
[citace_rtf] =>
[citace_bibtex] => @article{BUT175928,
author="Jaroslav {Pluskal} and Radovan {Šomplák} and Jakub {Kůdela}",
title="Novel Approaches for Transport Infrastructure Reduction to Effective Optimisation of Flow Tasks",
journal="Chemical Engineering transactions",
year="2021",
volume="88",
number="1",
pages="463--468",
doi="10.3303/CET21880777",
url="https://www.aidic.it/cet/21/88/077.pdf"
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[nazev_en] => Novel Approaches for Transport Infrastructure Reduction to Effective Optimisation of Flow Tasks
[popis_en] => Nowadays, increasing complexity of solved optimisation problems leads to necessity of dealing with computation time demand. In the case of network flow tasks, computation time is highly dependent on detail of transport infrastructure. The presented paper is concerned with developing novel approaches for transport infrastructure reduction using clustering analysis. According to the required outputs of the task, it is possible to variably change the detail of the network in individual territorial units to ensure the solvability of the task, but without significant distortion of the results. The main idea and novelty of the presented research is to have a finer construction only in the vicinity of the monitored subject. With a greater distance, it is possible to reduce the level of detail in the transport network. The principle of reduction technique is based on transformation of geographic coordinates with subsequent cluster analysis. K-means and hierarchical clustering are introduced and results of developed approach are shown on municipalities in Czech Republic. Consistency within clusters of both methods is evaluated using silhouettes. The presented methodology allows to solve optimisation of case studies more efficiently with greater detail in monitored region, which leads to more accurate solutions.
[klicova_slova_en] => Model-size reduction techniques, Cluster analysis, Infrastructure transformation
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url="https://link.springer.com/chapter/10.1007/978-3-031-09726-3_39"
}
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[nazev_en] => Composite Evolutionary Strategy and Differential Evolution Method for the ICSI’2022 Competition
[popis_en] => In this paper, a composite method for bound constrained optimization called Composite Evolutionary Strategy and Differential Evolution (CESDE) is described. This method combines two well-performing methods from the Congress on Evolutionary Computation Competitions. Through numerical investigation on the ICSI’2022 benchmark set, the favourite scheme for combining the two methods was determined, and it was found that CESDE outperforms both of its “parental” methods on all studied instances.
[klicova_slova_en] => ICSI’2022 competition; Evolutionary strategy; Differential evolution; Numerical optimization; Composite method
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[nazev] => Centroid based person detection using pixelwise prediction of the position
[nazev_orig] => Centroid based person detection using pixelwise prediction of the position
[duvernost_udaju_id] => S
[popis] => Implementations of person detection in tracking and counting systems tend towards processing of orthogonally captured images on edge computing devices. The ellipse-like shape of heads in orthogonally captured images inspired us to predict head centroids to determine positions of persons in images. We predict the centroids using a fully convolutional network (FCN). We combine the FCN with simple image processing operations to ensure fast inference of the detector. We experiment with the size of the FCN output to further decrease the inference time. We compare the proposed centroid-based detector with bounding box-based detectors on head detection task in terms of the inference time and the detection performance. We propose a performance measure which allows quantitative comparison of the two detection approaches. For the training and evaluation of the detectors, we form original datasets of 8000 annotated images, which are characterized by high variability in terms of lighting conditions, background, image quality, and elevation profile of scenes. We propose an approach which allows simultaneous annotation of the images for both bounding box-based and centroid-based detection. The centroid-based detector shows the best detection performance while keeping edge computing standards.
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[klicova_slova] => Persondetection; Fullyconvolutionalnetworks; Performancemeasure; Edgecomputing; Computervision
[klicova_slova_orig] => Persondetection; Fullyconvolutionalnetworks; Performancemeasure; Edgecomputing; Computervision
[url] => https://www.sciencedirect.com/science/article/pii/S1877750322001442
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[citace_text] => DOLEŽEL, P.; ŠKRABÁNEK, P.; ŠTURSA, D.; BARUQUE ZANON, B.; COGOLLOS ADRIAN, H.; KRÝDA, P. Centroid based person detection using pixelwise prediction of the position. Journal of Computational Science, 2022, vol. 63, no. 1, p. 1-12. ISSN: 1877-7503.
[citace_html] => DOLEŽEL, P.; ŠKRABÁNEK, P.; ŠTURSA, D.; BARUQUE ZANON, B.; COGOLLOS ADRIAN, H.; KRÝDA, P. Centroid based person detection using pixelwise prediction of the position. Journal of Computational Science, 2022, vol. 63, no. 1, p. 1-12. ISSN: 1877-7503.
[citace_rtf] =>
[citace_bibtex] => @article{BUT178514,
author="Petr {Doležel} and Pavel {Škrabánek} and Dominik {Štursa} and Bruno {Baruque Zanon} and Hector {Cogollos Adrian} and Pavel {Krýda}",
title="Centroid based person detection using pixelwise prediction of the position",
journal="Journal of Computational Science",
year="2022",
volume="63",
number="1",
pages="1--12",
doi="10.1016/j.jocs.2022.101760",
issn="1877-7503",
url="https://www.sciencedirect.com/science/article/pii/S1877750322001442"
}
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[nazev_en] => Centroid based person detection using pixelwise prediction of the position
[popis_en] => Implementations of person detection in tracking and counting systems tend towards processing of orthogonally captured images on edge computing devices. The ellipse-like shape of heads in orthogonally captured images inspired us to predict head centroids to determine positions of persons in images. We predict the centroids using a fully convolutional network (FCN). We combine the FCN with simple image processing operations to ensure fast inference of the detector. We experiment with the size of the FCN output to further decrease the inference time. We compare the proposed centroid-based detector with bounding box-based detectors on head detection task in terms of the inference time and the detection performance. We propose a performance measure which allows quantitative comparison of the two detection approaches. For the training and evaluation of the detectors, we form original datasets of 8000 annotated images, which are characterized by high variability in terms of lighting conditions, background, image quality, and elevation profile of scenes. We propose an approach which allows simultaneous annotation of the images for both bounding box-based and centroid-based detection. The centroid-based detector shows the best detection performance while keeping edge computing standards.
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[nazev] => Recent advances and applications of surrogate models for finite element method computations: a review
[nazev_orig] => Recent advances and applications of surrogate models for finite element method computations: a review
[duvernost_udaju_id] => S
[popis] => The utilization of surrogate models to approximate complex systems has recently gained increased popularity. Because of their capability to deal with black-box problems and lower computational requirements, surrogates were successfully utilized by researchers in various engineering and scientific fields. An efficient use of surrogates can bring considerable savings in computational resources and time. Since literature on surrogate modelling encompasses a large variety of approaches, the appropriate choice of a surrogate remains a challenging task. This review discusses significant publications where surrogate modelling for finite element method-based computations was utilized. We familiarize the reader with the subject, explain the function of surrogate modelling, sampling and model validation procedures, and give a description of the different surrogate types. We then discuss main categories where surrogate models are used: prediction, sensitivity analysis, uncertainty quantification, and surrogate-assisted optimization, and give detailed account of recent advances and applications. We review the most widely used and recently developed software tools that are used to apply the discussed techniques with ease. Based on a literature review of 180 papers related to surrogate modelling, we discuss major research trends, gaps, and practical recommendations. As the utilization of surrogate models grows in popularity, this review can function as a guide that makes surrogate modelling more accessible.
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[klicova_slova] => Surrogate model; Surrogate-assisted optimization; Sensitivity analysis; Uncertainty quantification; Finite element method
[klicova_slova_orig] => Surrogate model; Surrogate-assisted optimization; Sensitivity analysis; Uncertainty quantification; Finite element method
[url] => https://link.springer.com/article/10.1007/s00500-022-07362-8
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[citace_text] => KŮDELA, J.; MATOUŠEK, R. Recent advances and applications of surrogate models for finite element method computations: a review. SOFT COMPUTING, 2022, vol. 26, no. 1, p. 13709-13733. ISSN: 1432-7643.
[citace_html] => KŮDELA, J.; MATOUŠEK, R. Recent advances and applications of surrogate models for finite element method computations: a review. SOFT COMPUTING, 2022, vol. 26, no. 1, p. 13709-13733. ISSN: 1432-7643.
[citace_rtf] =>
[citace_bibtex] => @article{BUT178561,
author="Jakub {Kůdela} and Radomil {Matoušek}",
title="Recent advances and applications of surrogate models for finite element method computations: a review",
journal="SOFT COMPUTING",
year="2022",
volume="26",
number="1",
pages="13709--13733",
doi="10.1007/s00500-022-07362-8",
issn="1432-7643",
url="https://link.springer.com/article/10.1007/s00500-022-07362-8"
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[nazev_en] => Recent advances and applications of surrogate models for finite element method computations: a review
[popis_en] => The utilization of surrogate models to approximate complex systems has recently gained increased popularity. Because of their capability to deal with black-box problems and lower computational requirements, surrogates were successfully utilized by researchers in various engineering and scientific fields. An efficient use of surrogates can bring considerable savings in computational resources and time. Since literature on surrogate modelling encompasses a large variety of approaches, the appropriate choice of a surrogate remains a challenging task. This review discusses significant publications where surrogate modelling for finite element method-based computations was utilized. We familiarize the reader with the subject, explain the function of surrogate modelling, sampling and model validation procedures, and give a description of the different surrogate types. We then discuss main categories where surrogate models are used: prediction, sensitivity analysis, uncertainty quantification, and surrogate-assisted optimization, and give detailed account of recent advances and applications. We review the most widely used and recently developed software tools that are used to apply the discussed techniques with ease. Based on a literature review of 180 papers related to surrogate modelling, we discuss major research trends, gaps, and practical recommendations. As the utilization of surrogate models grows in popularity, this review can function as a guide that makes surrogate modelling more accessible.
[klicova_slova_en] => Surrogate model; Surrogate-assisted optimization; Sensitivity analysis; Uncertainty quantification; Finite element method
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[nazev] => A critical problem in benchmarking and analysis of evolutionary computation methods
[nazev_orig] => A critical problem in benchmarking and analysis of evolutionary computation methods
[duvernost_udaju_id] => S
[popis] => Benchmarking constitutes a cornerstone in the analysis and development of computational methods. Especially in the field of evolutionary computation, where theoretical analysis of the algorithms is almost impossible, benchmarking is at the center of attention. In this text, we show that some of the frequently used benchmark functions that have their respective optima in the center of the feasible set pose a critical problem for the analysis of evolutionary computation methods. We carry out the analysis of seven recent methods, published in respected journals, which contain a center-bias operator that lets them find these optima with ease. This makes their comparison with other methods (that do not have a center-bias) meaningless on such types of problems. We perform a computational comparison of these methods with two of the oldest methods in evolutionary computation on shifted problems and on more advanced benchmark problems. The results show a serious problem, as only one of the seven methods performed consistently better than the pair of old methods, three performed on par, two performed very badly, and the worst one performed barely better than a random search. We also give several suggestions that could help to resolve the presented issues.
[popis_orig] => Benchmarking constitutes a cornerstone in the analysis and development of computational methods. Especially in the field of evolutionary computation, where theoretical analysis of the algorithms is almost impossible, benchmarking is at the center of attention. In this text, we show that some of the frequently used benchmark functions that have their respective optima in the center of the feasible set pose a critical problem for the analysis of evolutionary computation methods. We carry out the analysis of seven recent methods, published in respected journals, which contain a center-bias operator that lets them find these optima with ease. This makes their comparison with other methods (that do not have a center-bias) meaningless on such types of problems. We perform a computational comparison of these methods with two of the oldest methods in evolutionary computation on shifted problems and on more advanced benchmark problems. The results show a serious problem, as only one of the seven methods performed consistently better than the pair of old methods, three performed on par, two performed very badly, and the worst one performed barely better than a random search. We also give several suggestions that could help to resolve the presented issues.
[klicova_slova] => Evolutionary computation; Metaheuristics; Benchmarking; Zero-bias
[klicova_slova_orig] => Evolutionary computation; Metaheuristics; Benchmarking; Zero-bias
[url] => https://www.nature.com/articles/s42256-022-00579-0
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[citace_text] => KŮDELA, J. A critical problem in benchmarking and analysis of evolutionary computation methods. Nature Machine Intelligence, 2022, no. 4, p. 1238-1245. ISSN: 2522-5839.
[citace_html] => KŮDELA, J. A critical problem in benchmarking and analysis of evolutionary computation methods. Nature Machine Intelligence, 2022, no. 4, p. 1238-1245. ISSN: 2522-5839.
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author="Jakub {Kůdela}",
title="A critical problem in benchmarking and analysis of evolutionary computation methods",
journal="Nature Machine Intelligence",
year="2022",
number="4",
pages="1238--1245",
doi="10.1038/s42256-022-00579-0",
url="https://www.nature.com/articles/s42256-022-00579-0"
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[nazev_en] => A critical problem in benchmarking and analysis of evolutionary computation methods
[popis_en] => Benchmarking constitutes a cornerstone in the analysis and development of computational methods. Especially in the field of evolutionary computation, where theoretical analysis of the algorithms is almost impossible, benchmarking is at the center of attention. In this text, we show that some of the frequently used benchmark functions that have their respective optima in the center of the feasible set pose a critical problem for the analysis of evolutionary computation methods. We carry out the analysis of seven recent methods, published in respected journals, which contain a center-bias operator that lets them find these optima with ease. This makes their comparison with other methods (that do not have a center-bias) meaningless on such types of problems. We perform a computational comparison of these methods with two of the oldest methods in evolutionary computation on shifted problems and on more advanced benchmark problems. The results show a serious problem, as only one of the seven methods performed consistently better than the pair of old methods, three performed on par, two performed very badly, and the worst one performed barely better than a random search. We also give several suggestions that could help to resolve the presented issues.
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[popis] => Semi-permeable barriers to geneflow in principle allow distantly related organisms to capture and exchange pre-adapted genes potentially speeding adaptation. However, describing barriers to geneflow on a genomic scale is non-trivial. We extend classic diagnostic allele counting measures of geneflow across a barrier to the case of genome-scale data. Diagnostic index expectation maximisation (diem) polarises the labelling of bistate markers with respect to the sides of a barrier. An initial state of ignorance is enforced by starting with randomly generated marker polarisations. This means there is no prior on population or taxon membership of the genomes concerned. Using a deterministic data labelling, small numbers of classic diagnostic markers can be replaced by large numbers of markers, each with a diagnostic index. Individuals' hybrid indices (genome admixture proportions) are then calculated genome wide conditioned on marker diagnosticity; within diploid, haplodiploid and/or haploid genome compartments; or indeed over any subset of markers, allowing classical cline width/barrier strength comparisons along genomes. Along-genome barrier strength heterogeneity allows for barrier regions to be identified. Furthermore, blocks of genetic material that have introgressed across a barrier are easily identified with high power. diem indicates panmixis among Myotis myotis bat genomes, with a barrier separating low data quality outliers. In a Mus musculus domesticus/Mus spretus system, diem adds multiple introgressions of olfactory (and vomeronasal) gene clusters in one direction to previous demonstrations of a pesticide resistance gene introgressing in the opposite direction across a strong species barrier. diem is a genome analysis solution, which scales over reduced representation genomics of thousands of markers to treatment of all variant sites in large genomes. While the method lends itself to visualisation, its output of markers with barrier-informative annotation will fuel research in population genetics, phylogenetics and association studies. diem can equip such downstream applications with millions of informative markers.
[popis_orig] => Semi-permeable barriers to geneflow in principle allow distantly related organisms to capture and exchange pre-adapted genes potentially speeding adaptation. However, describing barriers to geneflow on a genomic scale is non-trivial. We extend classic diagnostic allele counting measures of geneflow across a barrier to the case of genome-scale data. Diagnostic index expectation maximisation (diem) polarises the labelling of bistate markers with respect to the sides of a barrier. An initial state of ignorance is enforced by starting with randomly generated marker polarisations. This means there is no prior on population or taxon membership of the genomes concerned. Using a deterministic data labelling, small numbers of classic diagnostic markers can be replaced by large numbers of markers, each with a diagnostic index. Individuals' hybrid indices (genome admixture proportions) are then calculated genome wide conditioned on marker diagnosticity; within diploid, haplodiploid and/or haploid genome compartments; or indeed over any subset of markers, allowing classical cline width/barrier strength comparisons along genomes. Along-genome barrier strength heterogeneity allows for barrier regions to be identified. Furthermore, blocks of genetic material that have introgressed across a barrier are easily identified with high power. diem indicates panmixis among Myotis myotis bat genomes, with a barrier separating low data quality outliers. In a Mus musculus domesticus/Mus spretus system, diem adds multiple introgressions of olfactory (and vomeronasal) gene clusters in one direction to previous demonstrations of a pesticide resistance gene introgressing in the opposite direction across a strong species barrier. diem is a genome analysis solution, which scales over reduced representation genomics of thousands of markers to treatment of all variant sites in large genomes. While the method lends itself to visualisation, its output of markers with barrier-informative annotation will fuel research in population genetics, phylogenetics and association studies. diem can equip such downstream applications with millions of informative markers.
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[klicova_slova_orig] => gene capture; geneflow; genome admixture; genome polarisation; hybrid zone; hybridisation; introgression; reduced representation genomics
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[popis_en] => Semi-permeable barriers to geneflow in principle allow distantly related organisms to capture and exchange pre-adapted genes potentially speeding adaptation. However, describing barriers to geneflow on a genomic scale is non-trivial. We extend classic diagnostic allele counting measures of geneflow across a barrier to the case of genome-scale data. Diagnostic index expectation maximisation (diem) polarises the labelling of bistate markers with respect to the sides of a barrier. An initial state of ignorance is enforced by starting with randomly generated marker polarisations. This means there is no prior on population or taxon membership of the genomes concerned. Using a deterministic data labelling, small numbers of classic diagnostic markers can be replaced by large numbers of markers, each with a diagnostic index. Individuals' hybrid indices (genome admixture proportions) are then calculated genome wide conditioned on marker diagnosticity; within diploid, haplodiploid and/or haploid genome compartments; or indeed over any subset of markers, allowing classical cline width/barrier strength comparisons along genomes. Along-genome barrier strength heterogeneity allows for barrier regions to be identified. Furthermore, blocks of genetic material that have introgressed across a barrier are easily identified with high power. diem indicates panmixis among Myotis myotis bat genomes, with a barrier separating low data quality outliers. In a Mus musculus domesticus/Mus spretus system, diem adds multiple introgressions of olfactory (and vomeronasal) gene clusters in one direction to previous demonstrations of a pesticide resistance gene introgressing in the opposite direction across a strong species barrier. diem is a genome analysis solution, which scales over reduced representation genomics of thousands of markers to treatment of all variant sites in large genomes. While the method lends itself to visualisation, its output of markers with barrier-informative annotation will fuel research in population genetics, phylogenetics and association studies. diem can equip such downstream applications with millions of informative markers.
[klicova_slova_en] => gene capture; geneflow; genome admixture; genome polarisation; hybrid zone; hybridisation; introgression; reduced representation genomics
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[typ] => PV
[year] => 2022
[id_vav] => 178337
)
[9] => Array
(
[quotations] => DOLEŽEL, P.; ŠKRABÁNEK, P.; ŠTURSA, D.; BARUQUE ZANON, B.; COGOLLOS ADRIAN, H.; KRÝDA, P.
[title] => Centroid based person detection using pixelwise prediction of the position
[typ] => PV
[year] => 2022
[id_vav] => 178514
)
[10] => Array
(
[quotations] => KŮDELA, J.; MATOUŠEK, R.
[title] => Recent advances and applications of surrogate models for finite element method computations: a review
[typ] => PV
[year] => 2022
[id_vav] => 178561
)
[11] => Array
(
[quotations] => KŮDELA, J.
[title] => A critical problem in benchmarking and analysis of evolutionary computation methods
[typ] => PV
[year] => 2022
[id_vav] => 179505
)
[12] => Array
(
[quotations] => BAIRD, S.; PETRUŽELA, J.; IZAR, J.; ŠKRABÁNEK, P.; MARTÍNKOVÁ, N.
[title] => Genome polarisation for detecting barriers to geneflow
[typ] => PV
[year] => 2022
[id_vav] => 180422
)
[13] => Array
(
[quotations] => ŠKRABÁNEK, P.; MARTÍNKOVÁ, N.
[title] => fuzzyreg: Fuzzy Linear Regression
[typ] => AV
[year] => 2021
[id_vav] => 180423
)
)
)