supraHex 1.13.3

How many neighborhood kernels are supported and how to choose?

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    •       
    # The neighborhood kernel  dictates the final topology of the trained map, which is a non-increasing functions of: 1) the distance between the hexagon/rectangle and the winner, and 2) the radius. There are five kernels supported so far:
visKernels()
# As you have seen, these kernels are displayed within a plot for each fixed radius; two different radii (i.e. 1 and 2) are illustrated only. From the mathematical definitions and curve forms above, it is clear that the "gamma" and "gaussian" kernels exert more global influence, the "ep" kernel puts more emphasis on local topological relationships, and the other two "cutgaussian" and "bubble" keep the relative balance. 

# It becomes much clearer when using the function visHexMulComp to visualise trained maps using the same data input and the same trainology but choosing different kernels.

# Generate data
data <- cbind(
matrix(rnorm(1000*3,mean=0.5,sd=1), nrow=1000, ncol=3), 
matrix(rnorm(1000*3,mean=-0.5,sd=1), nrow=1000, ncol=3)
)

    


    colnames(data) <- c("S1","S1","S1","S2","S2","S2")

# with "gaussian" kernel (by default)
sMap_ga <- sPipeline(data=data, neighKernel="gaussian", init="uniform")

    
Start at 2017-03-27 18:59:46

First, define topology of a map grid (2017-03-27 18:59:46)...
Second, initialise the codebook matrix (169 X 6) using 'uniform' initialisation, given a topology and input data (2017-03-27 18:59:46)...
Third, get training at the rough stage (2017-03-27 18:59:46)...
	1 out of 2 (2017-03-27 18:59:46)
	updated (2017-03-27 18:59:46)
	2 out of 2 (2017-03-27 18:59:46)
	updated (2017-03-27 18:59:46)
Fourth, get training at the finetune stage (2017-03-27 18:59:46)...
	1 out of 7 (2017-03-27 18:59:46)
	updated (2017-03-27 18:59:46)
	2 out of 7 (2017-03-27 18:59:46)
	updated (2017-03-27 18:59:46)
	3 out of 7 (2017-03-27 18:59:46)
	updated (2017-03-27 18:59:46)
	4 out of 7 (2017-03-27 18:59:46)
	updated (2017-03-27 18:59:46)
	5 out of 7 (2017-03-27 18:59:46)
	updated (2017-03-27 18:59:46)
	6 out of 7 (2017-03-27 18:59:46)
	updated (2017-03-27 18:59:46)
	7 out of 7 (2017-03-27 18:59:46)
	updated (2017-03-27 18:59:46)
Next, identify the best-matching hexagon/rectangle for the input data (2017-03-27 18:59:46)...
Finally, append the response data (hits and mqe) into the sMap object (2017-03-27 18:59:46)...

Below are the summaries of the training results:
   dimension of input data: 1000x6
   xy-dimension of map grid: xdim=15, ydim=15, r=8
   grid lattice: hexa
   grid shape: suprahex
   dimension of grid coord: 169x2
   initialisation method: uniform
   dimension of codebook matrix: 169x6
   mean quantization error: 1.95201775253281

Below are the details of trainology:
   training algorithm: batch
   alpha type: invert
   training neighborhood kernel: gaussian
   trainlength (x input data length): 2 at rough stage; 7 at finetune stage
   radius (at rough stage): from 4 to 1
   radius (at finetune stage): from 1 to 1

End at 2017-03-27 18:59:46
Runtime in total is: 0 secs


    visHexMulComp(sMap_ga)
# with "gamma" kernel
sMap_gm <- sPipeline(data=data, neighKernel="gamma", init="uniform")

    
Start at 2017-03-27 18:59:47

First, define topology of a map grid (2017-03-27 18:59:47)...
Second, initialise the codebook matrix (169 X 6) using 'uniform' initialisation, given a topology and input data (2017-03-27 18:59:47)...
Third, get training at the rough stage (2017-03-27 18:59:47)...
	1 out of 2 (2017-03-27 18:59:47)
	updated (2017-03-27 18:59:47)
	2 out of 2 (2017-03-27 18:59:47)
	updated (2017-03-27 18:59:47)
Fourth, get training at the finetune stage (2017-03-27 18:59:47)...
	1 out of 7 (2017-03-27 18:59:47)
	updated (2017-03-27 18:59:47)
	2 out of 7 (2017-03-27 18:59:47)
	updated (2017-03-27 18:59:47)
	3 out of 7 (2017-03-27 18:59:47)
	updated (2017-03-27 18:59:47)
	4 out of 7 (2017-03-27 18:59:47)
	updated (2017-03-27 18:59:47)
	5 out of 7 (2017-03-27 18:59:47)
	updated (2017-03-27 18:59:47)
	6 out of 7 (2017-03-27 18:59:47)
	updated (2017-03-27 18:59:47)
	7 out of 7 (2017-03-27 18:59:47)
	updated (2017-03-27 18:59:47)
Next, identify the best-matching hexagon/rectangle for the input data (2017-03-27 18:59:47)...
Finally, append the response data (hits and mqe) into the sMap object (2017-03-27 18:59:47)...

Below are the summaries of the training results:
   dimension of input data: 1000x6
   xy-dimension of map grid: xdim=15, ydim=15, r=8
   grid lattice: hexa
   grid shape: suprahex
   dimension of grid coord: 169x2
   initialisation method: uniform
   dimension of codebook matrix: 169x6
   mean quantization error: 2.3688468448732

Below are the details of trainology:
   training algorithm: batch
   alpha type: invert
   training neighborhood kernel: gamma
   trainlength (x input data length): 2 at rough stage; 7 at finetune stage
   radius (at rough stage): from 4 to 1
   radius (at finetune stage): from 1 to 1

End at 2017-03-27 18:59:47
Runtime in total is: 0 secs



    visHexMulComp(sMap_gm)
# with "ep" kernel
sMap_ep <- sPipeline(data=data, neighKernel="ep", init="uniform")

    
Start at 2017-03-27 18:59:48

First, define topology of a map grid (2017-03-27 18:59:48)...
Second, initialise the codebook matrix (169 X 6) using 'uniform' initialisation, given a topology and input data (2017-03-27 18:59:48)...
Third, get training at the rough stage (2017-03-27 18:59:48)...
	1 out of 2 (2017-03-27 18:59:48)
	updated (2017-03-27 18:59:48)
	2 out of 2 (2017-03-27 18:59:48)
	updated (2017-03-27 18:59:48)
Fourth, get training at the finetune stage (2017-03-27 18:59:48)...
	1 out of 7 (2017-03-27 18:59:48)
	updated (2017-03-27 18:59:48)
	2 out of 7 (2017-03-27 18:59:48)
	updated (2017-03-27 18:59:48)
	3 out of 7 (2017-03-27 18:59:48)
	updated (2017-03-27 18:59:48)
	4 out of 7 (2017-03-27 18:59:48)
	updated (2017-03-27 18:59:48)
	5 out of 7 (2017-03-27 18:59:48)
	updated (2017-03-27 18:59:48)
	6 out of 7 (2017-03-27 18:59:48)
	updated (2017-03-27 18:59:48)
	7 out of 7 (2017-03-27 18:59:48)
	updated (2017-03-27 18:59:48)
Next, identify the best-matching hexagon/rectangle for the input data (2017-03-27 18:59:48)...
Finally, append the response data (hits and mqe) into the sMap object (2017-03-27 18:59:48)...

Below are the summaries of the training results:
   dimension of input data: 1000x6
   xy-dimension of map grid: xdim=15, ydim=15, r=8
   grid lattice: hexa
   grid shape: suprahex
   dimension of grid coord: 169x2
   initialisation method: uniform
   dimension of codebook matrix: 169x6
   mean quantization error: 0.97279930292498

Below are the details of trainology:
   training algorithm: batch
   alpha type: invert
   training neighborhood kernel: ep
   trainlength (x input data length): 2 at rough stage; 7 at finetune stage
   radius (at rough stage): from 4 to 1
   radius (at finetune stage): from 1 to 1

End at 2017-03-27 18:59:48
Runtime in total is: 0 secs



    visHexMulComp(sMap_ep)
# with "cutgaussian" kernel
sMap_cu <- sPipeline(data=data, neighKernel="cutgaussian", init="uniform")

    
Start at 2017-03-27 18:59:49

First, define topology of a map grid (2017-03-27 18:59:49)...
Second, initialise the codebook matrix (169 X 6) using 'uniform' initialisation, given a topology and input data (2017-03-27 18:59:49)...
Third, get training at the rough stage (2017-03-27 18:59:49)...
	1 out of 2 (2017-03-27 18:59:49)
	updated (2017-03-27 18:59:49)
	2 out of 2 (2017-03-27 18:59:49)
	updated (2017-03-27 18:59:49)
Fourth, get training at the finetune stage (2017-03-27 18:59:49)...
	1 out of 7 (2017-03-27 18:59:49)
	updated (2017-03-27 18:59:49)
	2 out of 7 (2017-03-27 18:59:49)
	updated (2017-03-27 18:59:49)
	3 out of 7 (2017-03-27 18:59:49)
	updated (2017-03-27 18:59:49)
	4 out of 7 (2017-03-27 18:59:49)
	updated (2017-03-27 18:59:49)
	5 out of 7 (2017-03-27 18:59:49)
	updated (2017-03-27 18:59:49)
	6 out of 7 (2017-03-27 18:59:49)
	updated (2017-03-27 18:59:49)
	7 out of 7 (2017-03-27 18:59:49)
	updated (2017-03-27 18:59:49)
Next, identify the best-matching hexagon/rectangle for the input data (2017-03-27 18:59:49)...
Finally, append the response data (hits and mqe) into the sMap object (2017-03-27 18:59:49)...

Below are the summaries of the training results:
   dimension of input data: 1000x6
   xy-dimension of map grid: xdim=15, ydim=15, r=8
   grid lattice: hexa
   grid shape: suprahex
   dimension of grid coord: 169x2
   initialisation method: uniform
   dimension of codebook matrix: 169x6
   mean quantization error: 1.52361772550777

Below are the details of trainology:
   training algorithm: batch
   alpha type: invert
   training neighborhood kernel: cutgaussian
   trainlength (x input data length): 2 at rough stage; 7 at finetune stage
   radius (at rough stage): from 4 to 1
   radius (at finetune stage): from 1 to 1

End at 2017-03-27 18:59:49
Runtime in total is: 0 secs



    visHexMulComp(sMap_cu)
# with "bubble" kernel
sMap_bu <- sPipeline(data=data, neighKernel="bubble", init="uniform")

    
Start at 2017-03-27 18:59:49

First, define topology of a map grid (2017-03-27 18:59:49)...
Second, initialise the codebook matrix (169 X 6) using 'uniform' initialisation, given a topology and input data (2017-03-27 18:59:49)...
Third, get training at the rough stage (2017-03-27 18:59:49)...
	1 out of 2 (2017-03-27 18:59:49)
	updated (2017-03-27 18:59:49)
	2 out of 2 (2017-03-27 18:59:49)
	updated (2017-03-27 18:59:50)
Fourth, get training at the finetune stage (2017-03-27 18:59:50)...
	1 out of 7 (2017-03-27 18:59:50)
	updated (2017-03-27 18:59:50)
	2 out of 7 (2017-03-27 18:59:50)
	updated (2017-03-27 18:59:50)
	3 out of 7 (2017-03-27 18:59:50)
	updated (2017-03-27 18:59:50)
	4 out of 7 (2017-03-27 18:59:50)
	updated (2017-03-27 18:59:50)
	5 out of 7 (2017-03-27 18:59:50)
	updated (2017-03-27 18:59:50)
	6 out of 7 (2017-03-27 18:59:50)
	updated (2017-03-27 18:59:50)
	7 out of 7 (2017-03-27 18:59:50)
	updated (2017-03-27 18:59:50)
Next, identify the best-matching hexagon/rectangle for the input data (2017-03-27 18:59:50)...
Finally, append the response data (hits and mqe) into the sMap object (2017-03-27 18:59:50)...

Below are the summaries of the training results:
   dimension of input data: 1000x6
   xy-dimension of map grid: xdim=15, ydim=15, r=8
   grid lattice: hexa
   grid shape: suprahex
   dimension of grid coord: 169x2
   initialisation method: uniform
   dimension of codebook matrix: 169x6
   mean quantization error: 1.59843633585734

Below are the details of trainology:
   training algorithm: batch
   alpha type: invert
   training neighborhood kernel: bubble
   trainlength (x input data length): 2 at rough stage; 7 at finetune stage
   radius (at rough stage): from 4 to 1
   radius (at finetune stage): from 1 to 1

End at 2017-03-27 18:59:50
Runtime in total is: 1 secs



    visHexMulComp(sMap_bu)

    Source faq

    FAQ7.r

    Functions used in this FAQ