R help - Nov 2010 - Issues with nnet.default for regression/classification

Hi,

I'm currently trying desperately to get the nnet function for training a
neural network (with one hidden layer) to perform a regression task.

So I run it like the following:

trainednet <- nnet(x=traindata, y=trainresponse, size = 30, linout = TRUE,
maxit=1000)
(where x is a matrix and y a numerical vector consisting of the target
values for one variable)

To see whether the network learnt anything at all, I checked the network
weights and those have definitely changed. However, when examining the
trainednet$fitted.values, those are all the same so it rather looks as if
the network is doing a classification. I can even set linout=FALSE and
then it outputs "1" (the class?) for each training example. The
trainednet$residuals are correct (difference between predicted/fitted
example and actual response), but rather useless.

The same happens if I run nnet with the formula/data.frame interface, btw.

As per the suggestion in the ?nnet page: "If the response is not a factor,
it is passed on unchanged to 'nnet.default'", I assume that the
network is
doing regression since my trainresponse variable is a numerical vector and
_not_ a factor.

I'm currently lost and I can't see that the AMORE/neuralnet packages are
any better (moreover, they don't implement the formula/dataframe/predict
things). I've read the manpages of nnet and predict.nnet a gazillion
times, but I can't really find an answer there. I don't want to do
classification, but regression.

Thanks for any help.

Georg.
--
Research Assistant
Otto-von-Guericke-Universit?t Magdeburg
research at georgruss.de
http://research.georgruss.de

Hi Georg,

The documentation (?nnet) says that y should be a matrix or data frame, but in
your case it is a vector. This is most likely the problem, if you do not have
other data issues going on. Convert y to a matrix (or data frame) using
'as.matrix' and see if this solves your problem. Library 'nnet'
can do both classification and regression. I was able to replicate your problem,
using an example from Modern Applied Statistics with S, Venables and Ripley,
pages 246 and 247), by turning y into a vector and verifying that all the
predicted values are the same when y is a vector. This is not the case when y is
part of a data frame. You can see this by running the code below. I tried about
4 neural network packages in the past, including AMORE, but found 'nnet'
to be the best for my needs.

Hope this helps.

Jude

# Neural Network model in Modern Applied Statistics with S, Venables and Ripley,
pages 246 and 247
library(nnet)
attach(rock)
dim(rock)
area1 <- area/10000; peri1 <- peri/10000
rock1 <- data.frame(perm, area = area1, peri = peri1, shape)
dim(rock1)
head(rock1,15)
# skip = T
rock.nn <- nnet(log(perm) ~ area + peri + shape, rock1, size=3, decay=1e-3,
linout=T, skip=T, maxit=1000, Hess=T)
rock1$actual <- log(perm)
rock1$predicted <- predict(rock.nn)
head(rock1,15)
summary(rock.nn)
sum((log(perm) - predict(rock.nn))^2)

y <- as.vector(log(rock1$perm))
head(rock1[,c(2:4)])
test.nn <- nnet(x=rock1[,c(2:4)], y=y, size=3, linout=T, maxit=1000)
head(predict(test.nn))

Georg wrote:


Hi,



I'm currently trying desperately to get the nnet function for training a

neural network (with one hidden layer) to perform a regression task.



So I run it like the following:



trainednet <- nnet(x=traindata, y=trainresponse, size = 30, linout = TRUE,
maxit=1000)

(where x is a matrix and y a numerical vector consisting of the target

values for one variable)



To see whether the network learnt anything at all, I checked the network

weights and those have definitely changed. However, when examining the

trainednet$fitted.values, those are all the same so it rather looks as if

the network is doing a classification. I can even set linout=FALSE and

then it outputs "1" (the class?) for each training example. The

trainednet$residuals are correct (difference between predicted/fitted

example and actual response), but rather useless.



The same happens if I run nnet with the formula/data.frame interface, btw.



As per the suggestion in the ?nnet page: "If the response is not a factor,

it is passed on unchanged to 'nnet.default'", I assume that the
network is

doing regression since my trainresponse variable is a numerical vector and

_not_ a factor.



I'm currently lost and I can't see that the AMORE/neuralnet packages are

any better (moreover, they don't implement the formula/dataframe/predict

things). I've read the manpages of nnet and predict.nnet a gazillion

times, but I can't really find an answer there. I don't want to do

classification, but regression.



Thanks for any help.



Georg.

--

Research Assistant

Otto-von-Guericke-Universit?t Magdeburg

research@georgruss.de

http://research.georgruss.de


Jude Ryan
MarketShare Partners
1270 Avenue of the Americas, Suite # 2702
New York, NY 10020
http://www.marketsharepartners.com
Work: (646)-745-9916 ext: 222
Cell: (973)-943-2029


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