This paper applies genetic simulated annealing algorithm (SAGA) to solving geometric constraint problems. This method makes full use of the advantages of SAGA and can handle under-/over- constraint problems naturally....This paper applies genetic simulated annealing algorithm (SAGA) to solving geometric constraint problems. This method makes full use of the advantages of SAGA and can handle under-/over- constraint problems naturally. It has advantages (due to its not being sensitive to the initial values) over the Newton-Raphson method, and its yielding of multiple solutions, is an advantage over other optimal methods for multi-solution constraint system. Our experiments have proved the robustness and efficiency of this method.展开更多
The least squares support vector regression (LS-SVR) is usually used for the modeling of single output system, but it is not well suitable for the actual multi-input-multi-output system. The paper aims at the modeling...The least squares support vector regression (LS-SVR) is usually used for the modeling of single output system, but it is not well suitable for the actual multi-input-multi-output system. The paper aims at the modeling of multi-output systems by LS-SVR. The multi-output LS-SVR is derived in detail. To avoid the inversion of large matrix, the recursive algorithm of the parameters is given, which makes the online algorithm of LS-SVR practical. Since the computing time increases with the number of training samples, the sparseness is studied based on the pro-jection of online LS-SVR. The residual of projection less than a threshold is omitted, so that a lot of samples are kept out of the training set and the sparseness is obtained. The standard LS-SVR, nonsparse online LS-SVR and sparse online LS-SVR with different threshold are used for modeling the isomerization of C8 aromatics. The root-mean-square-error (RMSE), number of support vectors and running time of three algorithms are compared and the result indicates that the performance of sparse online LS-SVR is more favorable.展开更多
A hybrid feature selection and classification strategy was proposed based on the simulated annealing genetic algonthrn and multiple instance learning (MIL). The band selection method was proposed from subspace decom...A hybrid feature selection and classification strategy was proposed based on the simulated annealing genetic algonthrn and multiple instance learning (MIL). The band selection method was proposed from subspace decomposition, which combines the simulated annealing algorithm with the genetic algorithm in choosing different cross-over and mutation probabilities, as well as mutation individuals. Then MIL was combined with image segmentation, clustering and support vector machine algorithms to classify hyperspectral image. The experimental results show that this proposed method can get high classification accuracy of 93.13% at small training samples and the weaknesses of the conventional methods are overcome.展开更多
The stochastic simulation algorithm (SSA) accurately depicts spatially homogeneous wellstirred chemically reacting systems with small populations of chemical species and properly represents noise, but it is often ab...The stochastic simulation algorithm (SSA) accurately depicts spatially homogeneous wellstirred chemically reacting systems with small populations of chemical species and properly represents noise, but it is often abandoned when modeling larger systems because of its computational complexity. In this work, a twin support vector regression based stochastic simulations algorithm (TS^3A) is proposed by combining the twin support vector regression and SSA, the former is a well-known robust regression method in machine learning. Numerical results indicate that this proposed algorithm can be applied to a wide range of chemically reacting systems and obtain significant improvements on efficiency and accuracy with fewer simulating runs over the existing methods.展开更多
In this study,we investigated the structural and dynamical properties of liquid water by using ab initio molecular dynamics simulation under periodic boundary conditions based on the fragment-based quantum mechanical ...In this study,we investigated the structural and dynamical properties of liquid water by using ab initio molecular dynamics simulation under periodic boundary conditions based on the fragment-based quantum mechanical approach.This study was carried out using the second-order Møller-Plesset perturbation theory(MP2)with the aug-cc-pVDZ basis set,which has been validated to be sufficiently accurate for describing water interactions.Diverse properties of liquid water,including radial distribution functions,diffusion coefficient,dipole moment,triplet oxygen-oxygen-oxygen angles,and hydrogen-bond structures,were simulated.This ab initio description leads to these properties in good agreement with experimental observations.This computational approach is general and transferable,providing a comprehensive framework for ab initio predictions of properties of condensed-phase matters.展开更多
A scheme of investigating the intracellular metabolic fluxes in central metabolism of Saccharomyces cerevisiae based on isotope model and tracer experiment was developed. The metabolic model applied in this study incl...A scheme of investigating the intracellular metabolic fluxes in central metabolism of Saccharomyces cerevisiae based on isotope model and tracer experiment was developed. The metabolic model applied in this study includes the Embden-Meyerhof-Parnas pathway,the pentose phosphate pathway,the tricarboxylic acid cycle,CO2 anaplerotic reactions,ethanol and acetate formation,and pathways involved in amino acid synthesis. The approach of hybridized genetic algorithm combined with the sequential simplex technique was used to optimize a quadratic error function without the requirement of the information on the partial derivatives. The impact of some key pa-rameters on the algorithm was studied. This approach was proved to be rapid and numerically stable in the analysis of the central metabolism of S.cerevisiae.展开更多
In this work we propose a quantum trajectory approach to the powerful molecular dynamics simulation with surface hopping, from an insight that an effective "observation" is actually implied in the simulation through...In this work we propose a quantum trajectory approach to the powerful molecular dynamics simulation with surface hopping, from an insight that an effective "observation" is actually implied in the simulation through tracking the forces experienced, just like checking the meter's result in quantum measurement process. This treatment can build the nonadiabatic surface hopping on a physical foundation, instead of the usual fictitious and conceptually inconsistent hopping algorithms. The effects and advantages of the proposed scheme are preliminarily illustrated by a two-surface model system.展开更多
文摘This paper applies genetic simulated annealing algorithm (SAGA) to solving geometric constraint problems. This method makes full use of the advantages of SAGA and can handle under-/over- constraint problems naturally. It has advantages (due to its not being sensitive to the initial values) over the Newton-Raphson method, and its yielding of multiple solutions, is an advantage over other optimal methods for multi-solution constraint system. Our experiments have proved the robustness and efficiency of this method.
基金Supported by the National Creative Research Groups Science Foundation of China (60721062)the National Basic Research Program of China (2007CB714000)
文摘The least squares support vector regression (LS-SVR) is usually used for the modeling of single output system, but it is not well suitable for the actual multi-input-multi-output system. The paper aims at the modeling of multi-output systems by LS-SVR. The multi-output LS-SVR is derived in detail. To avoid the inversion of large matrix, the recursive algorithm of the parameters is given, which makes the online algorithm of LS-SVR practical. Since the computing time increases with the number of training samples, the sparseness is studied based on the pro-jection of online LS-SVR. The residual of projection less than a threshold is omitted, so that a lot of samples are kept out of the training set and the sparseness is obtained. The standard LS-SVR, nonsparse online LS-SVR and sparse online LS-SVR with different threshold are used for modeling the isomerization of C8 aromatics. The root-mean-square-error (RMSE), number of support vectors and running time of three algorithms are compared and the result indicates that the performance of sparse online LS-SVR is more favorable.
文摘A hybrid feature selection and classification strategy was proposed based on the simulated annealing genetic algonthrn and multiple instance learning (MIL). The band selection method was proposed from subspace decomposition, which combines the simulated annealing algorithm with the genetic algorithm in choosing different cross-over and mutation probabilities, as well as mutation individuals. Then MIL was combined with image segmentation, clustering and support vector machine algorithms to classify hyperspectral image. The experimental results show that this proposed method can get high classification accuracy of 93.13% at small training samples and the weaknesses of the conventional methods are overcome.
基金This work was supported by the National Natural Science Foundation of China (No.30871341), the National High-Tech Research and Development Program of China (No.2006AA02-Z190), the Shanghai Leading Academic Discipline Project (No.S30405), and the Natural Science Foundation of Shanghai Normal University (No.SK200937).
文摘The stochastic simulation algorithm (SSA) accurately depicts spatially homogeneous wellstirred chemically reacting systems with small populations of chemical species and properly represents noise, but it is often abandoned when modeling larger systems because of its computational complexity. In this work, a twin support vector regression based stochastic simulations algorithm (TS^3A) is proposed by combining the twin support vector regression and SSA, the former is a well-known robust regression method in machine learning. Numerical results indicate that this proposed algorithm can be applied to a wide range of chemically reacting systems and obtain significant improvements on efficiency and accuracy with fewer simulating runs over the existing methods.
基金supported by the National Key R&D Program of China(No.2016YFA0501700 and No.2019YFA0905201)the National Natural Science Foundation of China(No.21703289,No.21922301,and No.21761132022)+2 种基金“Double First-Class”University Project(CPU2018GY09)the Fundamental Research Funds for China Pharmaceutical University(2632019FY01)the Fundamental Research Funds for the Central Universities。
文摘In this study,we investigated the structural and dynamical properties of liquid water by using ab initio molecular dynamics simulation under periodic boundary conditions based on the fragment-based quantum mechanical approach.This study was carried out using the second-order Møller-Plesset perturbation theory(MP2)with the aug-cc-pVDZ basis set,which has been validated to be sufficiently accurate for describing water interactions.Diverse properties of liquid water,including radial distribution functions,diffusion coefficient,dipole moment,triplet oxygen-oxygen-oxygen angles,and hydrogen-bond structures,were simulated.This ab initio description leads to these properties in good agreement with experimental observations.This computational approach is general and transferable,providing a comprehensive framework for ab initio predictions of properties of condensed-phase matters.
基金Supported by the National Natural Science Foundation of China (No.20276065)the Special Funds for Major State BasicResearch Program of China (973 Program, 2007CB707805).
文摘A scheme of investigating the intracellular metabolic fluxes in central metabolism of Saccharomyces cerevisiae based on isotope model and tracer experiment was developed. The metabolic model applied in this study includes the Embden-Meyerhof-Parnas pathway,the pentose phosphate pathway,the tricarboxylic acid cycle,CO2 anaplerotic reactions,ethanol and acetate formation,and pathways involved in amino acid synthesis. The approach of hybridized genetic algorithm combined with the sequential simplex technique was used to optimize a quadratic error function without the requirement of the information on the partial derivatives. The impact of some key pa-rameters on the algorithm was studied. This approach was proved to be rapid and numerically stable in the analysis of the central metabolism of S.cerevisiae.
基金Supported by the Major State Basic Research Project of China under Grant Nos.2011CB808502 and 2012CB932704the National Natural Science Foundation of China under Grant Nos.101202101 and 10874176
文摘In this work we propose a quantum trajectory approach to the powerful molecular dynamics simulation with surface hopping, from an insight that an effective "observation" is actually implied in the simulation through tracking the forces experienced, just like checking the meter's result in quantum measurement process. This treatment can build the nonadiabatic surface hopping on a physical foundation, instead of the usual fictitious and conceptually inconsistent hopping algorithms. The effects and advantages of the proposed scheme are preliminarily illustrated by a two-surface model system.