Getting errors while using neuralnet function - r

Question

I tried neural net in R on Boston data set available.
data("Boston",package="MASS")
data <- Boston
Retaining only those variable we want to use:
keeps <- c("crim", "indus", "nox", "rm" , "age", "dis", "tax" ,"ptratio", "lstat" ,"medv" )
data <- data[keeps]
In this case the formula is stored in an R object called f.
The response variable medv is to be “regressed” against the remaining nine attributes. I have done it as below:
f <- medv ~ crim + indus + nox + rm + age + dis + tax + ptratio + lstat
To set up train sample 400 of the 506 rows of data without replacement is collected using the sample method:
set.seed(2016)
n = nrow(data)
train <- sample(1:n, 400, FALSE)
neuralnet function of R is fitted.
library(neuralnet)
fit<- neuralnet(f, data = data[train ,], hidden=c(10 ,12 ,20),
algorithm = "rprop+", err.fct = "sse", act.fct = "logistic",
threshold =0.1, linear.output=TRUE)
But warning message is displayed as algorithm not converging.
Warning message:
algorithm did not converge in 1 of 1 repetition(s) within the stepmax
Tried Prediction using compute,
pred <- compute(fit,data[-train, 1:9])
Following error msg is displayed
Error in nrow[w] * ncol[w] : non-numeric argument to binary operator
In addition: Warning message:
In is.na(weights) : is.na() applied to non-(list or vector) of type 'NULL'
Why the error is coming up and how to recover from it for prediction. I want to use the neuralnet function on that data set.

Answer 1

When neuralnet doesn't converge, the resulting neural network is not complete. You can tell by calling attributes(fit)$names. When training converges, it will look like this:
[1] "call" "response" "covariate" "model.list" "err.fct"
[6] "act.fct" "linear.output" "data" "net.result" "weights"
[11] "startweights" "generalized.weights" "result.matrix"
When it doesn't, some attributes will not be defined:
[1] "call" "response" "covariate" "model.list" "err.fct" "act.fct" "linear.output"
[8] "data"
That explains why compute doesn't work.
When training doesn't converge, the first possible solution could be to increase stepmax (default 100000). You can also add lifesign = "full", to get better insight into the training process.
Also, looking at your code, I would say three layers with 10, 12 and 20 neurons is too much. I would start with one layer with the same number of neurons as the number of inputs, in your case 9.
EDIT:
With scaling (remember to scale both training and test data, and to 'de-scale' compute results), it converges much faster. Also note that I reduced the number of layers and neurons, and still lowered the error threshold.
data("Boston",package="MASS")
data <- Boston
keeps <- c("crim", "indus", "nox", "rm" , "age", "dis", "tax" ,"ptratio", "lstat" ,"medv" )
data <- data[keeps]
f <- medv ~ crim + indus + nox + rm + age + dis + tax + ptratio + lstat
set.seed(2016)
n = nrow(data)
train <- sample(1:n, 400, FALSE)
# Scale data. Scaling parameters are stored in this matrix for later.
scaledData <- scale(data)
fit<- neuralnet::neuralnet(f, data = scaledData[train ,], hidden=9,
algorithm = "rprop+", err.fct = "sse", act.fct = "logistic",
threshold = 0.01, linear.output=TRUE, lifesign = "full")
pred <- neuralnet::compute(fit,scaledData[-train, 1:9])
scaledResults <- pred$net.result * attr(scaledData, "scaled:scale")["medv"]
+ attr(scaledData, "scaled:center")["medv"]
cleanOutput <- data.frame(Actual = data$medv[-train],
Prediction = scaledResults,
diff = abs(scaledResults - data$medv[-train]))
# Show some results
summary(cleanOutput)

Answer 2

The problem seems to be in your argument linear.output = TRUE.
With your data, but changing the code a bit (not defining the formula and adding some explanatory comments):
library(neuralnet)
fit <- neuralnet(formula = medv ~ crim + indus + nox + rm + age + dis + tax + ptratio + lstat,
data = data[train,],
hidden=c(10, 12, 20), # number of vertices (neurons) in each hidden layer
algorithm = "rprop+", # resilient backprop with weight backtracking,
err.fct = "sse", # calculates error based on the sum of squared errors
act.fct = "logistic", # smoothing the cross product of neurons and weights with logistic function
threshold = 0.1, # of the partial derivatives for error function, stopping
linear.output=FALSE) # act.fct applied to output neurons
print(net)
Call: neuralnet(formula = medv ~ crim + indus + nox + rm + age + dis + tax + ptratio + lstat, data = data[train, ], hidden = c(10, 12, 20), threshold = 0.1, rep = 10, algorithm = "rprop+", err.fct = "sse", act.fct = "logistic", linear.output = FALSE)
10 repetitions were calculated.
Error Reached Threshold Steps
1 108955.0318 0.03436116236 4
5 108955.0339 0.01391790099 8
3 108955.0341 0.02193379592 3
9 108955.0371 0.01705056758 6
8 108955.0398 0.01983134293 8
4 108955.0450 0.02500006437 5
6 108955.0569 0.03689097762 5
7 108955.0677 0.04765829189 5
2 108955.0705 0.05052776877 5
10 108955.1103 0.09031966778 7
10 108955.1103 0.09031966778 7
# now compute will work
pred <- compute(fit, data[-train, 1:9])