| This is part of the dimred module |
| It is only available if you configure PLUMED with ./configure –enable-modules=dimred . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list. |
Construct a sketch map projection of the input data
- Examples
- Glossary of keywords and components
- Description of components
Quantity | Description |
.#!value | the sketch-map projection of the input points |
In addition the following quantities can be calculated by employing the keywords listed below
Quantity | Keyword | Description |
osample | PROJECT_ALL | the out-of-sample projections |
- Compulsory keywords
NLOW_DIM | number of low-dimensional coordinates required |
ARG | the matrix of high dimensional coordinates that you want to project in the low dimensional space |
HIGH_DIM_FUNCTION | the parameters of the switching function in the high dimensional space |
LOW_DIM_FUNCTION | the parameters of the switching function in the low dimensional space |
CGTOL | ( default=1E-6 ) The tolerance for the conjugate gradient minimization that finds the projection of the landmarks |
MAXITER | ( default=1000 ) maximum number of optimization cycles for optimisation algorithms |
NCYCLES | ( default=0 ) The number of cycles of pointwise global optimisation that are required |
BUFFER | ( default=1.1 ) grid extent for search is (max projection - minimum projection) multiplied by this value |
CGRID_SIZE | ( default=10 ) number of points to use in each grid direction |
FGRID_SIZE | ( default=0 ) interpolate the grid onto this number of points – only works in 2D |
OS_CGTOL | ( default=1E-6 ) The tolerance for the conjugate gradient minimization that finds the out of sample projections |
SMACTOL | ( default=1E-4 ) the tolerance for the smacof algorithm |
SMACREG | ( default=0.001 ) this is used to ensure that we don't divide by zero when updating weights for SMACOF algorithm |
- Options
PROJECT_ALL | ( default=off ) if the input are landmark coordinates then project the out of sample configurations |
USE_SMACOF | ( default=off ) find the projection in the low dimensional space using the SMACOF algorithm
|
WEIGHTS | a vector containing the weights of the points |