2051
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Grochowski P, Lesyng B. Extended Hellmann–Feynman forces, canonical representations, and exponential propagators in the mixed quantum-classical molecular dynamics. J Chem Phys 2003. [DOI: 10.1063/1.1624062] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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2052
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2053
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Stribeck N, Funari SS. Nanostructure evolution in a poly(ether ester) elastomer during drawing and the displacement of hard domains from lamellae. ACTA ACUST UNITED AC 2003. [DOI: 10.1002/polb.10550] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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2054
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Abstract
We demonstrate that the Nosé method for constant-temperature molecular-dynamics simulation [Mol. Phys. 52, 255 (1984)] can be substantially generalized by the addition of auxiliary variables to encompass an infinite variety of Hamiltonian thermostats. Such thermostats can be used to enhance ergodicity in systems, such as the one-dimensional harmonic oscillator or certain molecular systems, for which the standard Nosé-Hoover methods fail to reproduce converged canonical distributions. In this respect the method is similar in spirit to the method of Nosé-Hoover chains, but is both more general and Hamiltonian in structure (which allows for the use of efficient symplectic integration schemes). In particular, we show that, within the generalized Nosé formalism outlined herein, any Hamiltonian system can be thermostated with any other, including a copy of itself. This gives one an enormous flexibility in choosing the form of the thermostating bath. Numerical experiments are included in which a harmonic oscillator is thermostated with a collection of noninteracting harmonic oscillators as well as by a soft billiard system.
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Affiliation(s)
- Brian B Laird
- Department of Chemistry and Kansas Institute for Theoretical and Computational Science, University of Kansas, Lawrence, Kansas 66045, USA
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2055
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MARTIN JC, FORNIES-MARQUINA JM, BOTTREAU AM. Application of permittivity mixture laws to carbon black dielectric characterization by time domain reflectometry. Mol Phys 2003. [DOI: 10.1080/0026897021000018367] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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2056
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2057
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Affiliation(s)
- Heiko Briesen
- Lehrstuhl für Prozesstechnik, RWTH Aachen University, Turmstrasse 46, D-52056 Aachen, Germany
| | - Wolfgang Marquardt
- Lehrstuhl für Prozesstechnik, RWTH Aachen University, Turmstrasse 46, D-52056 Aachen, Germany
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2058
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Amisaki T, Toyoda S, Miyagawa H, Kitamura K. Development of hardware accelerator for molecular dynamics simulations: a computation board that calculates nonbonded interactions in cooperation with fast multipole method. J Comput Chem 2003; 24:582-92. [PMID: 12632472 DOI: 10.1002/jcc.10193] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Evaluation of long-range Coulombic interactions still represents a bottleneck in the molecular dynamics (MD) simulations of biological macromolecules. Despite the advent of sophisticated fast algorithms, such as the fast multipole method (FMM), accurate simulations still demand a great amount of computation time due to the accuracy/speed trade-off inherently involved in these algorithms. Unless higher order multipole expansions, which are extremely expensive to evaluate, are employed, a large amount of the execution time is still spent in directly calculating particle-particle interactions within the nearby region of each particle. To reduce this execution time for pair interactions, we developed a computation unit (board), called MD-Engine II, that calculates nonbonded pairwise interactions using a specially designed hardware. Four custom arithmetic-processors and a processor for memory manipulation ("particle processor") are mounted on the computation board. The arithmetic processors are responsible for calculation of the pair interactions. The particle processor plays a central role in realizing efficient cooperation with the FMM. The results of a series of 50-ps MD simulations of a protein-water system (50,764 atoms) indicated that a more stringent setting of accuracy in FMM computation, compared with those previously reported, was required for accurate simulations over long time periods. Such a level of accuracy was efficiently achieved using the cooperative calculations of the FMM and MD-Engine II. On an Alpha 21264 PC, the FMM computation at a moderate but tolerable level of accuracy was accelerated by a factor of 16.0 using three boards. At a high level of accuracy, the cooperative calculation achieved a 22.7-fold acceleration over the corresponding conventional FMM calculation. In the cooperative calculations of the FMM and MD-Engine II, it was possible to achieve more accurate computation at a comparable execution time by incorporating larger nearby regions.
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Affiliation(s)
- Takashi Amisaki
- Department of Biological Regulation, Faculty of Medicine, Tottori University, 86 Nishi-machi, Yonago, Tottori 683-8503, Japan
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2059
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Rajamäki T, Miani A, Halonen L. Vibrational energy levels for symmetric and asymmetric isotopomers of ammonia with an exact kinetic energy operator and new potential energy surfaces. J Chem Phys 2003. [DOI: 10.1063/1.1555801] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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2060
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2061
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Affiliation(s)
- Veroni Barbi
- Institute of Technical and Macromolecular Chemistry, University of Hamburg, Bundesstr. 45, 20146 Hamburg, Germany; Max-Planck-Institute of Colloids and Interfaces, c/o HASYLAB at DESY, Notkestr. 85, 22603 Hamburg, Germany; HASYLAB at DESY, Notkestr. 85, 22603 Hamburg, Germany; and GKSS Research Center, Postfach 1160, 21494 Geesthacht, Germany
| | - Sergio S. Funari
- Institute of Technical and Macromolecular Chemistry, University of Hamburg, Bundesstr. 45, 20146 Hamburg, Germany; Max-Planck-Institute of Colloids and Interfaces, c/o HASYLAB at DESY, Notkestr. 85, 22603 Hamburg, Germany; HASYLAB at DESY, Notkestr. 85, 22603 Hamburg, Germany; and GKSS Research Center, Postfach 1160, 21494 Geesthacht, Germany
| | - Rainer Gehrke
- Institute of Technical and Macromolecular Chemistry, University of Hamburg, Bundesstr. 45, 20146 Hamburg, Germany; Max-Planck-Institute of Colloids and Interfaces, c/o HASYLAB at DESY, Notkestr. 85, 22603 Hamburg, Germany; HASYLAB at DESY, Notkestr. 85, 22603 Hamburg, Germany; and GKSS Research Center, Postfach 1160, 21494 Geesthacht, Germany
| | - Nico Scharnagl
- Institute of Technical and Macromolecular Chemistry, University of Hamburg, Bundesstr. 45, 20146 Hamburg, Germany; Max-Planck-Institute of Colloids and Interfaces, c/o HASYLAB at DESY, Notkestr. 85, 22603 Hamburg, Germany; HASYLAB at DESY, Notkestr. 85, 22603 Hamburg, Germany; and GKSS Research Center, Postfach 1160, 21494 Geesthacht, Germany
| | - Norbert Stribeck
- Institute of Technical and Macromolecular Chemistry, University of Hamburg, Bundesstr. 45, 20146 Hamburg, Germany; Max-Planck-Institute of Colloids and Interfaces, c/o HASYLAB at DESY, Notkestr. 85, 22603 Hamburg, Germany; HASYLAB at DESY, Notkestr. 85, 22603 Hamburg, Germany; and GKSS Research Center, Postfach 1160, 21494 Geesthacht, Germany
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2062
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2063
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2064
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Plagianakos V, Magoulas G, Vrahatis M. Deterministic nonmonotone strategies for effective training of multilayer perceptrons. ACTA ACUST UNITED AC 2002; 13:1268-84. [DOI: 10.1109/tnn.2002.804225] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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2065
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Summanwar V, Jayaraman V, Kulkarni B, Kusumakar H, Gupta K, Rajesh J. Solution of constrained optimization problems by multi-objective genetic algorithm. Comput Chem Eng 2002; 26:1481-92. [DOI: 10.1016/s0098-1354(02)00125-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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2066
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2067
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Luo H, Kolb D, Flad HJ, Hackbusch W, Koprucki T. Wavelet approximation of correlated wave functions. II. Hyperbolic wavelets and adaptive approximation schemes. J Chem Phys 2002. [DOI: 10.1063/1.1494800] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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2068
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2069
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2070
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Stribeck N, Bayer R, von Krosigk G, Gehrke R. Nanostructure evolution of oriented high-pressure injection-molded poly(ethylene) during heating. POLYMER 2002. [DOI: 10.1016/s0032-3861(02)00171-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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2071
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Abstract
A common problem in neuroscience is to identify the features by which a set of measurements can be segregated into different classes, for example into different responses to sensory stimuli. A main difficulty is that the derived distributions are often high-dimensional and complex. Many multivariate analysis techniques, therefore, aim to find a simpler low-dimensional representation. Most of them either involve huge efforts in implementation and data handling or ignore important structures and relationships within the original data. We developed a dimension reduction method by means of radial basis functions (RBF), where only a system of linear equations has to be solved. We show that this approach can be regarded as an extension of a linear correlation-based classifier. The validity and reliability of this technique is demonstrated on artificial data sets. Its practical relevance is further confirmed by discriminating recordings from monkey visual cortex evoked by different stimuli.
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Affiliation(s)
- Alexander Kremper
- Neurophysics Group, Physics Department, Philipps-University, Renthof 7, D-35032, Marburg, Germany.
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2072
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Abstract
We are presenting here a model for processing space-time image sequences and applying them to 3D echo-cardiography. The non-linear evolutionary equations filter the sequence with keeping space-time coherent structures. They have been developed using ideas of regularized Perona-Malik an-isotropic diffusion and geometrical diffusion of mean curvature flow type (Malladi-Sethian), combined with Galilean invariant movie multi-scale analysis of Alvarez et al. A discretization of space-time filtering equations by means of finite volume method is discussed in detail. Computational results in processing of 3D echo-cardiographic sequences obtained by rotational acquisition technique and by real-time 3D echo volumetrics acquisition technique are presented. Quantitative error estimation is also provided.
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Affiliation(s)
- Alessandro Sarti
- Department of Mathematics, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, USA.
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2073
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Suri JS, Liu K, Singh S, Laxminarayan SN, Zeng X, Reden L. Shape recovery algorithms using level sets in 2-D/3-D medical imagery: a state-of-the-art review. IEEE Trans Inf Technol Biomed 2002; 6:8-28. [PMID: 11936600 DOI: 10.1109/4233.992158] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The class of geometric deformable models, also known as level sets, has brought tremendous impact to medical imagery due to its capability of topology preservation and fast shape recovery. In an effort to facilitate a clear and full understanding of these powerful state-of-the-art applied mathematical tools, this paper is an attempt to explore these geometric methods, their implementations and integration of regularizers to improve the robustness of these topologically independent propagating curves/surfaces. This paper first presents the origination of level sets, followed by the taxonomy of level sets. We then derive the fundamental equation of curve/surface evolution and zero-level curves/surfaces. The paper then focuses on the first core class of level sets, known as "level sets without regularizers." This class presents five prototypes: gradient, edge, area-minimization, curvature-dependent and application driven. The next section is devoted to second core class of level sets, known as "level sets with regularizers." In this class, we present four kinds: clustering-based, Bayesian bidirectional classifier-based, shape-based and coupled constrained-based. An entire section is dedicated to optimization and quantification techniques for shape recovery when used in the level set framework. Finally, the paper concludes with 22 general merits and four demerits on level sets and the future of level sets in medical image segmentation. We present applications of level sets to complex shapes like the human cortex acquired via MRI for neurological image analysis.
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Affiliation(s)
- Jasjit S Suri
- MR Clinical Science Division, Philips Medical Systems, Inc., Cleveland, OH 44143, USA
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2074
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Abstract
In a great variety of neuron models, neural inputs are combined using the summing operation. We introduce the concept of multiplicative neural networks that contain units that multiply their inputs instead of summing them and thus allow inputs to interact nonlinearly. The class of multiplicative neural networks comprises such widely known and well-studied network types as higher-order networks and product unit networks. We investigate the complexity of computing and learning for multiplicative neural networks. In particular, we derive upper and lower bounds on the Vapnik-Chervonenkis (VC) dimension and the pseudo-dimension for various types of networks with multiplicative units. As the most general case, we consider feedforward networks consisting of product and sigmoidal units, showing that their pseudo-dimension is bounded from above by a polynomial with the same order of magnitude as the currently best-known bound for purely sigmoidal networks. Moreover, we show that this bound holds even when the unit type, product or sigmoidal, may be learned. Crucial for these results are calculations of solution set components bounds for new network classes. As to lower bounds, we construct product unit networks of fixed depth with super-linear VC dimension. For sigmoidal networks of higher order, we establish polynomial bounds that, in contrast to previous results, do not involve any restriction of the network order. We further consider various classes of higher-order units, also known as sigma-pi units, that are characterized by connectivity constraints. In terms of these, we derive some asymptotically tight bounds. Multiplication plays an important role in both neural modeling of biological behavior and computing and learning with artificial neural networks. We briefly survey research in biology and in applications where multiplication is considered an essential computational element. The results we present here provide new tools for assessing the impact of multiplication on the computational power and the learning capabilities of neural networks.
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Affiliation(s)
- Michael Schmitt
- Lehrstuhl Mathematik und Informatik, Fakultät für Mathematik, Ruhr-Universität Bochum, D-44780 Bochum, Germany.
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2075
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Abstract
We review some of the most recent advances in the area of wavelet applications in medical imaging. We first review key concepts in the processing of medical images with wavelet transforms and multiscale analysis, including time-frequency tiling, overcomplete representations, higher dimensional bases, symmetry, boundary effects, translational invariance, orientation selectivity, and best-basis selection. We next describe some applications in magnetic resonance imaging, including activation detection and denoising of functional magnetic resonance imaging and encoding schemes. We then present an overview in the area of ultrasound, including computational anatomy with three-dimensional cardiac ultrasound. Next, wavelets in tomography are reviewed, including their relationship to the radon transform and applications in position emission tomography imaging. Finally, wavelet applications in digital mammography are reviewed, including computer-assisted diagnostic systems that support the detection and classification of small masses and methods of contrast enhancement.
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Affiliation(s)
- A F Laine
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, USA.
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2076
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2077
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2078
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Estep D, Holst M, Mikulencak D. Accounting for stability: a posteriori error estimates based on residuals and variational analysis. ACTA ACUST UNITED AC 2001. [DOI: 10.1002/cnm.461] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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2079
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Affiliation(s)
- D.G. Sathwell
- Centre for Nonlinear Dynamics, Department of Physics and Astronomy, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - T. Mullin
- Centre for Nonlinear Dynamics, Department of Physics and Astronomy, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
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2080
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2081
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Abstract
There has been an increasing interest in kernel-based techniques, such as support vector techniques, regularization networks, and gaussian processes. There are inner relationships among those techniques, with the kernel function playing a central role. This article discusses a new class of kernel functions derived from the so-called frames in a function Hilbert space.
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Affiliation(s)
- J B Gao
- Image, Speech and Intelligent System Research Group, Department of Electronics and Computer Science, University of Southampton, Southampton SO17 1BJ, UK
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2082
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2083
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Abstract
A general methodology is presented for the modeling, simulation, design, evaluation, and statistical analysis of (13)C-labeling experiments for metabolic flux analysis. The universal software framework 13C-FLUX was implemented to support all steps of this process. Guided by the example of anaplerotic flux determination in Corynebacterium glutamicum, the technical details of the model setup, experimental design, and data evaluation are discussed. It is shown how the network structure, the input substrate composition, the assumptions about fluxes, and the measurement configuration are specified within 13C-FLUX. Based on the network model, different experimental designs are computed depending on the goal of the investigations. Finally, a specific experiment is evaluated and the various statistical methods used to analyze the results are briefly explained. The appendix gives some details about the software implementation and availability.
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Affiliation(s)
- W Wiechert
- Department of Simulation, IMR, University of Siegen, Paul-Bonatz-Strasse 9-11, D-57068 Siegen, Germany.
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2084
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2085
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2086
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2087
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Kerkyacharian G, Picard D, Birgé L, Hall P, Lepski O, Mammen E, Tsybakov A, Kerkyacharian G, Picard D. Thresholding algorithms, maxisets and well-concentrated bases. TEST-SPAIN 2000; 9:283-344. [DOI: 10.1007/bf02595738] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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2088
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Abstract
This paper presents a literature survey of automatic 3D surface registration techniques emphasizing the mathematical and algorithmic underpinnings of the subject. The relevance of surface registration to medical imaging is that there is much useful anatomical information in the form of collected surface points which originate from complimentary modalities and which must be reconciled. Surface registration can be roughly partitioned into three issues: choice of transformation, elaboration of surface representation and similarity criterion, and matching and global optimization. The first issue concerns the assumptions made about the nature of relationships between the two modalities, e.g. whether a rigid-body assumption applies, and if not, what type and how general a relation optimally maps one modality onto the other. The second issue determines what type of information we extract from the 3D surfaces, which typically characterizes their local or global shape, and how we organize this information into a representation of the surface which will lead to improved efficiency and robustness in the last stage. The last issue pertains to how we exploit this information to estimate the transformation which best aligns local primitives in a globally consistent manner or which maximizes a measure of the similarity in global shape of two surfaces. Within this framework, this paper discusses in detail each surface registration issue and reviews the state-of-the-art among existing techniques.
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Affiliation(s)
- M A Audette
- Montreal Neurological Institute, McGill University, Quebec, Canada.
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2089
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Binder T, Cruse A, Cruz Villar C, Marquardt W. Dynamic optimization using a wavelet based adaptive control vector parameterization strategy. Comput Chem Eng 2000. [DOI: 10.1016/s0098-1354(00)00357-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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2090
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2091
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Affiliation(s)
- E. Gallestey
- Institute for Dynamical Systems, University of Bremen, 28334 Bremen, Germany
| | - D. Hinrichsen
- Institute for Dynamical Systems, University of Bremen, 28334 Bremen, Germany
| | - A. J. Pritchard
- Department of Mathematics, University of Warwick, Coventry CV4 7AL, UK
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2092
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2093
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2094
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2095
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Bieniasz L. Use of dynamically adaptive grid techniques for the solution of electrochemical kinetic equations. J Electroanal Chem (Lausanne) 2000; 481:115-33. [DOI: 10.1016/s0022-0728(99)00460-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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2096
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2097
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2098
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2099
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2100
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