This study was conducted to establish a Support Vector Machines(SVM)-Markov Chain prediction model for prediction of mining water inflow. According to the raw data sequence, the Support Vector Machines(SVM) model was ...This study was conducted to establish a Support Vector Machines(SVM)-Markov Chain prediction model for prediction of mining water inflow. According to the raw data sequence, the Support Vector Machines(SVM) model was built, and then revised by means of a Markov state change probability matrix. Through dividing the state and analyzing absolute errors and relative errors and other indexes of the measured value and the fitted value of SVM, the prediction results were improved. Finally,the model was used to calculate relative errors. Through predicting and analyzing mining water inflow, the prediction results of the model were satisfactory. The results of this study enlarge the application scope of the Support Vector Machines(SVM) prediction model and provide a new method for scientific forecasting water inflow in coal mining.展开更多
Molecular dynamics （MD） simulation has become a powerful tool to investigate the structure- function relationship of proteins and other biological macromolecules at atomic resolution and biologically relevant timesc...Molecular dynamics （MD） simulation has become a powerful tool to investigate the structure- function relationship of proteins and other biological macromolecules at atomic resolution and biologically relevant timescales. MD simulations often produce massive datasets con- taining millions of snapshots describing proteins in motion. Therefore, clustering algorithms have been in high demand to be developed and applied to classify these MD snapshots and gain biological insights. There mainly exist two categories of clustering algorithms that aim to group protein conformations into clusters based on the similarity of their shape （geometric clustering） and kinetics （kinetic clustering）. In this paper, we review a series of frequently used clustering algorithms applied in MD simulations, including divisive algorithms, ag- glomerative algorithms （single-linkage, complete-linkage, average-linkage, centroid-linkage and ward-linkage）, center-based algorithms （K-Means, K-Medoids, K-Centers, and APM）, density-based algorithms （neighbor-based, DBSCAN, density-peaks, and Robust-DB）, and spectral-based algorithms （PCCA and PCCA＋）. In particular, differences between geomet- ric and kinetic clustering metrics will be discussed along with the performances of diflhrent clustering algorithms. We note that there does not exist a one-size-fits-all algorithm in the classification of MD datasets. For a specific application, the right choice of clustering algo- rithm should be based on the purpose of clustering, and the intrinsic properties of the MD conformational ensembles. Therefore, a main focus of our review is to describe the merits and limitations of each clustering algorithm. We expect that this review would be helpful to guide researchers to choose appropriate clustering algorithms for their own MD datasets.展开更多
文摘This study was conducted to establish a Support Vector Machines(SVM)-Markov Chain prediction model for prediction of mining water inflow. According to the raw data sequence, the Support Vector Machines(SVM) model was built, and then revised by means of a Markov state change probability matrix. Through dividing the state and analyzing absolute errors and relative errors and other indexes of the measured value and the fitted value of SVM, the prediction results were improved. Finally,the model was used to calculate relative errors. Through predicting and analyzing mining water inflow, the prediction results of the model were satisfactory. The results of this study enlarge the application scope of the Support Vector Machines(SVM) prediction model and provide a new method for scientific forecasting water inflow in coal mining.
基金supported by Shenzhen Science and Technology Innovation Committee(JCYJ20170413173837121)the Hong Kong Research Grant Council(HKUST C6009-15G,14203915,16302214,16304215,16318816,and AoE/P-705/16)+2 种基金King Abdullah University of Science and Technology(KAUST) Office of Sponsored Research(OSR)(OSR-2016-CRG5-3007)Guangzhou Science Technology and Innovation Commission(201704030116)Innovation and Technology Commission(ITCPD/17-9and ITC-CNERC14SC01)
文摘Molecular dynamics （MD） simulation has become a powerful tool to investigate the structure- function relationship of proteins and other biological macromolecules at atomic resolution and biologically relevant timescales. MD simulations often produce massive datasets con- taining millions of snapshots describing proteins in motion. Therefore, clustering algorithms have been in high demand to be developed and applied to classify these MD snapshots and gain biological insights. There mainly exist two categories of clustering algorithms that aim to group protein conformations into clusters based on the similarity of their shape （geometric clustering） and kinetics （kinetic clustering）. In this paper, we review a series of frequently used clustering algorithms applied in MD simulations, including divisive algorithms, ag- glomerative algorithms （single-linkage, complete-linkage, average-linkage, centroid-linkage and ward-linkage）, center-based algorithms （K-Means, K-Medoids, K-Centers, and APM）, density-based algorithms （neighbor-based, DBSCAN, density-peaks, and Robust-DB）, and spectral-based algorithms （PCCA and PCCA＋）. In particular, differences between geomet- ric and kinetic clustering metrics will be discussed along with the performances of diflhrent clustering algorithms. We note that there does not exist a one-size-fits-all algorithm in the classification of MD datasets. For a specific application, the right choice of clustering algo- rithm should be based on the purpose of clustering, and the intrinsic properties of the MD conformational ensembles. Therefore, a main focus of our review is to describe the merits and limitations of each clustering algorithm. We expect that this review would be helpful to guide researchers to choose appropriate clustering algorithms for their own MD datasets.
