Showing posts with label R. Show all posts
Showing posts with label R. Show all posts

## Friday, 17 January 2014

### Particle approximation to probability density functions: Dirac delta function representation

In the previous post, I have briefly shown the idea of using dirac delta function for discrete data representation. In the second example there, a histogram locations for a given set of points are presented as spike trains, where as heights are somehow given in a second sum. This is hard to follow and visualise, of course if you are not that good in reading formulation with different indexes. Due to pedagocial reasons, an easier representation of arbitrary probability density function (PDF), $p(x)$, one would simply need to couple each discrete points with a corresponding weight.

Hence, a set  $\{x_{i}, \omega^{i}\}_{i=1}^{N}$ would be an estimation of PDF, $\hat{p}(x)$ . At this point we can invoke dirac delta function,

$\hat{p}(x) = \sum_{i=1}^{N} \omega^{i} \delta(x-x_{i})$

Let's revisit the R code given there, this time let's draw uniform numbers between $[-2, 2]$ to get 100  $x_{i}$ values. Simply these numbers will indicate the locations on the x-axis, a spike train.  For simplicity, let's use Gausian distribution for target PDF, $\mathcal{N}(0, 1)$.  Than, for weights we need to draw numbers using the spike locations. This approach is easier to understand compare to my previous double index notation.

R Example code

Above explained procedure is trivial to implement in R.

  1 2 3 4 5 6 7 8 9 10 # Generate locations 100 x locations # out out 1000 points in [-2.0, 2.0] set.seed(42) # Domain where Dirac comb operates Xj = seq(-2,2,0.002) Xi = sample(Xj, 100) # Now generate weights from N(0,1) at those given locations Wi = dnorm(Xi) # Now visualise plot(Xi, Wi, type="h",xlim=c(-2.0,2.0),ylim=c(0,0.6),lwd=2,col="blue",ylab="p") 

Conclusion

Above notation introduces second  abuse of notation while actually there must be a secondary regular grid that pics $x_{i}$ values using dirac delta in practice. Because, the argument of $\hat{p}(x)$, is in the discrete domain. So a little better notation that reflects the above code would be

$\hat{p}(x_j) = \sum_{i=1}^{N} \omega^{i} \delta(x_{j}-x_{i})$

The set $x_j$ is simply defined in a certain domain, for example regularly. Hence I only recommend not to introduce dirac delta for explaining a particle approximation to PDFs for novice students in the class. It will only confuse them even more.
 Figure: Spike trains with weights $\hat{p}(x) = \sum_{i=1}^{N} \omega^{i} \delta(x-x_{i})$

## Wednesday, 20 November 2013

### Demystify Dirac delta function for data representation on discrete space

Dirac delta function is an important tool in Fourier Analysis. It is used specially in electrodynamics and signal processing routinely.  A function over set of data points
is often shown with a delta function representation. A novice reader relying on integral properties of the delta function may found this notation quite confusing.  Probably, the notation itself is an example of  abuse of notation.

One dimensional function/distribution: Sum of delta functions

Let's define a one dimensional function, $f(x)$ as follows, $x \in \mathbb{R}$ and $a$ being constant:

$f(x) = a \sum_{i=-n}^{n} \delta(x - x_{i})$

This representation is inspired from Dirac comb and used in spike trains.  Note that set of data points in one dimension $\{x_{i} \}$ will determine the graph of this function. Using the shifting property of delta function, the value of the function will be zero every where except on data points. The constant $a$ will simply be the height of the graph at the data point.

 Figure: A spike train.

Numeric Example

Let's plot $f(x)$ for some specific values of the set $\{x_{i} \} = {-0.5, -0.2, -0.1, 0.2, 0.4}$ and $a=0.5$. Here is the R code for plotting this spike train.

x_i = c(-0.5, -0.2, -0.1, 0.2, 0.4)
a   = c(0.5, 0.5, 0.5, 0.5, 0.5)
plot(x_i,a,type="h",xlim=c(-0.6,0.6),ylim=c(0,0.6),lwd=2,col="blue",ylab="p")


Representing Histograms: One dimensional example

Particularly convenient representation of histograms can be developed similarly. Consider set of points $\{x_{i}\}_{i=1}^{n}$ where we would like to establish a histogram out of this set, let's say $h(x)$. If we set our histogram intervals as $\{x_{j}\}_{j=1}^{m}$. The histogram $h(x)$ then can be written as

$h(x_{j}) = \sum_{i=1}^{n} \sum_{j=1}^{m} \delta(x_{j}- x_{i}^{min})$
where set $x_{i}^{min}$  represents the value from set $\{x_{j}\}_{j=1}^{m}$ that is closest to given $x_{i}$. Where as, second sum determines the height at a given point, i.e., frequency. This is just a confusing mathematical representation and practical implementation only counts the frequency of $x_{i}^{min}$ directly.

Conclusion

However it is quite trivial, the above usage of sum of delta functions appear in mathematical physics as well, not limited to statistics.

## Tuesday, 9 April 2013

### Matrix Cumulative Coherence: Fourier Bases, Random and Sensing Matrices

Compressive sampling (CS) is revolutionizing the way we process analog to digital conversion, our understanding of linear systems and the limits of information theory. One of the key concept in CS is that a signal can be represented in a sparse bases or it is already sparse. The novelty of sparsity bases is that when signal is randomly sampled, in a nutshell it can be recovered (or a solution can be found to a linear problem) with fewer samples. A land mark example is being sparse MRI.

The concept of choosing "more" sparse bases or CS sensing matrix lies in the measure of mutual coherence. It is defined as follows for a given matrix at order k.
$$M(A, k) = max_{p} max_{p \ne q, q \in \Omega } \sum_{q} | <a_{p}, a_{q}> | / ( |a_{p}| |a_{q}|)$$ When k=1, it is easy to understand what it means. Basically we find the largest inner product among columns of the given matrix. Lower the value better the sparsity i.e. incoherence. However a single number may not be so informative, after all how low is better.  With the definition of David Donoho and Joel Tropp,  if M is slowly increasing then matrix said to be enchances sparsity. Larger value of k forms a set of columns $\Omega$, and the second colums are selected from this set i.e. second max argument in the above definition.

In a recent post I have shortly reviewed my R package for CS called R1magic. Its recent version 0.2 contains a functionality to compute $M(A, k)$.  Also now there is a public Github repository of the package. mutualCoherence function is written fully functional way. All operations for computing $M(A,k)$ performed in vectorial fashion in R, using function closures and apply. However, for much larger matrices, a low level implementation may be required.

Example

Here we shortly investigate coherence of Fourier, random and mixed bases in R.

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 require("R1magic") set.seed(42) A <- DFTMatrix0(10) # Fourier Bases B <- matrix(rnorm(100), 10, 10) # Gaussian Random Matrix C <- A %*% B # A sensing matrix with A and B as above aa<-mutualCoherence(A, 8) bb<-mutualCoherence(A, 8) bb<-mutualCoherence(A, 8) aa [1] 1 1 1 1 1 1 1 1 bb [1] 0.6784574 1.2011489 1.7001046 2.1713561 2.4664608 2.7302690 2.7908302 [8] 2.9623327 cc [1] 0.7506222 1.3448452 1.8047043 2.1105348 2.3350516 2.4703822 2.5898766 [8] 2.6882250 
We observe that mixed bases, where we define so called a CS matrix, matrix $C$ in above notation, with Fourier ($A$) and Random basis ($B$). Its mutual coherence increases slower than the pure random matrix with unit measure. This may signify a better incoherent basis.  However, since this is a "syntetic data', it does not tell any universal behaviour at all. A real data or signal measurement matrix  shall be tested for a better judgement of which bases is better to use in sparse recovery.  A recent paper in optical tomography uses this concept to identify a better sensing matrix in tomographic image reconstruction.

## Friday, 25 January 2013

### Tensor Algebra: Efficient Operations on Multidimensional Arrays with R

Multidimensional arrays are ubiquitous. Any complex problem having multivariate observables would easily generate a need to represent corresponding data in multidimensional arrays. Most of the practitioners would choose to apply operations on these objects with an index notation.  For example a 3-D array would have 3 indices A[i, j, k] or A[i][j][k] depending on the syntax. However there are languages which takes array operations as their native component, for example APL. More familiar examples are matrix operations in MATLAB, Fortran 90 and alike. Of course this concept is noting more than vectorisation.

Mathematical objects called tensors can be used to represent multidimensional objects. In reality a scalar is rank 0 tensor,  so scalar is the simplest tensor. Rank of a tensor can be thought as objects spatial dimension.  Let's consider matrix multiplication, where there are two indices, tensor of rank 2. If we have two matrices $A_{ij}$ and $B_{ij}$. We can multiply them with index notation as follows using an obscure language R with a naive algorithm:

> set.seed(42)
> A <- matrix(rnorm(4), 2, 2)
> B <- matrix(rnorm(4), 2, 2)
> C <- matrix(0, 2, 2)
> for(i in 1:2) {
+  for(j in 1:2) {
+   for(k in 1:2) {
+     C[i,j] = C[i,j] + A[i, k] * B[k,j]
+    }
+   }
+ }
> C
[,1]       [,2]
[1,]  6.413566 -2.5178879
[2,] -2.249789  0.4908884
> A %*% B
[,1]       [,2]
[1,]  0.5156982  2.0378605
[2,] -0.2954518 -0.9134599


You should have noticed that we introduce a third index. That is called a dummy index which we actually do the sum. This approach is technically called Einstein summation rule. So we represent the multiplication as follows: $C_{ij} = \sum_{k=1}^{m} A_{ik} B_{kj}$. Normally sum is dropped for short notation. It is quite intuitive from this notation that number of columns of A should be equal to number of rows in B to perform the sum consistently.

There are software packages that can do symbolic and numerical tensor algebra . Here we demonstrate an R package called tensorA developed by Professor van den Boogaart of TU Freiberg. We can repeat the matrix multiplication by using this package as follows.

> library("tensorA")
> set.seed(42)
> At <- to.tensor(rnorm(4), c(i=2, k=2))
> Bt <- to.tensor(rnorm(4), c(k=2, j=2))
> At %e% Bt
j
i            [,1]       [,2]
[1,]  0.5156982  2.0378605
[2,] -0.2954518 -0.9134599
attr(,"class")
[1] "tensor" "matrix"


Note that here $\%e\%$ implies tensor multiplication with Einstein summation rule. This is pretty trivial example but if you imagine higher dimensional objects, tracking indices would be cumbersome so multi-linear algebra makes life easy.

In conclusion,  I think,  using tensor arithmetic for multidimensional arrays looks more compacts and efficient (~ 2-3 times).  A discussion related to this appeared in R help list.

## Monday, 15 October 2012

### Compressed Sensing with R

Compressed sensing (CS) is pretty much appealing all current signal processing research community. At the same time, popularity of R language gaining a strong foot in the research and industry. Even though historically MATLAB is a de-facto standard in signal processing community, R is becoming a serious alternative to this. For example, the quality of R in time-series analysis or medical imaging is now an accepted fact.

Last year, I have demonstrated how one can use R in compressed sensing research in a
short tutorial in the pub, close to Liverpool street in London.  The package R1magic is available in CRAN. Package provides basic interface to perform 1-D compressed sensing with l1, TV penalized minimization. There are other packages doing similar regularized minimization. However the interface of R1magic is particularly designed for CS i.e. appearance of sparse bases in the objective function.

Here is one simple example (
Version 0.1):

library(R1magic)#  Signal components
N <- 100
# Sparse components

K <- 4
#  Up to Measurements  > K LOG (N/K)
M <- 40
# Measurement Matrix (Random Sampling Sampling)
phi <- GaussianMatrix(N,M)
# R1magic generate random signal
xorg <- sparseSignal(N, K, nlev=1e-3)
y <- phi %*% xorg ;# generate measurement
T <- diag(N) ;# Do identity transform
p <- matrix(0, N, 1) ;# initial guess
# R1magic Convex Minimization ! (unoptimized-parameter)
ll <- solveL1(phi, y, T, p)
x1 <- ll\$estimate
plot( 1:100, seq(0.011,1.1,0.011), type = "n",xlab="",ylab="")
title(main="Random Sparse Signal Recovery",
xlab="Signal Component",ylab="Spike Value")
lines(1:100, xorg , col = "red")
lines(1:100, x1, col = "blue", cex = 1.5)

# shifted by 5 for clearity

Blue line is the reconstructed signal with R1magic.