44 results on '"Sushko, I."'
Search Results
2. Causes of fragile stock market stability
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Gardini, L., Radi, D., Schmitt, N., Sushko, I., and Westerhoff, F.
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- 2022
- Full Text
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3. Exchange Rate Dynamics and Central Bank Interventions: On the (De)Stabilizing Nature of Targeting Long-Run Fundamentals Interventions.
- Author
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Gardini, L., Radi, D., Schmitt, N., Sushko, I., and Westerhoff, F.
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FOREIGN exchange rates ,CENTRAL banking industry ,FOREIGN exchange market ,BEAR markets ,MARKET makers - Abstract
We develop a foreign exchange market model in which a market maker adjusts the exchange rate with respect to the trading behavior of chartists, fundamentalists and a central bank. While chartists bet on the persistence of bull and bear markets, fundamentalists speculate on mean reversion. The central bank seeks to stabilize the foreign exchange market by placing buy (sell) orders when the undervaluation (overvaluation) of the exchange rate exceeds a certain threshold. Since a one-dimensional piecewise-linear discontinuous map with three branches determines the evolution of the exchange rate, we use a combination of analytical and numerical tools to explore the extent to which the central bank is able to tame the behavior of the foreign exchange market. [ABSTRACT FROM AUTHOR]
- Published
- 2024
4. Lozi map embedded into the 2D border collision normal form.
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Sushko, I., Avrutin, V., and Gardini, L.
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ROTATIONAL motion - Abstract
A 2D piecewise linear continuous two-parameter map known as the Lozi map is a special case of the 2D border collision normal form depending on four parameters. In the present paper, we investigate how the bifurcation structure of the Lozi map is incorporated into the bifurcation structure of the 2D border collision normal form using an analytical representation of the boundaries of the largest periodicity regions related to the cycles with rotation number 1/n, n ⩾ 3. At the centre bifurcation boundary of the stability domain of the fixed point both maps are conservative which leads to a quite intricate bifurcation structure near this boundary. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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5. Pattern recognition of 1D and 2D signals using normalization and normal transformation
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Rybin, A. I., Melnyk, A. D., Nizhebetskaya, Yu. Kh., Sushko, I. A., and Litvintsev, S. N.
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- 2016
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6. Research of the problem of deceleration of computations in multiprocessional computing systems when solving applied problems
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Ivashchenko, V., Ivashchenko, O., Kabak, I., Sushko, I., Mamuzić, Ilija, and Mamuzić, Ilija
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multiprocessional computing systems ,applied problems ,deceleration factor - Abstract
The research is aimed at determining the deceleration factor associated with the increase in computing of a multiprocessor system. It should be noted that the research of these problems is important and relevant. The aim of the research is the further approach development associated with methodology defi nition for evaluation of the multiprocessor modular computing system effectiveness and this value impact of the computational deceleration.
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- 2022
7. Speeding up the Tikhonov regularization iterative procedure in solving the inverse problem of electrical impedance tomography
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Sushko, I. A. and Rybin, A. I.
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- 2015
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8. Thermonuclear Energy
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Sushko, I., Shevchenko, D., and Lukashevich, K.
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- 2021
9. Visualization of surface conductivity distributions of tomography cross-section using conductivity zones method
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Sushko, I. A.
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- 2013
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10. Border collision bifurcation of a resonant closed invariant curve.
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Zhusubaliyev, Zh. T., Avrutin, V., Sushko, I., and Gardini, L.
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NEIGHBORHOODS ,BIFURCATION diagrams - Abstract
This paper contributes to studying the bifurcations of closed invariant curves in piecewise-smooth maps. Specifically, we discuss a border collision bifurcation of a repelling resonant closed invariant curve (a repelling saddle-node connection) colliding with the border by a point of the repelling cycle. As a result, this cycle becomes attracting and the curve is destroyed, while a new repelling closed invariant curve appears (not in a neighborhood of the previously existing invariant curve), being associated with quasiperiodic dynamics. This leads to a global restructuring of the phase portrait since both curves mentioned above belong to basin boundaries of coexisting attractors. [ABSTRACT FROM AUTHOR]
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- 2022
- Full Text
- View/download PDF
11. Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information
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Sushko I, Pandey AK, Novotarskyi S, Körner R, Rupp M, Teetz W, Brandmaier S, Abdelaziz A, Prokopenko VV, Tanchuk VY, Todeschini R, Varnek A, Marcou G, Ertl P, Potemkin V, Grishina M, Gasteiger J, Baskin II, Palyulin VA, Radchenko EV, Welsh WJ, Kholodovych V, Chekmarev D, Cherkasov A, Aires-de-Sousa J, Zhang Q-Y, Bender A, Nigsch F, Patiny L, Williams A, Tkachenko V, and Tetko IV
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Information technology ,T58.5-58.64 ,Chemistry ,QD1-999 - Published
- 2011
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12. Online chemical modeling environment
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Tetko I, Sushko I, and Novotarskyi S
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Chemistry ,QD1-999 - Published
- 2009
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13. Emerging trade patterns in a 3-region linear NEG model: three examples
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Commendatore P, Kubin I, Sushko I, Commendatore P, Kubin I, Bougheas S, Kirman A, Kopel M, Bischi GI, Commendatore, P, Kubin, I, and Sushko, I
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Two-dimensional piecewise smooth map, Multistability, Basin of attraction, New Economic Geography model, Three-region models, Trade patterns - Abstract
This chapter draws attention to a specific feature of a NEG model that uses linear (and not iso-elastic) demand functions, namely its ability to account for zero trade. Thus, it represents a suitable framework to study how changes in parameters that are typical for NEG models, such as trade costs and regional market size, not only shape the regional distribution of economic activity, but at the same time determine the emergence of additional trade links between formerly autarkic regions. We survey some related papers and present a three-region framework that potentially nests many possible trade patterns. To focus the analysis, we study in more detail three specific trade patterns frequently found in the EU trade network. We start with three autarkic regions; then we introduce the possibility that two regions trade with each other; and, finally, we allow for one region trading with the other two, but the latter are still not trading with each other. We find a surprising plethora of long-run equilibria each involving a specific regional distribution of economic activity and a specific pattern of trade links. We show how a reduction in trade costs shapes simultaneously industry location and the configuration of the trade network.
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- 2018
14. Hicks’ trade cycle revisited: cycles and bifurcations
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Gallegati, M., Gardini, L., Puu, T., and Sushko, I.
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- 2003
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15. Obtaining a hub position: A New Economic Geography analysis of industry location and trade network structures.
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Commendatore, P., Kubin, I., and Sushko, I.
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INDUSTRIAL location ,ECONOMIC geography ,ECONOMIC research ,LOCATION analysis ,RELIEF models - Abstract
We present a linear New Economic Geography model with three regions, one remote region and two regions that entertain a trade agreement with low bilateral trade costs. Only one of these two integrated regions has the outside option to conclude an additional trade agreement with the remote region and to obtain a hub position. We show that the new trade agreement has a substantial impact on industry location and trade patterns and that the effects strongly depend upon level of integration between the initial two regions. It is not always the region with the outside option that profits from using it. Finally, we also show that higher firm mobility may lead to complex dynamics. [ABSTRACT FROM AUTHOR]
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- 2021
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16. Trade Agreements in a linear FE model
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COMMENDATORE, PASQUALE, Kubin I., Sushko I., Bednar-Friedl B., Kleiner J., Commendatore, Pasquale, Kubin, I., and Sushko, I.
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New Economic Geography, Agglomeration, Trade agreements - Abstract
The treaty of Rome was signed in 1957 and it started a continuous process of strengthening the internal integration of the EU. In this study, we consider the economic effects of intensified trade integration within the Union in which productive factors are also mobile. We argue that a New Economic Geography (NEG) perspective is preferable to the Heckscher-Ohlin approach. We show that trade integration leads to specialization, trade creation, and trade diversion (as predicted by a standard Heckscher-Ohlin framework), but it may also lead to agglomeration within the Union, which is typical of a NEG framework. We show that these agglomeration processes reinforce the specialization and trade effects of trade integration. Finally, we provide insights into the dynamic processes and show that the coexistence of attractors in our modeling approach is more pervasive than in a standard NEG framework.
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- 2016
17. The role of centrality and market size in a 4-region asymmetric new economic geography model
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Pasquale commendatore, Kubin I, Mossay P, Sushko I, Commendatore, Pasquale, I, Kubin, P, Mossay, and I, Sushko
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New economic geography, Market access, Centrality, Transit traffic, Industrial agglomeration, Two-dimensional piecewise smooth map, Local and global dynamics - Abstract
In this paper, we put forward a four-region new economic geography footloose entrepreneur model in which regions are differentiated by their size and their geographical position along a line. There are two distinct trade blocs, each of them consisting of a pair of regions. Direct and indirect trade between all regions is allowed, whereas factor mobility can occur only between regions of the same bloc. Given this more general geographical structure, as compared to previous studies, we are able to disentangle two manifestations of the market access effect: firms can take advantage of locating both in a more central region (centrality effect) and/or in a bigger region (local market size effect). The model is able to generate a plethora of long-term outcomes, including four equilibria with full agglomeration in each trade bloc that can be ranked by factor owners. Equilibria where industry is dispersed or agglomerated in a bloc and dispersed in the other one, are also possible as well as more complex attractors. Finally, by allowing direct and indirect trade between regions, we are able to look at the effect of trade integration on transit traffic by evaluating in a preliminary analysis the consequences of policies aiming at limiting transport volumes in a model with shifting industry.
- Published
- 2017
18. Online chemical modeling environment
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Novotarskyi, S, Sushko, I, and Tetko, I
- Published
- 2009
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19. Consistency of linear forecasts in a nonlinear stochastic economy
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Hommes, C., Sorger, G., Wagener, F., Bischi, G.I., Chiarella, C., Sushko, I., and Equilibrium, Expectations & Dynamics / CeNDEF (ASE, FEB)
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Nonlinear system ,Economy ,Stochastic process ,Consistency (statistics) ,Econometrics ,Economics ,Adaptive learning ,Overlapping generations model ,Conditional expectation ,Bounded rationality ,Path dependence - Abstract
The notion of consistent expectations equilibrium is extended to economies that are described by a nonlinear stochastic system. Agents in the model do not know the nonlinear law of motion and use a simple linear forecasting rule to form their expectations. Along a stochastic consistent expectations equilibrium (SCEE), these expectations are correct in a linear statistical sense, i.e., the unconditional mean and autocovariances of the actual (but unknown) nonlinear stochastic process coincide with those of the linear stochastic process on which the agents base their beliefs. In general, the linear forecasts do not coincide with the true conditional expectation, but an SCEE is an ‘approximate rational expectations equilibrium’ in the sense that forecasting errors are unbiased and uncorrelated. Adaptive learning of SCEE is studied in an overlapping generations framework.
- Published
- 2013
20. 2D discontinuous piecewise linear map: Emergence of fashion cycles.
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Gardini, L., Sushko, I., and Matsuyama, K.
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DISCRETE-time systems , *FASHION , *PIECEWISE linear approximation , *BIFURCATION theory , *CONTINUOUS time systems - Abstract
We consider a discrete-time version of the continuous-time fashion cycle model introduced in Matsuyama, 1992. Its dynamics are defined by a 2D discontinuous piecewise linear map depending on three parameters. In the parameter space of the map periodicity, regions associated with attracting cycles of different periods are organized in the period adding and period incrementing bifurcation structures. The boundaries of all the periodicity regions related to border collision bifurcations are obtained analytically in explicit form. We show the existence of several partially overlapping period incrementing structures, that is, a novelty for the considered class of maps. Moreover, we show that if the time-delay in the discrete time formulation of the model shrinks to zero, the number of period incrementing structures tends to infinity and the dynamics of the discrete time fashion cycle model converges to those of continuous-time fashion cycle model. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
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21. Border Collision Bifurcation in a simple oligopoly model with constraints
- Author
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Bischi, GIAN ITALO, Lamantia, F., and Sushko, I.
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Border collision bifurcations ,Piecewise-smooth dynamical system ,Cournot oligopoly - Published
- 2012
22. Study of strange matter production in the heavy ion collisions at NUCLOTRON
- Author
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Ablyazimov, Timur O., Aichelin, J., Andreev, V. V., Avdejchikov, V. V., Averianov, A. V., Avramenko, S. V., Akishina, V. P., Akishin, P. G., Aksinenko, V. D., Alfeev, A. V., Alfeev, V. S., Babkin, V. A., Baginyan, S. A., Balandin, V. P., Baranova, A. V., Barznat, M. I., Basylev, S. N., Belyakov, Dmitry V., Bogdanova, G. A., Boguslavsky, I. V., Bolshakova, I. A., Boos, E. E., Bratkovskaya, Elena L., Cassing, W., Chernenko, S. P., Davkov, V., Davkov, K., Demidova, V. I., Deng, Z., Derenovskaya, O. Yu., Donskov, S. V., Dunin, V. B., Ershov, A. A., Fateev, O. V., Fedorov, Yu. I., Gapienko, V. A., Gavrishuk, O. P., Genchev, S. G., Golovatyuk, V. M., Golokhvastov, A. I., Golovnya, S. N., Grigalashvili, N., Guber, F. F., Gudima, K. K., Gumen, S., Gurchin, Yu. V., Hartnack, Christoph, Hayduchok, V., Heuser, J., Huang, X., Ivanov, V. V., Ivashkin, A. P., Ierusalimov, A. P., Ilgenfritz, E.-M., Isupov, A. Yu., Ivanets, V., Janek, M., Karachuk, Yu.-T., Karmanov, D. E., Kekelidze, V. D., Kekelidze, G. D., Khabarov, V. S., Khabarov, S. V., Kholodenko, A. G., Khrenov, A. N., Kireev, V. I., Kiryushin, Yu. T., Kisel, P. I., Kisel, Ivan, Kogut, I., Kokoulina, E. S., Kolesnikov, Vadim Ivanovith, Konchakovski, V., Kopko, B., Korolev, M. G., Korotkova, A. M., Kost, Y., Kovaljova, N., Kovtun, V. E., Kozachenko, L., Kravets, M., Kugler, A., Kurbatov, E. O., Kurepin, A. B., Kurilkin, Alexei. K., Kurilkin, Pavel. K., Kushpil, V., Kutov, A. Yu., Kuznezov, A. V., Kuzmin, N. A., Ladygin, E. A., Ladygin, Vladimir P., Ladygina, N. B., Lebedev, A. A., Lenok, V. V., Levchenko, A., Li, Y., Linnyk, O., Lipchinski, D., Litvinenko, E. P., Lobastov, S. P., Lokhtin, I. P., Lukstins, J., Lyashchenko, V. N., Madigozhin, D. T., Makido, O., Maksimenko, N. V., Malakhov, A. I., Malinina, L. V., Martinska, M., Merkin, M. M., Mikhaylov, Yu. V., Mialkovsky, V. V., Moroz, A., Murin, Yu. N., Nagorny, S. N., Nakalov, Y., Nikitin, V. A., Nomokonov, P. V., Okhrimenko, O. V., Palynyak, I., Pavljuchkov, V. V., Parfenov, A. N., Petukhov, Yu. P., Pechenov, V. N., Pechenova, O. Yu., Peshekhonov, V. D., Piyadin, S. M., Polyakov, V. A., Popovichi, J., Radkov, I. S., Radnev, S. V., Rakhlin, L., Raportirenko, A. M., Rashevski, G., Reva, S. N., Reznikov, S. G., Riadovikov, V. N., Rukoyatkin, P. A., Rufanov, I. A., Sadovsky, A. S., Semak, A. A., Senger, P., Shabunov, A. V., Shapovalov, H., Shejnast, V., Shkilyov, A. L., Shurygin, F., Shutov, A. V., Slepnev, V. M., Slepnev, I. V., Snigirev, A. M., Sushko, I., Suzdalev, V. I., Svoboda, O., Syschenko, V. V., Sychkov, S. Yu., Terekhin, A .A., Terlezky, A. V., Teryaev, O. V., Tiflov, V. V., Tikhomirov, V. V., Tlusty, P., Topilin, N. D., Trpisova, B., Tsupa, Yu. P., Turchin, A. A., Tymoshyn, S., Ukhanov, M. N., Usenko, E. A., Urban, J., Vasendina, V. A., Vasiliev, T. A., Vassiliev, Yuri, Vladimirova, N. M., Vishnevsky, A. V., Vnukov, I. E., Vokal, S., Volgin, S. V., Volkov, V. Yu., Vorobiev, A. P., Voronin, A. G., Voronyuk, V. V., Voroshylo, H., Wang, J., Wang, Y., Yerashok, V., Yukaev, A. I., Zagachevskyi, Y., Zaljyubovsky, I. I., Zanevsky, Yu. V., Zenkov, A., Zhu, X., Zinchenko, A. P., Zrelov, P. V., and Zryuev, V. N.
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Physics::Instrumentation and Detectors ,Nuclear Theory ,ddc:530 ,Nuclear Experiment - Abstract
It is proposed to install an experimental setup in the fixed-target hall of the Nuclotron with the final goal to perform a research program focused on the production of strange matter in heavyion collisions at beam energies between 2 and 6 A GeV. The basic setup will comprise a large acceptance dipole magnet with inner tracking detector modules based on double-sided Silicon micro-strip sensors and GEMs. The outer tracking will be based on the drift chambers and straw tube detector. Particle identification will be based on the time-of-flight measurements. This setup will be sufficient perform a comprehensive study of strangeness production in heavy-ion collisions, including multi-strange hyperons, multi-strange hypernuclei, and exotic multi-strange heavy objects. These pioneering measurements would provide the first data on the production of these particles in heavy-ion collisions at Nuclotron beam energies, and would open an avenue to explore the third (strangeness) axis of the nuclear chart. The extension of the experimental program is related with the study of in-medium effects for vector mesons decaying in hadronic modes. The studies of the NN and NA reactions for the reference is assumed.
- Published
- 2012
23. Organizing centers in parameter space of discontinuous 1D maps with one increasing and one decreasing branches
- Author
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Gardini, Laura, Avrutin, V., Schanz, M., Granados, A., and Sushko, I.
- Published
- 2012
24. Applicability domain of QSAR models
- Author
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Sushko, I.
- Subjects
QSAR ,chemoinformatics ,applicability domain ,machine learning - Abstract
In recent decades, computational models have gained popularity for predictions of biological activities and physico-chemical properties. The major limiting point of computational models is a lack for a clear definition of their applicability domain. The work introduces the methodology for the AD assessment and performs a comprehensive benchmarking analysis of existing and new approaches. The practical AD assessment is demonstrated in a number of studies on the prediction of such properties as mutagenicity (Ames test), toxicity (inhibition growth concentration), lipophilicity and cytochromes inhibition. It is shown that the AD approaches allow to estimate the prediction accuracy for every compound individually and, thereby, to identify highly accurate predictions with the accuracy close to that of experimental measurements. All the introduced AD methods are implemented as a part of a new platform for chemical modeling (OCHEM) and are publicly available online at http://ochem.eu.
- Published
- 2011
25. Corruption in Public Procurement: Border Collision Bifurcations in a One-dimensional Piecewise Smooth Map
- Author
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Michetti, Elisabetta, Brianzoni, S., and Sushko, I.
- Published
- 2010
26. The research of L-type matching filter parameters.
- Author
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Movchanyuk, A., Fesich, V., Sushko, I., and Vistyzenko, Ye.
- Published
- 2016
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27. Nonsmooth one-dimensional maps: some basic concepts and definitions.
- Author
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Sushko, I., Gardini, L., and Avrutin, V.
- Subjects
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SMOOTHING (Numerical analysis) , *DYNAMICAL systems , *DIFFERENCE equations - Abstract
The main purpose of the present survey is to contribute to the theory of dynamical systems defined by one-dimensionalpiecewise monotone maps. We recall some definitions known from the theory ofsmoothmaps, which are applicable to piecewise smooth ones, and discuss the notions specific for the considered class of maps. To keep the presentation clear for the researchers working in other fields, especially in applications, many examples are provided. We focus mainly on the notions and concepts which are used for the investigation of various kinds of attractors of a map and related bifurcation structures observed in its parameter space. [ABSTRACT FROM PUBLISHER]
- Published
- 2016
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28. On Chaotic attractors at the transition from homeomorphism to endomorphismsin a family of two-dimensional piece-wise linear maps
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Sushko, I. M., Maistrenko, Y. L., and Gardini, Laura
- Published
- 1999
29. Bifurcation structure in the skew tent map and its application as a border collision normal form.
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Sushko, I., Avrutin, V., and Gardini, L.
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- *
BIFURCATION theory , *DYNAMICAL systems , *LINEAR operators - Abstract
The goal of the present paper is to collect the results related to dynamics of a one-dimensional piecewise linear map widely known as the skew tent map. These results may be useful for the researchers working on theoretical and applied problems in the field of nonsmooth dynamical systems. In particular, we propose the complete description of the bifurcation structure of the parameter space of the skew tent map, providing the related proofs. It is also shown how these results can be used to classify border collision bifurcations in one-dimensional piecewise smooth maps. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
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30. A propos Brexit: on the breaking up of integration areas – an NEG analysis
- Author
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Iryna Sushko, Pasquale Commendatore, Ingrid Kubin, Commendatore, P., Kubin, I., and Sushko, I.
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05 social sciences ,Geography, Planning and Development ,0211 other engineering and technologies ,021107 urban & regional planning ,02 engineering and technology ,JEL C62, F2, F12, R12 ,industry agglomeration, trade patterns, economic disintegration, New Economic Geography ,Brexit ,0502 economics and business ,Earth and Planetary Sciences (miscellaneous) ,Economics ,Economic geography ,050207 economics ,Statistics, Probability and Uncertainty ,General Economics, Econometrics and Finance - Abstract
Inspired by Brexit, the paper explores the effects of splitting an integration area or "Union" on trade Patterns and the spatial distribution of industry. A linear three-region New Economic Geography (NEG) model is developed and two possible situations before separation are considered: agglomeration and dispersion. By analogy with the Brexit options, soft and hard separation scenarios are considered. Firms in the leaving region may move to the larger Union market, even on the periphery, relocation substituting trade; or firms in the Union may move in the more isolated leaving region, escaping from competition. The paper also analyses deeper Union integration following separation. Instances of multistability and complex Dynamics are found.
- Published
- 2021
31. Some dynamical models in regional economics: Economic structure and analytic tools
- Author
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Pasquale Commendatore, Iryna Sushko, Ingrid Kubin, Bischi G.I., Panchuk A., Radi D., Commendatore, Pasquale, Kubin, I., and Sushko, I.
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Mathematical theory ,Structure (mathematical logic) ,Dynamical systems theory ,Dynamic models ,Management science ,Regional economics ,Simple (abstract algebra) ,Computer science ,New Economic Geography, Dynamical models, Multi-regional modelling ,Focus (optics) ,Mathematical economics - Abstract
This chapter acquaints the reader with the use of dynamic models in regional economics. The focus is on the New Economic Geography (NEG) approach. A brief comparison is provided between NEG and other economic approaches to investigate regional inequalities. The analytic structure of a general multi-regional model is described, and some simple examples are presented, where the number of regions is assumed to be small to obtain more easily analytic and numerical results. Tools from the mathematical theory of dynamical systems are drawn to study the qualitative properties of such multi-regional model.
- Published
- 2016
32. A three-Region New Economic Geography Model in Discrete Time: Preliminary Results on Global Dynamics
- Author
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COMMENDATORE, PASQUALE, Kubin I., Bischi G. I., Chiarella C., Sushko I., Commendatore, Pasquale, and Kubin, I.
- Subjects
New Economic Geography ,Multiregional economic model ,footloose entrepreneur - Abstract
In this paper, we deal with a three-region new economic geography model. The dynamic law which governs the migration of the mobile factor – in our context, “footloose” entrepreneurs (Commendatore et al. (Spat Econ Anal 3(1):115–141, 2008); Forslid and Ottaviano (J Econ Geogr 3:229–240, 2003)) – across three identical regions is formulated in discrete time. The resulting dynamical model belongs to the class of two-dimensional noninvertible maps (Mira et al. (1996) Chaotic dynamics in two-dimensional noninverible maps. World Scientific, Singapore). We present the local stability analysis of the map’s fixed points, corresponding to long term stationary equilibria of the economic system, and a preliminary study of its global stability properties. Our results show that the presence of a third region matters and that there are crucial differences with respect to the symmetric two-region footloose entrepreneurs model: firstly, when the manufacturing sector is absent in one of the three regions, stable asymmetric equilibria may emerge; secondly, we detect complex/strange two-dimensional attractors that cannot exist in two-region new economic geography models, which are typically one-dimensional; finally, we highlight the complex self-similar structure of the basins of attraction of some of the two-dimensional attractors.
- Published
- 2013
33. Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information
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Gilles Marcou, Florian Nigsch, Ahmed Abdelaziz, Qingyou Zhang, Vladyslav Kholodovych, William J. Welsh, Matthias Rupp, Antony J. Williams, Vsevolod Yu. Tanchuk, Valery Tkachenko, Volodymyr V. Prokopenko, Sergii Novotarskyi, Alexandre Varnek, Igor I. Baskin, Christof H. Schwab, Peter Ertl, João Aires-de-Sousa, Eugene V. Radchenko, Johann Gasteiger, Robert Körner, Igor V. Tetko, Iurii Sushko, Andreas Bender, Maria Grishina, Vladimir A. Palyulin, Dmitriy Chekmarev, Luc Patiny, Wolfram Teetz, Artem Cherkasov, Stefan Brandmaier, Roberto Todeschini, Anil Kumar Pandey, Vladimir Potemkin, Sushko, I, Novotarskyi, S, Körner, R, Pandey, A, Rupp, M, Teetz, W, Brandmaier, S, Abdelaziz, A, Prokopenko, V, Tanchuk, V, Todeschini, R, Varnek, A, Marcou, G, Ertl, P, Potemkin, V, Grishina, M, Gasteiger, J, Schwab, C, Baskin, I, Palyulin, V, Radchenko, E, Welsh, W, Kholodovych, V, Chekmarev, D, Cherkasov, A, Aires de Sousa, J, Zhang, Q, Bender, A, Nigsch, F, Patiny, L, and Williams, A
- Subjects
Information management ,Databases, Factual ,Computer science ,Estimation of accuracy of predictions ,Information Management ,Molecular Similarity ,Modeling workflow ,Quantitative Structure-Activity Relationship ,01 natural sciences ,Partition-Coefficients ,Descriptors ,Article ,Set (abstract data type) ,World Wide Web ,03 medical and health sciences ,User-Computer Interface ,Resource (project management) ,CHIM/01 - CHIMICA ANALITICA ,Applicability domain ,Drug Discovery ,Physical and Theoretical Chemistry ,030304 developmental biology ,0303 health sciences ,Internet ,On-line web platform ,business.industry ,Information Dissemination ,Open access ,E-State Indexes ,0104 chemical sciences ,Variety (cybernetics) ,Computer Science Applications ,Data sharing ,010404 medicinal & biomolecular chemistry ,On-line web platform, Modeling workflow, Estimation of accuracy of predictions, Applicability domain, Data sharing, Open access ,In-Silico ,Models, Chemical ,Cheminformatics ,Shape Signatures ,Associative Neural Networks ,The Internet ,ddc:004 ,business ,Prediction - Abstract
The Online Chemical Modeling Environment is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. A user-contributed database contains a set of tools for easy input, search and modification of thousands of records. The OCHEM database is based on the wiki principle and focuses primarily on the quality and verifiability of the data. The database is tightly integrated with the modeling framework, which supports all the steps required to create a predictive model: data search, calculation and selection of a vast variety of molecular descriptors, application of machine learning methods, validation, analysis of the model and assessment of the applicability domain. As compared to other similar systems, OCHEM is not intended to re-implement the existing tools or models but rather to invite the original authors to contribute their results, make them publicly available, share them with other users and to become members of the growing research community. Our intention is to make OCHEM a widely used platform to perform the QSPR/QSAR studies online and share it with other users on the Web. The ultimate goal of OCHEM is collecting all possible chemoinformatics tools within one simple, reliable and user-friendly resource. The OCHEM is free for web users and it is available online at http://www.ochem.eu . © 2011 The Author(s).
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34. Complexity in Environment and Space - Sensitivity on Model Specification.
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Commendatore P, Kubin I, and Sushko I
- Abstract
In this paper, we study the complex interaction between environmental damage and location in space of firms and entrepreneurial households. We use a New Economic Geography (NEG) framework, suitably extended to account for environmental damage and the two mobility processes. The resulting model is a two-dimensional piecewise smooth map with two constraints for each variable, and we use analytic and numerical tools to explore its long-run dynamics. We pay special attention to the different types of fixed points and the structure of the respective basins of attraction. Their complexity re-enforces a core theme of the NEG: History matters for the long run location in space of economic activity.
- Published
- 2024
35. A financial market model with two discontinuities: Bifurcation structures in the chaotic domain.
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Panchuk A, Sushko I, and Westerhoff F
- Abstract
We continue the investigation of a one-dimensional piecewise linear map with two discontinuity points. Such a map may arise from a simple asset-pricing model with heterogeneous speculators, which can help us to explain the intricate bull and bear behavior of financial markets. Our focus is on bifurcation structures observed in the chaotic domain of the map's parameter space, which is associated with robust multiband chaotic attractors. Such structures, related to the map with two discontinuities, have been not studied before. We show that besides the standard bandcount adding and bandcount incrementing bifurcation structures, associated with two partitions, there exist peculiar bandcount adding and bandcount incrementing structures involving all three partitions. Moreover, the map's three partitions may generate intriguing bistability phenomena.
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- 2018
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36. The QSPR-THESAURUS: the online platform of the CADASTER project.
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Brandmaier S, Peijnenburg W, Durjava MK, Kolar B, Gramatica P, Papa E, Bhhatarai B, Kovarich S, Cassani S, Roy PP, Rahmberg M, Öberg T, Jeliazkova N, Golsteijn L, Comber M, Charochkina L, Novotarskyi S, Sushko I, Abdelaziz A, D'Onofrio E, Kunwar P, Ruggiu F, and Tetko IV
- Subjects
- Linear Models, Research Design, Vocabulary, Controlled, Hazardous Substances toxicity, Internet, Quantitative Structure-Activity Relationship, Risk Assessment
- Abstract
The aim of the CADASTER project (CAse Studies on the Development and Application of in Silico Techniques for Environmental Hazard and Risk Assessment) was to exemplify REACH-related hazard assessments for four classes of chemical compound, namely, polybrominated diphenylethers, per and polyfluorinated compounds, (benzo)triazoles, and musks and fragrances. The QSPR-THESAURUS website (http: / /qspr-thesaurus.eu) was established as the project's online platform to upload, store, apply, and also create, models within the project. We overview the main features of the website, such as model upload, experimental design and hazard assessment to support risk assessment, and integration with other web tools, all of which are essential parts of the QSPR-THESAURUS., (2014 FRAME.)
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- 2014
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37. Development of dimethyl sulfoxide solubility models using 163,000 molecules: using a domain applicability metric to select more reliable predictions.
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Tetko IV, Novotarskyi S, Sushko I, Ivanov V, Petrenko AE, Dieden R, Lebon F, and Mathieu B
- Subjects
- Linear Models, Neural Networks, Computer, Reproducibility of Results, Solubility, Support Vector Machine, Artificial Intelligence, Databases, Pharmaceutical, Dimethyl Sulfoxide chemistry, Informatics methods
- Abstract
The dimethyl sulfoxide (DMSO) solubility data from Enamine and two UCB pharma compound collections were analyzed using 8 different machine learning methods and 12 descriptor sets. The analyzed data sets were highly imbalanced with 1.7-5.8% nonsoluble compounds. The libraries' enrichment by soluble molecules from the set of 10% of the most reliable predictions was used to compare prediction performances of the methods. The highest accuracies were calculated using a C4.5 decision classification tree, random forest, and associative neural networks. The performances of the methods developed were estimated on individual data sets and their combinations. The developed models provided on average a 2-fold decrease of the number of nonsoluble compounds amid all compounds predicted as soluble in DMSO. However, a 4-9-fold enrichment was observed if only 10% of the most reliable predictions were considered. The structural features influencing compounds to be soluble or nonsoluble in DMSO were also determined. The best models developed with the publicly available Enamine data set are freely available online at http://ochem.eu/article/33409 .
- Published
- 2013
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38. From descriptors to predicted properties: experimental design by using applicability domain estimation.
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Brandmaier S, Novotarskyi S, Sushko I, and Tetko IV
- Subjects
- Regression Analysis, Research Design, Risk Assessment methods, Hazardous Substances toxicity
- Abstract
The importance of reliable methods for representative sub-sampling in terms of experimental design and risk assessment within the European Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) system is crucial. We developed experimental design approaches, by utilising predicted properties and the 'distance to model' parameter, to estimate the benefits of certain compounds to the quality of a resulting model. A statistical evaluation of four regression data sets and one classification data set showed that the adaptive concept of iteratively refining the representation of the chemical space contributes to a more efficient and more reliable selection in comparison to traditional approaches. The evaluation of compounds with regard to the uncertainty and the correlation of prediction is beneficial, and in particular, for regression data sets of sufficient size, whereas the use of predicted properties to define the chemical space is beneficial for classification models., (2013 FRAME.)
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- 2013
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39. ToxAlerts: a Web server of structural alerts for toxic chemicals and compounds with potential adverse reactions.
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Sushko I, Salmina E, Potemkin VA, Poda G, and Tetko IV
- Subjects
- Drug Evaluation, Preclinical, Humans, Quantitative Structure-Activity Relationship, Databases, Chemical, Drug-Related Side Effects and Adverse Reactions, Internet, Pharmaceutical Preparations chemistry
- Abstract
The article presents a Web-based platform for collecting and storing toxicological structural alerts from literature and for virtual screening of chemical libraries to flag potentially toxic chemicals and compounds that can cause adverse side effects. An alert is uniquely identified by a SMARTS template, a toxicological endpoint, and a publication where the alert was described. Additionally, the system allows storing complementary information such as name, comments, and mechanism of action, as well as other data. Most importantly, the platform can be easily used for fast virtual screening of large chemical datasets, focused libraries, or newly designed compounds against the toxicological alerts, providing a detailed profile of the chemicals grouped by structural alerts and endpoints. Such a facility can be used for decision making regarding whether a compound should be tested experimentally, validated with available QSAR models, or eliminated from consideration altogether. The alert-based screening can also be helpful for an easier interpretation of more complex QSAR models. The system is publicly accessible and tightly integrated with the Online Chemical Modeling Environment (OCHEM, http://ochem.eu). The system is open and expandable: any registered OCHEM user can introduce new alerts, browse, edit alerts introduced by other users, and virtually screen his/her data sets against all or selected alerts. The user sets being passed through the structural alerts can be used at OCHEM for other typical tasks: exporting in a wide variety of formats, development of QSAR models, additional filtering by other criteria, etc. The database already contains almost 600 structural alerts for such endpoints as mutagenicity, carcinogenicity, skin sensitization, compounds that undergo metabolic activation, and compounds that form reactive metabolites and, thus, can cause adverse reactions. The ToxAlerts platform is accessible on the Web at http://ochem.eu/alerts, and it is constantly growing.
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- 2012
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40. A comparison of different QSAR approaches to modeling CYP450 1A2 inhibition.
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Novotarskyi S, Sushko I, Körner R, Pandey AK, and Tetko IV
- Subjects
- Enzyme Inhibitors chemistry, Humans, Molecular Conformation, Artificial Intelligence, Cytochrome P-450 CYP1A2 Inhibitors, Enzyme Inhibitors pharmacology, Quantitative Structure-Activity Relationship
- Abstract
Prediction of CYP450 inhibition activity of small molecules poses an important task due to high risk of drug-drug interactions. CYP1A2 is an important member of CYP450 superfamily and accounts for 15% of total CYP450 presence in human liver. This article compares 80 in-silico QSAR models that were created by following the same procedure with different combinations of descriptors and machine learning methods. The training and test sets consist of 3745 and 3741 inhibitors and noninhibitors from PubChem BioAssay database. A heterogeneous external test set of 160 inhibitors was collected from literature. The studied descriptor sets involve E-state, Dragon and ISIDA SMF descriptors. Machine learning methods involve Associative Neural Networks (ASNN), K Nearest Neighbors (kNN), Random Tree (RT), C4.5 Tree (J48), and Support Vector Machines (SVM). The influence of descriptor selection on model accuracy was studied. The benefits of "bagging" modeling approach were shown. Applicability domain approach was successfully applied in this study and ways of increasing model accuracy through use of applicability domain measures were demonstrated as well as fragment-based model interpretation was performed. The most accurate models in this study achieved values of 83% and 68% correctly classified instances on the internal and external test sets, respectively. The applicability domain approach allowed increasing the prediction accuracy to 90% for 78% of the internal and 17% of the external test sets, respectively. The most accurate models are available online at http://ochem.eu/models/Q5747 .
- Published
- 2011
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41. Applicability domains for classification problems: Benchmarking of distance to models for Ames mutagenicity set.
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Sushko I, Novotarskyi S, Körner R, Pandey AK, Cherkasov A, Li J, Gramatica P, Hansen K, Schroeter T, Müller KR, Xi L, Liu H, Yao X, Öberg T, Hormozdiari F, Dao P, Sahinalp C, Todeschini R, Polishchuk P, Artemenko A, Kuz'min V, Martin TM, Young DM, Fourches D, Muratov E, Tropsha A, Baskin I, Horvath D, Marcou G, Muller C, Varnek A, Prokopenko VV, and Tetko IV
- Subjects
- Mutagenicity Tests standards, Principal Component Analysis, Benchmarking methods, Classification methods, Mutagenicity Tests methods, Quantitative Structure-Activity Relationship
- Abstract
The estimation of accuracy and applicability of QSAR and QSPR models for biological and physicochemical properties represents a critical problem. The developed parameter of "distance to model" (DM) is defined as a metric of similarity between the training and test set compounds that have been subjected to QSAR/QSPR modeling. In our previous work, we demonstrated the utility and optimal performance of DM metrics that have been based on the standard deviation within an ensemble of QSAR models. The current study applies such analysis to 30 QSAR models for the Ames mutagenicity data set that were previously reported within the 2009 QSAR challenge. We demonstrate that the DMs based on an ensemble (consensus) model provide systematically better performance than other DMs. The presented approach identifies 30-60% of compounds having an accuracy of prediction similar to the interlaboratory accuracy of the Ames test, which is estimated to be 90%. Thus, the in silico predictions can be used to halve the cost of experimental measurements by providing a similar prediction accuracy. The developed model has been made publicly available at http://ochem.eu/models/1 .
- Published
- 2010
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42. Endogenous Business Cycle Dynamics within Metzlers Inventory Model: Adding an Inventory Floor.
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Sushko I, Wegener M, Westerhoff F, and Zaklan G
- Abstract
Metzlers inventory model may produce dampened fluctuations in economic activity, thus contributing to our understanding of business cycle dynamics. For some parameter combinations, however, the model generates oscillations with increasing amplitude, implying that the inventory stock of firms eventually turns negative. Taking this observation into account, we reformulate Metzlers model by simply putting a floor to the inventory level. Within the new piecewise linear model, endogenous business cycle dynamics may now be triggered via a center bifurcation, i.e. for certain parameter combinations production changes are (quasi-)periodic.
- Published
- 2009
43. Critical assessment of QSAR models of environmental toxicity against Tetrahymena pyriformis: focusing on applicability domain and overfitting by variable selection.
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Tetko IV, Sushko I, Pandey AK, Zhu H, Tropsha A, Papa E, Oberg T, Todeschini R, Fourches D, and Varnek A
- Subjects
- Animals, Computer Simulation, Databases, Factual, Models, Statistical, Normal Distribution, Predictive Value of Tests, Reproducibility of Results, Environmental Pollutants chemistry, Environmental Pollutants toxicity, Models, Biological, Quantitative Structure-Activity Relationship, Tetrahymena pyriformis drug effects, Toxicity Tests standards
- Abstract
The estimation of the accuracy of predictions is a critical problem in QSAR modeling. The "distance to model" can be defined as a metric that defines the similarity between the training set molecules and the test set compound for the given property in the context of a specific model. It could be expressed in many different ways, e.g., using Tanimoto coefficient, leverage, correlation in space of models, etc. In this paper we have used mixtures of Gaussian distributions as well as statistical tests to evaluate six types of distances to models with respect to their ability to discriminate compounds with small and large prediction errors. The analysis was performed for twelve QSAR models of aqueous toxicity against T. pyriformis obtained with different machine-learning methods and various types of descriptors. The distances to model based on standard deviation of predicted toxicity calculated from the ensemble of models afforded the best results. This distance also successfully discriminated molecules with low and large prediction errors for a mechanism-based model developed using log P and the Maximum Acceptor Superdelocalizability descriptors. Thus, the distance to model metric could also be used to augment mechanistic QSAR models by estimating their prediction errors. Moreover, the accuracy of prediction is mainly determined by the training set data distribution in the chemistry and activity spaces but not by QSAR approaches used to develop the models. We have shown that incorrect validation of a model may result in the wrong estimation of its performance and suggested how this problem could be circumvented. The toxicity of 3182 and 48774 molecules from the EPA High Production Volume (HPV) Challenge Program and EINECS (European chemical Substances Information System), respectively, was predicted, and the accuracy of prediction was estimated. The developed models are available online at http://www.qspr.org site.
- Published
- 2008
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44. Synchronization and desynchronization under the influence of quasiperiodic forcing.
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Neumann E, Sushko I, Maistrenko Y, and Feudel U
- Abstract
We study the influence of quasiperiodic forcing on synchronization and desynchronization using two coupled quasiperiodically forced logistic maps as a paradigm. We show that due to the forcing the synchronization region in parameter space shrinks. The loss of transverse stability of the synchronized attractors leads to desynchronization. Two types of such blowout bifurcations are described, namely, the blowout bifurcations of synchronized quasiperiodic motion on invariant curves and synchronized strange nonchaotic attractors, both yielding desynchronized chaotic attractors.
- Published
- 2003
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