I'm trying to calculate this regression formula, but I have problem with the dimension calculation, they are not correct:
Where:
X-a matrix with dimensions 200x20, n=200 samples, p=20 predictors,
y-a matrix with dimensions 200x1,
- a sequence of coefficients, dimensions 20x1, and k=1,2,3...
- dimensions 20x200
j- and value from 1...p so from 1...20,
The problem is when I calculate
For example for k=20, k-1=19 i have and the dimensions do not match to do a substraction 200x1 - 200x20 x 1x1 =200x1 - 200x20 will not work.
If I take all the beta vector then it is correct. does this: mean to take the 19th value of Beta and to multiply it with the matrix X?
Source of the formula:
You should be using the entire beta vector at each stage of the calculation.
(Tibshirani has been a bit permissive with his use of notation, perhaps...)
The k is just a counter for which step of the algorithm we are on. Right at the start (k = 0 or "step 0") we initialise the entire beta vector to have all elements equal to zero:
At each step of the algorithm (steps k = 1, 2, 3... and so on) we use our previous estimate of the vector beta ( calculated in step k - 1) to calculate a new improved estimate for the vector beta (). The superscript number is not an index into the vector, rather it is a label telling us at which stage of the algorithm that beta vector was produced.
I hope this makes sense. The important point is that each of the values is a different 20x1 vector.
Related
I am currently in an online class in genomics, coming in as a wetlab physician, so my statistical knowledge is not the best. Right now we are working on PCA and SVD in R. I got a big matrix:
head(mat)
ALL_GSM330151.CEL ALL_GSM330153.CEL ALL_GSM330154.CEL ALL_GSM330157.CEL ALL_GSM330171.CEL ALL_GSM330174.CEL ALL_GSM330178.CEL ALL_GSM330182.CEL
ENSG00000224137 5.326553 3.512053 3.455480 3.472999 3.639132 3.391880 3.282522 3.682531
ENSG00000153253 6.436815 9.563955 7.186604 2.946697 6.949510 9.095092 3.795587 11.987291
ENSG00000096006 6.943404 8.840839 4.600026 4.735104 4.183136 3.049792 9.736803 3.338362
ENSG00000229807 3.322499 3.263655 3.406379 9.525888 3.595898 9.281170 8.946498 3.473750
ENSG00000138772 7.195113 8.741458 6.109578 5.631912 5.224844 3.260912 8.889246 3.052587
ENSG00000169575 7.853829 10.428492 10.512497 13.041571 10.836815 11.964498 10.786381 11.953912
Those are just the first few columns and rows, it has 60 columns and 1000 rows. Columns are cancer samples, rows are genes
The task is to:
removing the eigenvectors and reconstructing the matrix using SVD, then we need to calculate the reconstruction error as the difference between the original and the reconstructed matrix. HINT: You have to use the svd() function and equalize the eigenvalue to $0$ for the component you want to remove.
I have been all over google, but can't find a way to solve this task, which might be because I don't really get the question itself.
so i performed SVD on my matrix m:
d <- svd(mat)
Which gives me 3 matrices (Eigenassays, Eigenvalues and Eigenvectors), which i can access using d$u and so on.
How do I equalize the eigenvalue and ultimately calculate the error?
https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/svd
the decomposition expresses your matrix mat as a product of 3 matrices
mat = d$u x diag(d$d) x t(d$v)
so first confirm you are able to do the matrix multiplications to get back mat
once you are able to do this, set the last couple of elements of d$d to zero before doing the matrix multiplication
It helps to create a function that handles the singular values.
Here, for instance, is one that zeros out any singular value that is too small compared to the largest singular value:
zap <- function(d, digits = 3) ifelse(d < 10^(-digits) * max(abs(d))), 0, d)
Although mathematically all singular values are guaranteed non-negative, numerical issues with floating point algorithms can--and do--create negative singular values, so I have prophylactically wrapped the singular values in a call to abs.
Apply this function to the diagonal matrix in the SVD of a matrix X and reconstruct the matrix by multiplying the components:
X. <- with(svd(X), u %*% diag(zap(d)) %*% t(v))
There are many ways to assess the reconstruction error. One is the Frobenius norm of the difference,
sqrt(sum((X - X.)^2))
My problem is the following:
I'm trying to use R in order to compute numerically this problem.
So I've correctly setup the problem in my console, and then I tried to compute the eigenvectors.
But I expect that the eigenvector associated with lambda = 1 is (1,2,1) instead of what I've got here. So, the scaling is correct (0.4082483 is effectively half of 0.8164966), but I would like to obtain a consistent result.
My original problem is to find a stationary distribution for a Markov Chain using R instead of doing it on paper. So from a probabilistic point of view, my stationary distribution is a vector whose sum of the components is equal to 1. For that reason I was trying to change the scale in order to obtain what I've defined "a consistent result".
How can I do that ?
The eigen vectors returned by R are normalized (for the square-norm). If V is a eigen vector then s * V is a eigen vector as well for any non-zero scalar s. If you want the stationary distribution as in your link, divide by the sum:
V / sum(V)
and you will get (1/4, 1/2, 1/4).
So:
ev <- eigen(t(C))$vectors
ev / colSums(ev)
to get all the solutions in one shot.
C <- matrix(c(0.5,0.25,0,0.5,0.5,0.5,0,0.25,0.5),
nrow=3)
ee <- eigen(t(C))$vectors
As suggested by #Stéphane Laurent in the comments, the scaling of eigenvectors is arbitrary; only the relative value is specified. The default in R is that the sum of squares of the eigenvectors (their norms) are equal to 1; colSums(ee^2) is a vector of 1s.
Following the link, we can see that you want each eigenvector to sum to 1.
ee2 <- sweep(ee,MARGIN=2,STATS=colSums(ee),FUN=`/`)
(i.e., divide each eigenvector by its sum).
(This is a good general solution, but in this case the sum of the second and third eigenvectors are both approximately zero [theoretically, they are exactly zero], so this only really makes sense for the first eigenvector.)
I have a vector epsilon of length N. I am applying the function bw.CDF.pi(x, pilot="UCV") from the sROC package to compute bandwidths for cdf Kernel estimation.
My goal is to repeat this bandwidth function for every subvector from epsilon from the beginning value on. Stated otherwise, I would like to apply this function for the first value in epsilon, then for the first two values in epsilon, then for the first three values in epsilon, continiuing until the function is applied fot the total vector epsilon. Finally i want to have then N values for the bandwidth.
How can I accomplish this?
Apparently you need a vector of 2 elements for the function bw.CDF.pi to run. If you want to run it for the first 2 elemts of a vector, then the first 3, etc, you can do the following. Note that the data example is the one in the help page for the function.
library(sROC)
set.seed(100)
n <- 200
x <- c(rnorm(n/2, mean=-2, sd=1), rnorm(n/2, mean=3, sd=0.8))
lapply(seq_along(x)[-1], function(m) bw.CDF.pi(x[seq_len(m)], pilot="UCV"))
Rao QE is a weighted Euclidian distance matrix. I have the vectors for the elements of the d_ijs in a data table dt, one column per element (say there are x of them). p is the final column. nrow = S. The double sums are for the lower left (or upper right since it is symmetric) elements of the distance matrix.
If I only needed an unweighted distance matrix I could simply do dist() over the x columns. How do I weight the d_ijs by the product of p_i and p_j?
And example data set is at https://github.com/GeraldCNelson/nutmod/blob/master/RaoD_example.csv with the ps in the column called foodQ.ratio.
You still start with dist for the raw Euclidean distance matrix. Let it be D. As you will read from R - How to get row & column subscripts of matched elements from a distance matrix, a "dist" object is not a real matrix, but a 1D array. So first do D <- as.matrix(D) or D <- dist2mat(D) to convert it to a complete matrix before the following.
Now, let p be the vector of weights, the Rao's QE is just a quadratic form q'Dq / 2:
c(crossprod(p, D %*% p)) / 2
Note, I am not doing everything in the most efficient way. I have performed a symmetric matrix-vector multiplication D %*% p using the full D rather than just its lower triangular part. However, R does not have a routine doing triangular matrix-vector multiplication. So I compute the full version than divide 2.
This doubles computation amount that is necessary; also, making D a full matrix doubles memory costs. But if your problem is small to medium size this is absolutely fine. For large problem, if you are R and C wizard, call BLAS routine dtrmv or even dtpmv for the triangular matrix-vector computation.
Update
I just found this simple paper: Rao's quadratic entropy as a measure of functional diversity based on multiple traits for definition and use of Rao's EQ. It mentions that we can replace Euclidean distance with Mahalanobis distance. In case we want to do this, use my code in Mahalanobis distance of each pair of observations for fast computation of Mahalanobis distance matrix.
How does it actually reduce noise..can you suggest some nice tutorials?
SVD can be understood from a geometric sense for square matrices as a transformation on a vector.
Consider a square n x n matrix M multiplying a vector v to produce an output vector w:
w = M*v
The singular value decomposition M is the product of three matrices M=U*S*V, so w=U*S*V*v. U and V are orthonormal matrices. From a geometric transformation point of view (acting upon a vector by multiplying it), they are combinations of rotations and reflections that do not change the length of the vector they are multiplying. S is a diagonal matrix which represents scaling or squashing with different scaling factors (the diagonal terms) along each of the n axes.
So the effect of left-multiplying a vector v by a matrix M is to rotate/reflect v by M's orthonormal factor V, then scale/squash the result by a diagonal factor S, then rotate/reflect the result by M's orthonormal factor U.
One reason SVD is desirable from a numerical standpoint is that multiplication by orthonormal matrices is an invertible and extremely stable operation (condition number is 1). SVD captures any ill-conditioned-ness in the diagonal scaling matrix S.
One way to use SVD to reduce noise is to do the decomposition, set components that are near zero to be exactly zero, then re-compose.
Here's an online tutorial on SVD.
You might want to take a look at Numerical Recipes.
Singular value decomposition is a method for taking an nxm matrix M and "decomposing" it into three matrices such that M=USV. S is a diagonal square (the only nonzero entries are on the diagonal from top-left to bottom-right) matrix containing the "singular values" of M. U and V are orthogonal, which leads to the geometric understanding of SVD, but that isn't necessary for noise reduction.
With M=USV, we still have the original matrix M with all its noise intact. However, if we only keep the k largest singular values (which is easy, since many SVD algorithms compute a decomposition where the entries of S are sorted in nonincreasing order), then we have an approximation of the original matrix. This works because we assume that the small values are the noise, and that the more significant patterns in the data will be expressed through the vectors associated with larger singular values.
In fact, the resulting approximation is the most accurate rank-k approximation of the original matrix (has the least squared error).
To answer to the tittle question: SVD is a generalization of eigenvalues/eigenvectors to non-square matrices.
Say,
$X \in N \times p$, then the SVD decomposition of X yields X=UDV^T where D is diagonal and U and V are orthogonal matrices.
Now X^TX is a square matrice, and the SVD decomposition of X^TX=VD^2V where V is equivalent to the eigenvectors of X^TX and D^2 contains the eigenvalues of X^TX.
SVD can also be used to greatly ease global (i.e. to all observations simultaneously) fitting of an arbitrary model (expressed in an formula) to data (with respect to two variables and expressed in a matrix).
For example, data matrix A = D * MT where D represents the possible states of a system and M represents its evolution wrt some variable (e.g. time).
By SVD, A(x,y) = U(x) * S * VT(y) and therefore D * MT = U * S * VT
then D = U * S * VT * MT+ where the "+" indicates a pseudoinverse.
One can then take a mathematical model for the evolution and fit it to the columns of V, each of which are a linear combination the components of the model (this is easy, as each column is a 1D curve). This obtains model parameters which generate M? (the ? indicates it is based on fitting).
M * M?+ * V = V? which allows residuals R * S2 = V - V? to be minimized, thus determining D and M.
Pretty cool, eh?
The columns of U and V can also be inspected to glean information about the data; for example each inflection point in the columns of V typically indicates a different component of the model.
Finally, and actually addressing your question, it is import to note that although each successive singular value (element of the diagonal matrix S) with its attendant vectors U and V does have lower signal to noise, the separation of the components of the model in these "less important" vectors is actually more pronounced. In other words, if the data is described by a bunch of state changes that follow a sum of exponentials or whatever, the relative weights of each exponential get closer together in the smaller singular values. In other other words the later singular values have vectors which are less smooth (noisier) but in which the change represented by each component are more distinct.