Do you know if we can implement Bayesian Hierarchical clustering (python or R) on vectors with float values? I have searched through the web, and just found some random matrices with the values of 0,1,2. In the related paper nothing has mentioned. I also tried to implement it with R, which returned a fatal error and R studio and RGui were closed suddenly, which I am not sure if it is because of the float values or not.
BHC Package in R is specially designed for bayesian hierarchical clustering
Related
I am new to machine learning field and right now trying to get a grasp of how the most common learning algorithms work and understand when to apply each one of them. At the moment I am learning on how Support Vector Machines work and have a question on custom kernel functions.
There is plenty of information on the web on more standard (linear, RBF, polynomial) kernels for SVMs. I, however, would like to understand when it is reasonable to go for a custom kernel function. My questions are:
1) What are other possible kernels for SVMs?
2) In which situation one would apply custom kernels?
3) Can custom kernel substantially improve prediction quality of SVM?
1) What are other possible kernels for SVMs?
There are infinitely many of these, see for example list of ones implemented in pykernels (which is far from being exhaustive)
https://github.com/gmum/pykernels
Linear
Polynomial
RBF
Cosine similarity
Exponential
Laplacian
Rational quadratic
Inverse multiquadratic
Cauchy
T-Student
ANOVA
Additive Chi^2
Chi^2
MinMax
Min/Histogram intersection
Generalized histogram intersection
Spline
Sorensen
Tanimoto
Wavelet
Fourier
Log (CPD)
Power (CPD)
2) In which situation one would apply custom kernels?
Basically in two cases:
"simple" ones give very bad results
data is specific in some sense and so - in order to apply traditional kernels one has to degenerate it. For example if your data is in a graph format, you cannot apply RBF kernel, as graph is not a constant-size vector, thus you need a graph kernel to work with this object without some kind of information-loosing projection. also sometimes you have an insight into data, you know about some underlying structure, which might help classifier. One such example is a periodicity, you know that there is a kind of recuring effect in your data - then it might be worth looking for a specific kernel etc.
3) Can custom kernel substantially improve prediction quality of SVM?
Yes, in particular there always exists a (hypothethical) Bayesian optimal kernel, defined as:
K(x, y) = 1 iff arg max_l P(l|x) == arg max_l P(l|y)
in other words, if one has a true probability P(l|x) of label l being assigned to a point x, then we can create a kernel, which pretty much maps your data points onto one-hot encodings of their most probable labels, thus leading to Bayes optimal classification (as it will obtain Bayes risk).
In practise it is of course impossible to get such kernel, as it means that you already solved your problem. However, it shows that there is a notion of "optimal kernel", and obviously none of the classical ones is not of this type (unless your data comes from veeeery simple distributions). Furthermore, each kernel is a kind of prior over decision functions - closer you get to the actual one with your induced family of functions - the more probable is to get a reasonable classifier with SVM.
Newbie here typesetting my question, so excuse me if this don't work.
I am trying to give a bayesian classifier for a multivariate classification problem where input is assumed to have multivariate normal distribution. I choose to use a discriminant function defined as log(likelihood * prior).
However, from the distribution,
$${f(x \mid\mu,\Sigma) = (2\pi)^{-Nd/2}\det(\Sigma)^{-N/2}exp[(-1/2)(x-\mu)'\Sigma^{-1}(x-\mu)]}$$
i encounter a term -log(det($S_i$)), where $S_i$ is my sample covariance matrix for a specific class i. Since my input actually represents a square image data, my $S_i$ discovers quite some correlation and resulting in det(S_i) being zero. Then my discriminant function all turn Inf, which is disastrous for me.
I know there must be a lot of things go wrong here, anyone willling to help me out?
UPDATE: Anyone can help how to get the formula working?
I do not analyze the concept, as it is not very clear to me what you are trying to accomplish here, and do not know the dataset, but regarding the problem with the covariance matrix:
The most obvious solution for data, where you need a covariance matrix and its determinant, and from numerical reasons it is not feasible is to use some kind of dimensionality reduction technique in order to capture the most informative dimensions and simply discard the rest. One such method is Principal Component Analysis (PCA), which applied to your data and truncated after for example 5-20 dimensions would yield the reduced covariance matrix with non-zero determinant.
PS. It may be a good idea to post this question on Cross Validated
Probably you do not have enough data to infer parameters in a space of dimension d. Typically, the way you would get around this is to take an MAP estimate as opposed to an ML.
For the multivariate normal, this is a normal-inverse-wishart distribution. The MAP estimate adds the matrix parameter of inverse Wishart distribution to the ML covariance matrix estimate and, if chosen correctly, will get rid of the singularity problem.
If you are actually trying to create a classifier for normally distributed data, and not just doing an experiment, then a better way to do this would be with a discriminative method. The decision boundary for a multivariate normal is quadratic, so just use a quadratic kernel in conjunction with an SVM.
I got Memory Error when I was running dbscan algorithm of scikit.
My data is about 20000*10000, it's a binary matrix.
(Maybe it's not suitable to use DBSCAN with such a matrix. I'm a beginner of machine learning. I just want to find a cluster method which don't need an initial cluster number)
Anyway I found sparse matrix and feature extraction of scikit.
http://scikit-learn.org/dev/modules/feature_extraction.html
http://docs.scipy.org/doc/scipy/reference/sparse.html
But I still have no idea how to use it. In DBSCAN's specification, there is no indication about using sparse matrix. Is it not allowed?
If anyone knows how to use sparse matrix in DBSCAN, please tell me.
Or you can tell me a more suitable cluster method.
The scikit implementation of DBSCAN is, unfortunately, very naive. It needs to be rewritten to take indexing (ball trees etc.) into account.
As of now, it will apparently insist of computing a complete distance matrix, which wastes a lot of memory.
May I suggest that you just reimplement DBSCAN yourself. It's fairly easy, there exists good pseudocode e.g. on Wikipedia and in the original publication. It should be just a few lines, and you can then easily take benefit of your data representation. E.g. if you already have a similarity graph in a sparse representation, it's usually fairly trivial to do a "range query" (i.e. use only the edges that satisfy your distance threshold)
Here is a issue in scikit-learn github where they talk about improving the implementation. A user reports his version using the ball-tree is 50x faster (which doesn't surprise me, I've seen similar speedups with indexes before - it will likely become more pronounced when further increasing the data set size).
Update: the DBSCAN version in scikit-learn has received substantial improvements since this answer was written.
You can pass a distance matrix to DBSCAN, so assuming X is your sample matrix, the following should work:
from sklearn.metrics.pairwise import euclidean_distances
D = euclidean_distances(X, X)
db = DBSCAN(metric="precomputed").fit(D)
However, the matrix D will be even larger than X: n_samples² entries. With sparse matrices, k-means is probably the best option.
(DBSCAN may seem attractive because it doesn't need a pre-determined number of clusters, but it trades that for two parameters that you have to tune. It's mostly applicable in settings where the samples are points in space and you know how close you want those points to be to be in the same cluster, or when you have a black box distance metric that scikit-learn doesn't support.)
Yes, since version 0.16.1.
Here's a commit for a test:
https://github.com/scikit-learn/scikit-learn/commit/494b8e574337e510bcb6fd0c941e390371ef1879
Sklearn's DBSCAN algorithm doesn't take sparse arrays. However, KMeans and Spectral clustering do, you can try these. More on sklearns clustering methods: http://scikit-learn.org/stable/modules/clustering.html
Hello I am working on a project involving in face recognition for which I am using Linear Discriminant Analysis(LDA). LDA demands to find the generalized eigen vectors for the between class scatter matrix and with in class scatter matrix and that is where I am struck. I am using opencv with DevC++ for coding. Basically the problem looks like
A*v=lambda*B*v
where A and B are matrices for which generalized eigen vectors should be found
lambda is eigen values and v is vectors
Upon searching about this problem many people suggested to go for calculating the inverse of B and then multiplying with A*v
(inv(B)*A)*v=lambda*v
and then calculate eigen vectors for inv(B)*A.
It seems to be a good solution but in my case the scatter matrix B is almost sigular. I found its determinant is in the order of 10^-36 .So I cant find its inverse and proceed with the above solution. So Can some one suggest me a way to get out of this problem except saying to code for generalized eigen value problem separately.
I am providing a Fisherfaces implementation in my github repository at https://github.com/bytefish/opencv/tree/master/lda. This includes the implementation of an eigenvalue solver for general matrices, see: https://github.com/bytefish/opencv/blob/master/lda/include/decomposition.hpp (I've ported the great JAMA solver), which is exactely what you are looking for.
If you have problems with the code, please drop me a note on the projects page at http://www.bytefish.de/blog/fisherfaces_in_opencv.
I am trying to implement image search based on paper "Scalable Recognition with a Vocabulary Tree". I am using SURF for extracting the features and key points. For example, for an image i'm getting say 300 key points and each key point has 128 descriptor values. My Question is how can I apply the K-Means Clustering algorithm on the data. I mean Do I need to apply clustering algorithm on all the points i.e., 300*128 values or Do I need to find the distance between the consecutive descriptor values and store the values and apply the clustering algorithm on that. I am confused and any help will be appreciated.
Thanks,
Rocky.
From your question I would say you are quite confused. The vocabulary tree technique is grounded on the us of k-means hierarchical clustering and a TF-IDF weighting scheme for the leaf nodes.
In a nutshell the clustering algorithm employed for the vocabulary tree construction runs k-means once over all the d-dimensional data (d=128 for the case of SIFT) and then runs k-means again over each of the obtained clusters until some depth level. Hence the two main parameters for the vocabulary tree construction are the branching factor k and the tree depth L. Some improvements consider only the branching factor while the depth is automatically determined by cutting the tree to fulfill a minimum variance measure.
As for the implementation, cv::BOWTrainer from OpenCV is a good starting point though is not very well generalized for the case of a hierarchical BoW scheme since it imposes the centers to be stored in a simple cv::Mat while vocabulary tree is typically unbalanced and mapping it to a matrix in a level-wise fashion might not be efficient from the memory use point of view when the number of nodes is much lower than the theoretical number of nodes in a balanced tree with depth L and branching factor k, that is:
n << (1-k^L)/(1-k)
For what I know I think that you have to store all the descriptors on a cv::Mat and then add this to a "Kmeans Trainer", thus you can finally apply the clustering algorithm. Here a snippet that can give you an idea about what I am talking:
BOWKMeansTrainer bowtrainer(1000); //num clusters
bowtrainer.add(training_descriptors); // we add the descriptors
Mat vocabulary = bowtrainer.cluster(); // apply the clustering algorithm
And this maybe can be interesting to you: http://www.morethantechnical.com/2011/08/25/a-simple-object-classifier-with-bag-of-words-using-opencv-2-3-w-code/
Good luck!!
Checkout out the code in libvot, in src/vocab_tree/clustering.*, you can find a detailed implementation of the clustering algorithm.