How to work with binary contraints in linear optimization? - r

I have two input matrices, dt(10,3) & wt(3,3), that i need to use to find the optimal decision matrix (same dimension), Par(10,3) so as to maximize an objective function. Below R code would give some direction into the problem (used Sample inputs here) -
#Input Matrices
dt <- matrix(runif(300),100,3)
wt <- matrix(c(1,0,0,0,2,0,0,0,1),3,3) #weights
#objective function
Obj <- function(Par) {
P = matrix(Par, nrow = 10, byrow=F) # Reshape
X = t((dt%*%wt)[,1])%*%P[,1]
Y = t((dt%*%wt)[,2])%*%P[,2]
Z = t((dt%*%wt)[,3])%*%P[,3]
as.numeric(X+Y+Z) #maximize
}
Now I am struggling to apply the following constraints to the problem :
1) Matrix, Par can only have binary values (0 or 1)
2) rowSums(Par) = 1 (Basically a row can only have 1 in one of the three columns)
3) colSums(Par[,1]) <= 5, colSums(Par[,2]) <= 6, & colSums(Par[,3]) <= 4
4) X/(X+Y+Z) < 0.35, & Y/(X+Y+Z) < 0.4 (X,Y,Z are defined in the objective function)
I tried coding the constraints in constrOptim, but not sure how to input binary & integer constraints. I am reading up on lpSolve, but not able to figure out. Any help much appreciated. Thanks!

I believe this is indeed a MIP so no issues with convexity. If I am correct the model can look like:
This model can be easily transcribed into R. Note that LP/MIP solvers do not use functions for the objective and constraints (opposed to NLP solvers). In R typically one builds up matrices with the LP coefficients.
Note: I had to make the limits on the column sums much larger (I used 50,60,40).

Based on Erwin's response, I am able to formulate the model using lpSolve in R. However still struggling to add the final constraint to the model (4th constraint in my question above). Here's what I am able to code so far :
#input dimension
r <- 10
c <- 3
#input matrices
dt <- matrix(runif(r*c),r,c)
wt <- matrix(c(1,0,0,0,2,0,0,0,1),3,3) #weights
#column controller
c.limit <- c(60,50,70)
#create structure for lpSolve
ncol <- r*c
lp.create <- make.lp(ncol=ncol)
set.type(lp.create, columns=1:ncol, type = c("binary"))
#create objective values
obj.vals <- as.vector(t(dt%*%wt))
set.objfn(lp.create, obj.vals)
lp.control(lp.create,sense='max')
#Add constraints to ensure sum of parameters for every row (rowSum) <= 1
for (i in 1:r){
add.constraint(lp.create, xt=c(1,1,1),
indices=c(3*i-2,3*i-1,3*i), rhs=1, type="<=")
}
#Add constraints to ensure sum of parameters for every column (colSum) <= column limit (defined above)
for (i in 1:c){
add.constraint(lp.create, xt=rep(1,r),
indices=seq(i,ncol,by=c), rhs=c.limit[i], type="<=")
}
#Add constraints to ensure sum of column objective (t((dt%*%wt)[,i])%*%P[,i) <= limits defined in the problem)
#NOT SURE HOW TO APPLY A CONSTRAINT THAT IS DEPENDENT ON THE OBJECTIVE FUNCTION
solve(lp.create)
get.objective(lp.create) #20
final.par <- matrix(get.variables(lp.create), ncol = c, byrow=T) # Reshape
Any help that can get me to the finish line is much appreciated :)
Thanks

Related

Mclust() - NAs in model selection

I recently tried to perform a GMM in R on a multivariate matrix (400 obs of 196 var), which elements belong to known categories. The Mclust() function (from package mclust) gave very poor results (around 30% of individuals were well classified, whereas with k-means the result reaches more than 90%).
Here is my code :
library(mclust)
X <- read.csv("X.csv", sep = ",", h = T)
y <- read.csv("y.csv", sep = ",")
gmm <- Mclust(X, G = 5) #I want 5 clusters
cl_gmm <- gmm$classification
cl_gmm_lab <- cl_gmm
for (k in 1:nclusters){
ii = which(cl_gmm == k) # individuals of group k
counts=table(y[ii]) # number of occurences for each label
imax = which.max(counts) # Majority label
maj_lab = attributes(counts)$dimnames[[1]][imax]
print(paste("Group ",k,", majority label = ",maj_lab))
cl_gmm_lab[ii] = maj_lab
}
conf_mat_gmm <- table(y,cl_gmm_lab) # CONFUSION MATRIX
The problem seems to come from the fact that every other model than "EII" (spherical, equal volume) is "NA" when looking at gmm$BIC.
Until now I did not find any solution to this problem...are you familiar with this issue?
Here is the link for the data: https://drive.google.com/file/d/1j6lpqwQhUyv2qTpm7KbiMRO-0lXC3aKt/view?usp=sharing
Here is the link for the labels: https://docs.google.com/spreadsheets/d/1AVGgjS6h7v6diLFx4CxzxsvsiEm3EHG7/edit?usp=sharing&ouid=103045667565084056710&rtpof=true&sd=true
I finally found the answer. GMMs simply cannot apply every model when two much explenatory variables are involved. The right thing to do is first reduce dimensions and select an optimal number of dimensions that make it possible to properly apply GMMs while preserving as much informations as possible about the data.

Generate numbers with specific correlation [with only positive values in the output]

I want to obtain a dataframe with simulated values which have a specific correlation to each other.
I need to use this function, but in the returned output there are also negative values, which do not have meaning for my purposes:
COR <- function (n, xmean, xsd, ymean, ysd, correlation) {
x <- rnorm(n)
y <- rnorm(n)
z <- correlation * scale(x)[,1] + sqrt(1 - correlation^2) *
scale(resid(lm(y ~ x)))[,1]
xresult <- xmean + xsd * scale(x)[,1]
yresult <- ymean + ysd * z
data.frame(x=xresult,y=yresult)
}
Please note that my question starts from this previous post (currently closed):
another similar discussion
Is there a method able to exclude from the final output all the rows which have at least one negative value? (in another terms, x and y must be always positives).
I spent many hours without any concrete result.....
Filtering rows which have at least one negative value can be done with the apply function, e.g.
df <- simcor(100, 1, 1, 1, 1, 0.8)
filter <- apply(df, 1, function(x) sum(x < 0) > 0)
df <- df[!filter,]
plot(df)
First, I create a dataframe df from your funcion. Then, I apply the function sum(x < 0) > 0 rowwise to the dataframe (the second argument of apply, 1 indicates to go along the first dimension of the dataframe or array). This will create a logical vector that is TRUE for every row with at least one negative value. Subsetting the dataframe with the inverse of that (!filter) leaves you with all rows that have no negative values.
UPDATE:
Seems like the package VineCopula offers functions to create distributions with a given correlation. However, I did not dive into the math as deep so I was not able to fully grasp how copulas (i.e. multivariate probability distributions) work. Using this package, you can at least create e.g. two gaussian distributions.
library(VineCopula)
BC <- BiCop(family = 1, par = 0.9)
sim <- BiCopSim(N = 1000, obj = BC)
cor(sim[,1], sim[,2])
plot(sim)
You might be able to then scale the resulting matrix to achieve a certain standard derivation.

Permutations and combinations of all the columns in R

I want to check all the permutations and combinations of columns while selecting models in R. I have 8 columns in my data set and the below piece of code lets me check some of the models, but not all. Models like column 1+6, 1+2+5 will not be covered by this loop. Is there any better way to accomplish this?
best_model <- rep(0,3) #store the best model in this array
for(i in 1:8){
for(j in 1:8){
for(x in k){
diabetes_prediction <- knn(train = diabetes_training[, i:j], test = diabetes_test[, i:j], cl = diabetes_train_labels, k = x)
accuracy[x] <- 100 * sum(diabetes_test_labels == diabetes_prediction)/183
if( best_model[1] < accuracy[x] ){
best_model[1] = accuracy[x]
best_model[2] = i
best_model[3] = j
}
}
}
}
Well, this answer isn't complete, but maybe it'll get you started. You want to be able to subset by all possible subsets of columns. So instead of having i:j for some i and j, you want to be able to subset by c(1,6) or c(1,2,5), etc.
Using the sets package, you can for the power set (set of all subsets) of a set. That's the easy part. I'm new to R, so the hard part for me is understanding the difference between sets, lists, vectors, etc. I'm used to Mathematica, in which they're all the same.
library(sets)
my.set <- 1:8 # you want column indices from 1 to 8
my.power.set <- set_power(my.set) # this creates the set of all subsets of those indices
my.names <- c("a") #I don't know how to index into sets, so I created names (that are numbers, but of type characters)
for(i in 1:length(my.power.set)) {my.names[i] <- as.character(i)}
names(my.power.set) <- my.names
my.indices <- vector("list",length(my.power.set)-1)
for(i in 2:length(my.power.set)) {my.indices[i-1] <- as.vector(my.power.set[[my.names[i]]])} #this is the line I couldn't get to work
I wanted to create a list of lists called my.indices, so that my.indices[i] was a subset of {1,2,3,4,5,6,7,8} that could be used in place of where you have i:j. Then, your for loop would have to run from 1:length(my.indices).
But alas, I have been spoiled by Mathematica, and thus cannot decipher the incredibly complicated world of R data types.
Solved it, below is the code with explanatory comments:
# find out the best model for this data
number_of_columns_to_model <- ncol(diabetes_training)-1
best_model <- c()
best_model_accuracy = 0
for(i in 2:2^number_of_columns_to_model-1){
# ignoring the first case i.e. i=1, as it doesn't represent any model
# convert the value of i to binary, e.g. i=5 will give combination = 0 0 0 0 0 1 0 1
combination = as.binary(i, n=number_of_columns_to_model) # from the binaryLogic package
model <- c()
for(i in 1:length(combination)){
# choose which columns to consider depending on the combination
if(combination[i])
model <- c(model, i)
}
for(x in k){
# for the columns decides by model, find out the accuracies of model for k=1:27
diabetes_prediction <- knn(train = diabetes_training[, model, with = FALSE], test = diabetes_test[, model, with = FALSE], cl = diabetes_train_labels, k = x)
accuracy[x] <- 100 * sum(diabetes_test_labels == diabetes_prediction)/length(diabetes_test_labels)
if( best_model_accuracy < accuracy[x] ){
best_model_accuracy = accuracy[x]
best_model = model
print(model)
}
}
}
I trained with Pima.tr and tested with Pima.te. KNN Accuracy for pre-processed predictors was 78% and 80% without pre-processing (and this because of the large influence of some variables).
The 80% performance is at par with a Logistic Regression model. You don't need to preprocess variables in Logistic Regression.
RandomForest, and Logistic Regression provide a hint on which variables to drop, so you don't need to go and perform all possible combinations.
Another way is to look at a matrix Scatter plot
You get a sense that there is difference between type 0 and type 1 when it comes to npreg, glu, bmi, age
You also notice the highly skewed ped and age, and you notice that there may be an anomaly data point between skin and and and other variables (you may need to remove that observation before going further)
Skin Vs Type box plot shows that for type Yes, an extreme outlier exist (try removing it)
You also notice that most of the boxes for Yes type are higher than No type=> the variables may add prediction to the model (you can confirm this through a Wilcoxon Rank Sum Test)
The high correlation between Skin and bmi means that you can use one or the other or an interact of both.
Another approach to reducing the number of predictors is to use PCA

How to Generate Normal Random Samples within Mean±3Sigma

I want to draw normal random numbers in an array of order ((100*8)*5000) with a specific Mean (M) and Standard Deviation (S) but I want them to be only within the range M±3S, so that I don't have any outliers in my array exceeding those limits.
Any Suggestion? I want to write a program in R based on this array for some simulation studies. I am using following R Code to generate my Data Set:
for(i in 1:5000){
for(j in 1:8){
Dat[,j,i]=rnorm(100,mean=muu[j],sd=sigma[j])
}
}
Now, We want to get rid of those values which are higher than muu±3sigma in the above data. Definitely, We have to replace discarded values with fresh values so that the dimension of the Dat array keep intact.
First Solution
Here is a start but I bet there is a more elegant solution.
First generate a sample next step is to subset it to your desired values. Of course you have to adjust values to your desire.
set.seed(123)
rs <- rnorm(10000, mean = 10, sd = 3)
rs1 <- rs[ rs >= -19 & rs <= 19 ]
Second (better) solution
I think my first solutions didn't work so well. I have just written some code that might be perfect for your purposes. Here are the steps.
create an array of NAs with the required dimensions
fill it with random numbers
create a logical vector where TRUEs are for the desired conditions
subset the data based on that vector and replace the values where TRUE is TRUE (pardon my words game) with the mean used to generate samples
data <- array(NA, dim = c(100, 8, 5000))
for(i in 1:5000){
data[ , , i] <- rnorm(800, 3, 1)
}
bound <- 3 + c(-1, 1)*3*1
pr <- data <= bound[1] | data >= bound[2]
data[pr] <- 3

Using a for loop for performing several regressions

I am currently performing a style analysis using the following method: http://www.r-bloggers.com/style-analysis/ . It is a constrained regression of one asset on a number of benchmarks, over a rolling 36 month window.
My problem is that I need to perform this regression for a fairly large number of assets and doing it one by one would take a huge amount of time. To be more precise: Is there a way to tell R to regress columns 1-100 one by one on colums 101-116. Of course this also means printing 100 different plots, one for each asset. I am new to R and have been stuck for several days now.
I hope it doesn't matter that the following excerpt isn't reproducible, since the code works as originally intended.
# Style Regression over Window, constrained
#--------------------------------------------------------------------------
# setup
load.packages('quadprog')
style.weights[] = NA
style.r.squared[] = NA
# Setup constraints
# 0 <= x.i <= 1
constraints = new.constraints(n, lb = 0, ub = 1)
# SUM x.i = 1
constraints = add.constraints(rep(1, n), 1, type = '=', constraints)
# main loop
for( i in window.len:ndates ) {
window.index = (i - window.len + 1) : i
fit = lm.constraint( hist.returns[window.index, -1], hist.returns[window.index, 1], constraints )
style.weights[i,] = fit$coefficients
style.r.squared[i,] = fit$r.squared
}
# plot
aa.style.summary.plot('Style Constrained', style.weights, style.r.squared, window.len)
Thank you very much for any tips!
"Is there a way to tell R to regress columns 1-100 one by one on colums 101-116."
Yes! You can use a for loop, but you there's also a whole family of 'apply' functions which are appropriate. Here's a generalized solution with a random / toy dataset and using lm(), but you can sub in whatever regression function you want
# data frame of 116 cols of 20 rows
set.seed(123)
dat <- as.data.frame(matrix(rnorm(116*20), ncol=116))
# with a for loop
models <- list() # empty list to store models
for (i in 1:100) {
models[[i]] <-
lm(formula=x~., data=data.frame(x=dat[, i], dat[, 101:116]))
}
# with lapply
models2 <-
lapply(1:100,
function(i) lm(formula=x~.,
data=data.frame(x=dat[, i], dat[, 101:116])))
# compare. they give the same results!
all.equal(models, models2)
# to access a single model, use [[#]]
models2[[1]]

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