I found a similar question asked here Determining cluster membership in SOM (Self Organizing Map) for time series data
and I want to learn how to apply self organizing map in binarizing or assigning more than 2 kinds of symbols to data.
For example, let data = rand(100,1)
In general, I would be doing data_quantized = 2*(data>=0.5)-1
to get a binary valued transformed series where the threshold 0.5 is assumed and fixed. It may have been possible to quantize data using more that 2 symbols. Can kmeans or SOM be applied to do this task? What should be the input and output if I were to use SOM in quantizing the data?
X = {x_i(t)}
for i =1:N and t = 1:T number of time series, N
represents the number of components/ variables. To get the quantized value for any vector x_i is to use the value of the BMU, which is nearest. The quantization error will be the Euclidean norm of the difference of the input vector and the best-matching model. Then a new time series is compared / matched using the symbols representation of the time series. WOuld BMU be a scalar valued number or a vector of floating point numbers? It is very hard to picturize what SOM is doing.
Matlab implementation https://www.mathworks.com/matlabcentral/fileexchange/39930-self-organizing-map-simple-demonstration
I cannot understand how to work for time series in quantization. Assuming N = 1
, a 1 dimensional array/ vector of elements obtained from a white noise process, how can I quantize / partition this data using self organizing map?
http://www.mathworks.com/help/nnet/ug/cluster-with-self-organizing-map-neural-network.html
is provided by the Matlab but it works for N dimensional data but I have a 1 dimensional data containing 1000 data points (t =1,...,1000).
It shall be of immense help if a toy example is provided which explain how a time series can be quantized into multiple levels. Let, trainingData = x_i;
T = 1000;
N = 1;
x_i = rand(T,N) ;
How can I apply the code below of SOM so that the numerical valued data can be represented by symbols such as 1,2,3 i.e clustered using 3 symbols? A data point (scalar valued) can be either represented by symbol 1 or 2 or 3.
function som = SOMSimple(nfeatures, ndim, nepochs, ntrainingvectors, eta0, etadecay, sgm0, sgmdecay, showMode)
%SOMSimple Simple demonstration of a Self-Organizing Map that was proposed by Kohonen.
% sommap = SOMSimple(nfeatures, ndim, nepochs, ntrainingvectors, eta0, neta, sgm0, nsgm, showMode)
% trains a self-organizing map with the following parameters
% nfeatures - dimension size of the training feature vectors
% ndim - width of a square SOM map
% nepochs - number of epochs used for training
% ntrainingvectors - number of training vectors that are randomly generated
% eta0 - initial learning rate
% etadecay - exponential decay rate of the learning rate
% sgm0 - initial variance of a Gaussian function that
% is used to determine the neighbours of the best
% matching unit (BMU)
% sgmdecay - exponential decay rate of the Gaussian variance
% showMode - 0: do not show output,
% 1: show the initially randomly generated SOM map
% and the trained SOM map,
% 2: show the trained SOM map after each update
%
% For example: A demonstration of an SOM map that is trained by RGB values
%
% som = SOMSimple(1,60,10,100,0.1,0.05,20,0.05,2);
% % It uses:
% % 1 : dimensions for training vectors
% % 60x60: neurons
% % 10 : epochs
% % 100 : training vectors
% % 0.1 : initial learning rate
% % 0.05 : exponential decay rate of the learning rate
% % 20 : initial Gaussian variance
% % 0.05 : exponential decay rate of the Gaussian variance
% % 2 : Display the som map after every update
nrows = ndim;
ncols = ndim;
nfeatures = 1;
som = rand(nrows,ncols,nfeatures);
% Generate random training data
x_i = trainingData;
% Generate coordinate system
[x y] = meshgrid(1:ncols,1:nrows);
for t = 1:nepochs
% Compute the learning rate for the current epoch
eta = eta0 * exp(-t*etadecay);
% Compute the variance of the Gaussian (Neighbourhood) function for the ucrrent epoch
sgm = sgm0 * exp(-t*sgmdecay);
% Consider the width of the Gaussian function as 3 sigma
width = ceil(sgm*3);
for ntraining = 1:ntrainingvectors
% Get current training vector
trainingVector = trainingData(ntraining,:);
% Compute the Euclidean distance between the training vector and
% each neuron in the SOM map
dist = getEuclideanDistance(trainingVector, som, nrows, ncols, nfeatures);
% Find the best matching unit (bmu)
[~, bmuindex] = min(dist);
% transform the bmu index into 2D
[bmurow bmucol] = ind2sub([nrows ncols],bmuindex);
% Generate a Gaussian function centered on the location of the bmu
g = exp(-(((x - bmucol).^2) + ((y - bmurow).^2)) / (2*sgm*sgm));
% Determine the boundary of the local neighbourhood
fromrow = max(1,bmurow - width);
torow = min(bmurow + width,nrows);
fromcol = max(1,bmucol - width);
tocol = min(bmucol + width,ncols);
% Get the neighbouring neurons and determine the size of the neighbourhood
neighbourNeurons = som(fromrow:torow,fromcol:tocol,:);
sz = size(neighbourNeurons);
% Transform the training vector and the Gaussian function into
% multi-dimensional to facilitate the computation of the neuron weights update
T = reshape(repmat(trainingVector,sz(1)*sz(2),1),sz(1),sz(2),nfeatures);
G = repmat(g(fromrow:torow,fromcol:tocol),[1 1 nfeatures]);
% Update the weights of the neurons that are in the neighbourhood of the bmu
neighbourNeurons = neighbourNeurons + eta .* G .* (T - neighbourNeurons);
% Put the new weights of the BMU neighbouring neurons back to the
% entire SOM map
som(fromrow:torow,fromcol:tocol,:) = neighbourNeurons;
end
end
function ed = getEuclideanDistance(trainingVector, sommap, nrows, ncols, nfeatures)
% Transform the 3D representation of neurons into 2D
neuronList = reshape(sommap,nrows*ncols,nfeatures);
% Initialize Euclidean Distance
ed = 0;
for n = 1:size(neuronList,2)
ed = ed + (trainingVector(n)-neuronList(:,n)).^2;
end
ed = sqrt(ed);
I don't know that I might be misunderstanding your question, but from what I understand it is really quite straight forward, both with kmeans
and with Matlab's own selforgmap
. The implementation you have posted for SOMSimple I cannot really comment on.
Let's take your initial example:
rng(1337);
T = 1000;
x_i = rand(1,T); %rowvector for convenience
Assuming you want to quantize to three symbols, your manual version could be:
nsyms = 3;
symsthresh = [1:-1/nsyms:1/nsyms];
x_i_q = zeros(size(x_i));
for i=1:nsyms
x_i_q(x_i<=symsthresh(i)) = i;
end
Using Matlab's own selforgmap
you can achieve a similar result:
net = selforgmap(nsyms);
net.trainParam.showWindow = false;
net = train(net,x_i);
net(x_i);
y = net(x_i);
classes = vec2ind(y);
Lastly, the same can be done straightforwardly with kmeans
:
clusters = kmeans(x_i',nsyms)';