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Subject: newrbe
Message: 1 of 10
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Hi, I am working on radial basis network to predict protein conc. Part of the task is to compare result between newrb
& newrbe. I have no problem with the newrb but for newrbe I got this warning:
K=TRAINOPTIMIZE;
[r,c]=size(K);
GOAL=0.5;%SPREAD=input
SPREAD=20;
MN=24; % sample points
DF=1;
%net.layers{1}.transferFcn='radbas';
%net.layers{2}.transferFcn='purelin';
net=newrbe(P,T,SPREAD);
Y=sim(net,P);
GOAL=0.5; %SPREAD=input
SPREAD=20;
MN=24; % sample points
DF=1;
%net.layers{1}.transferFcn='radbas';
%net.layers{2}.transferFcn='purelin';
net=newrb(P,T,GOAL,SPREAD);
Y=sim(net,P);
Message: 2 of 10
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On Nov 15, 9:15 pm, "aurikel Radzali" <suriar...@gmail.com> wrote:
> Hi, I am working on radial basis network to predict protein conc. Part of the task is to compare result between
newrb & newrbe. I have no problem with the newrb but for newrbe I got this warning:
>
> Warning: Rank deficient, rank = 5, tol = 2.7195e-014.
> > In newrbe>designrbe at 122
>
>
In newrbe at 105
In RBFnormBnewrbe01_VCC_TRAINOPTIMIZE at 64
>
> 1.below are my source (newrbe):
>
> K=TRAINOPTIMIZE;
> [r,c]=size(K);
>
> GOAL=0.5;%SPREAD=input
> SPREAD=20;
> MN=24; % sample points
> DF=1;
> %net.layers{1}.transferFcn='radbas';
> %net.layers{2}.transferFcn='purelin';
>
> net=newrbe(P,T,SPREAD);
> Y=sim(net,P);
>
> 2.below are my source (newrb):
>
> GOAL=0.5; %SPREAD=input
> SPREAD=20;
> MN=24; % sample points
> DF=1;
> %net.layers{1}.transferFcn='radbas';
> %net.layers{2}.transferFcn='purelin';
>
> net=newrb(P,T,GOAL,SPREAD);
> Y=sim(net,P);
>
> note: i got the result as follow:
> NEWRB, neurons = 0, MSE = 0.130203
>
> where i could be wrong?or did i miss something important?
Greg
Subject: newrbe
Message: 3 of 10
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Greg Heath <heath@alumni.brown.edu> wrote in message <dc9ef436-338f-40fb-aa39d679e47f6b1d@j11g2000vbi.googlegroups.com>...
>
> which makes no sense to me. Furthermore, the value 0.13
> means nothing unless it is compared to a reference.
> What is mean(var(T))?
>
> Greg
Hi, actually i have a problem with newrb too except it does not produce warning like the newrbe.
GOAL=0.5;
SPREAD=5;
MN=24; % sample points
DF=1;
%net.layers{1}.transferFcn='radbas';
%net.layers{2}.transferFcn='purelin';
net=newrb(P,T,GOAL,SPREAD);
Y=sim(net,P);
e=T-Y;
msetrain=mse(e)
msetrain =
0.0018
Message: 4 of 10
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>
> > > where i could be wrong?or did i miss something important?
>
> > You say "I have no problem with the newrb".
> > However, you report "neurons = 0, MSE = 0.130203"
>
> > which makes no sense to me. Furthermore, the value 0.13
> > means nothing unless it is compared to a reference.
> > What is mean(var(T))?
>
> >Greg
>
> Hi, actually i have a problem with newrb too except
> it does not produce warning like the newrbe.
>
> --> this is the newrb code:
size(P) = ?
minmax(P) = ?
size(T) = ?
minmax(T) = ?
> GOAL=0.5;
y00 = repmat(mean(T,2),1,size(T,2));
e00 = T-y00;
SSE00 = sse(e00)
so that
> SPREAD=5;
0.5*mean(median(dist(P,P')))?
> Y=sim(net,P);
> e=T-Y;
> msetrain=mse(e)
> msetrain =
>
> 0.0018
MSE(neurons = 0) = (N-1)*mean(var(T'))/N
Greg
Subject: newrb
Message: 5 of 10
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Greg Heath <heath@alumni.brown.edu> wrote in message <9bfd2ece-92b5-432f-a82c61238af4d20c@j4g2000yqe.googlegroups.com>...
> On Nov 16, 4:23 am, "aurikel Radzali" <suriar...@gmail.com> wrote:
> > GregHeath<he...@alumni.brown.edu> wrote in message <dc9ef436-338f-40fb-aa39d679e47f6...@j11g2000vbi.googlegroups.com>...
> > > On Nov 15, 9:15?pm, "aurikel Radzali" <suriar...@gmail.com> wrote:
> > > > Hi, I am working on radial basis network to predict protein conc. Part of the task is to compare result between
newrb & newrbe. I have no problem with the newrb but for newrbe I got this warning:
>>
> > > > Warning: Rank deficient, rank = 5, ?tol = ? 2.7195e-014.
> > > > ?> ?In newrbe>designrbe at 122
> > > > ? ? ?In newrbe at 105
> > > > ? ? ?In RBFnormBnewrbe01_VCC_TRAINOPTIMIZE at 64
>>
> > > > 1.below are my source (newrbe):
>>
> > > > K=TRAINOPTIMIZE;
> > > > [r,c]=size(K);
>>
> > > > GOAL=0.5;%SPREAD=input
> minmax(T) = ?
>
> > GOAL=0.5;
>
> Note: In my version 6.5 this is SSEgoal, NOT MSEgoal;
> -----------> I just put random value, I do not know what value should i choose.
>
> [net, tr] = newrb(P,T,GOAL,SPREAD);
>
-----------------> what is the different between the those two? What is the purpose of putting [net,tr]?
>
> Greg
based on your advice, %For newrb, it is desirable to have SSEgoal < SSE00/100
SSE00=3.1249
SSEm=SSE00/100 %produce 0.0312
Message: 6 of 10
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On Nov 19, 1:36 am, "aurikel Radzali" <suriar...@gmail.com> wrote:
> Greg Heath <he...@alumni.brown.edu> wrote in message <9bfd2ece-92b5-432f-a82c61238af4d...@j4g2000yqe.googlegroups.com>...
> > On Nov 16, 4:23 am, "aurikel Radzali" <suriar...@gmail.com> wrote:
> > > GregHeath<he...@alumni.brown.edu> wrote in message <dc9ef436-338f-40fb-aa39d679e47f6...@j11g2000vbi.googlegroups.com>...
> > > > On Nov 15, 9:15?pm, "aurikel Radzali" <suriar...@gmail.com> wrote:
> > > > > Hi, I am working on radial basis network to predict protein conc.
Part of the task is to compare result between newrb & newrbe. I have
no
problem with the newrb but for newrbe I got this warning:
>
> > > > > Warning: Rank deficient, rank = 5, ?tol = ? 2.7195e-014.
> > > > > ?> ?In newrbe>designrbe at 122
> > > > > ? ? ?In newrbe at 105
> > > > > ? ? ?In RBFnormBnewrbe01_VCC_TRAINOPTIMIZE at 64
>
> > > > > 1.below are my source (newrbe):
>
> > > > > K=TRAINOPTIMIZE;
> > > > > [r,c]=size(K);
>
> > > > > GOAL=0.5;%SPREAD=input
> > > > > SPREAD=20;
> > > > > MN=24; % sample points
> > > > > DF=1;
> > > > > %net.layers{1}.transferFcn='radbas';
> > > > > %net.layers{2}.transferFcn='purelin';
>
> > > > > net=newrbe(P,T,SPREAD);
> > > > > Y=sim(net,P);
>
> > > > > 2.below are my source (newrb):
>
> > > > > GOAL=0.5; %SPREAD=input
> > > > > SPREAD=20;
> > > > > MN=24; % sample points
> > > > > DF=1;
> > > > > %net.layers{1}.transferFcn='radbas';
> > > > > %net.layers{2}.transferFcn='purelin';
>
> > > > > net=newrb(P,T,GOAL,SPREAD);
> > > > > Y=sim(net,P);
>
> > > > > note: i got the result as follow:
> > > > > NEWRB, neurons = 0, MSE = 0.130203
>
> > > > > where i could be wrong?or did i miss something important?
>
> > > > You say "I have no problem with the newrb".
> > > > However, you report "neurons = 0, MSE = 0.130203"
>
> > > > which makes no sense to me. Furthermore, the value 0.13
> > > > means nothing unless it is compared to a reference.
> > > > What is mean(var(T))?
>
> > > >Greg
>
> > > Hi, actually i have a problem with newrb too except
> > > it does not produce warning like the newrbe.
>
> > > --> this is the newrb code:
>
> > size(P) = ?
http://en.wikipedia.org/wiki/Coefficient_of_determination
True, but why whistle in the dark when you can quickly estimate
a few charcteristic distances to help limit the search?
Yes.
help newrb
doc newrb
> --------------tr.perf(end)=0.0018
Greg
Subject: newrb
Message: 7 of 10
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Greg Heath <heath@alumni.brown.edu> wrote in message <f88c4240-7211-4544-9ca1f5a6568454cf@f20g2000vbl.googlegroups.com>...
> On Nov 19, 1:36 am, "aurikel Radzali" <suriar...@gmail.com> wrote:
> > Greg Heath <he...@alumni.brown.edu> wrote in message <9bfd2ece-92b5-432f-a82c61238af4d...@j4g2000yqe.googlegroups.com>...
> > > On Nov 16, 4:23 am, "aurikel Radzali" <suriar...@gmail.com> wrote:
> > > > GregHeath<he...@alumni.brown.edu> wrote in message <dc9ef436-338f-40fb-aa39d679e47f6...@j11g2000vbi.googlegroups.com>...
> > > > > On Nov 15, 9:15?pm, "aurikel Radzali" <suriar...@gmail.com> wrote:
> > > > > > Hi, I am working on radial basis network to predict protein conc.
> Part of the task is to compare result between newrb & newrbe. I have
> no
> problem with the newrb but for newrbe I got this warning:
>>
> > > > > > Warning: Rank deficient, rank = 5, ?tol = ? 2.7195e-014.
> > > > > > ?> ?In newrbe>designrbe at 122
>>
> > > > Hi, actually i have a problem with newrb too except
> > > > it does not produce warning like the newrbe.
>>
> > > > --> this is the newrb code:
>>
> > > size(P) = ?
> > > minmax(P) = ?
> > > size(T) = ?
> > > minmax(T) = ?
>
>
> Please answer the questions.
---->size(P) =3 24
size(T) =1 24
>
> > > > GOAL=0.5;
>>
> > > Note: In my version 6.5 this is SSEgoal, NOT MSEgoal;
>
> > -----------> I just put random value, I do not know what
> > value should i choose.
>
> > > Why did you choose this value?
>>
> > > For the best constant model y = mean of targets:
>>
> > > y00 = repmat(mean(T,2),1,size(T,2));
> > > e00 = T-y00;
> > > SSE00 = sse(e00)
>>
> > > For newrb, it is desirable to have
>>
> > > SSEgoal < SSE00/100
>>
> > > so that
>>
> > > R^2 = 1-SSE/SSE00 > 0.99
>
> > -----------> i do not understand, what is the purpose of this?
>
> R^2 (coefficient of determination) is a measure of the
-----------> is this some kind of guideline to choose the spread? the spread should be around that value, it is?less or
more but not too far away?
>>
> > > > net=newrb(P,T,GOAL,SPREAD);
>>
> > > [net, tr] = newrb(P,T,GOAL,SPREAD);
>>
> > -----------------> what is the different between the those two?
> >What is the purpose of putting [net,tr]?
>
> tr is the training record
>
> help newrb
> doc newrb
>
> > > > Y=sim(net,P);
> > > > e=T-Y;
> > > > msetrain=mse(e)
>>
> > > compare with tr.perf(end)
>
> > --------------tr.perf(end)=0.0018
>
> > > > --> this is the result:
> > > > NEWRB, neurons = 0, MSE = 0.130203
>>
> > > If N ~ 24, This is not inconsistent with
> > > mean(var(T)) = 0.1359.
>
> > ___________> I'm really sorry, but i truly do not
> understand what do you by If N ~ 24,
> This is not inconsistent with mean(var(T)) = 0.1359
>>
> > ----------------------->how it suppose to be??
>
> If neurons = 0. Then the the output is a constant
> equal to the bias. To minimize SSE, the constant must
> be mean(T). The resulting MSE is (N-1)*var(T)/N
>
---------->forgive me, i still don't understand.
mean(T)=0.5389
mean(var(T)) = 0.1359
MSE i= (N-1)*var(T)/N= 0.1302 so?
--->To minimize SSE, 'the constant' must be mean(T). 'the constant' refer to?
Message: 8 of 10
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On Nov 19, 4:14 am, "aurikel Radzali" <suriar...@gmail.com> wrote:
> Greg Heath <he...@alumni.brown.edu> wrote > > > > size(P) = ?
> > > > minmax(P) = ?
> > > > size(T) = ?
> > > > minmax(T) = ?
>
> > Please answer the questions.
>
> ---->size(P) =3
>
24
size(T) =1 24
MINMAX??
Greg
Subject: newrb
Message: 9 of 10
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Greg Heath <heath@alumni.brown.edu> wrote in message <85397222-7dfd-4f31-a3f76e2a088e47e9@p33g2000vbn.googlegroups.com>...
> On Nov 19, 4:14?am, "aurikel Radzali" <suriar...@gmail.com> wrote:
> > Greg Heath <he...@alumni.brown.edu> wrote > > > > size(P) = ?
> > > > > minmax(P) = ?
> > > > > size(T) = ?
> > > > > minmax(T) = ?
>>
> > > Please answer the questions.
>>
MINMAXP =
01
01
01
MINMAXT =
01
Subject: newrb
Message: 10 of 10
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On Nov 19, 4:14 am, "aurikel Radzali" <suriar...@gmail.com> wrote:
> Greg Heath <he...@alumni.brown.edu> wrote in message <f88c4240-7211-4544-9ca1f5a656845...@f20g2000vbl.googlegroups.com
-----SNIP
> > > > size(P) = ?
> > > > minmax(P) = ?
> > > > size(T) = ?
> > > > minmax(T) = ?
>
> > Please answer the questions.
>
> ---->size(P) =3 24
> size(T) =1 24
MINMAX?
-----SNIP
Now that you realize that the input data is contained in a unit cube
it should be obvious the spread = 5 is inappropriate.
> > True, but why whistle in the dark when you can quickly estimate
> > a few charcteristic distances to help limit the search?
>
> ------------------>how do i estimate characteristic distances to help
limit the search? i even do not know what no should i start with
.
What can you tell about the data from N, minmax(P) and summary
statistics of dist(P,P') (exclude the diagonal)?
What if the data was uniformly distributed over the cube?
The input data is only 3-D. Therefore you can obtain 1,2,and
3-D scatter plots.
etc
>
> > > > How does it compare to
>
> > > > 0.5*mean(median(dist(P,P')))?
>
> > Typical half-distance between data points. More useful
> > when the data points are either cluster centers from a previous
> > cluster analysis or data points selected as neurons.
>
> > > ---------> do you mean compare this and spread=5?
>
> > Yes.
>
> > > ------------->btw, 0.5*mean(median(dist(P,P')))=1.0815
>
> -----------> is this some kind of guideline to choose the spread?
the spread should be around that value, it is?less or more but not too
far
away?
>
> > > > compare with tr.perf(end)
>
> > > --------------tr.perf(end)=0.0018
>
> > > > > --> this is the result:
> > > > > NEWRB, neurons = 0, MSE = 0.130203
>
> > > > If N ~ 24, This is not inconsistent with
> > > > mean(var(T)) = 0.1359.
>
> > > ___________> I'm really sorry, but i truly do not
> > understand what do you by If N ~ 24,
> > This is not inconsistent with mean(var(T)) = 0.1359
>
> > > ----------------------->how it suppose to be??
>
> > If neurons = 0. Then the the output is a constant
> > equal to the bias. To minimize SSE, the constant must
> > be mean(T). The resulting MSE is (N-1)*var(T)/N
>
> ---------->forgive me, i still don't understand.
> mean(T)=0.5389
> mean(var(T)) = 0.1359
> MSE i= (N-1)*var(T)/N= 0.1302 so?
Yes
> > > > Where is the tabulation for neurons > 0?
>
> > > > > msetrain =
>
> > > > > 0.0018
>
> > > > For how many neurons?
> > > > -------------->Number of nodes in hidden layer=2.0000e+000
> > > > > why the mse value is different?
>
> > > > Different number of neurons
> > > > What is tr.epoch(end)?
> > > > ---------> 2
> > > > >the mean(var(T)) is 0.1359
>
> > > > MSE(neurons = 0) = (N-1)*mean(var(T'))/N
> > > > -------------> owhh..thats why i get the MSE=0.1302
> > > > Hope this helps.
>
> > > > Greg
>
> > > ==============> Thanks, I still have some questions.
>
> > > based on your advice, %For newrb, it is desirable to have SSEgoal < SSE00/100
> > > SSE00=3.1249
> > > SSEm=SSE00/100 %produce 0.0312
>
> > > so i choose my goal 0.0005 % since SSEgoal < SSE00/100. is this right?
>
> > I would use 0.02.
GregGreg-