I have extracted words from a set of URLs and calculated cosine similarity between each URL's contents.And also I have normalized the values between 0-1(using Min-Max).Now i need to cluster the URLs based on cosine similarity values to find out similar URLs.which clustering algorithm will be most suitable?.Please suggest me a Dynamic clustering method because it will be useful since i could increase number of URL's on demand and also it will be more natural.Please correct me if you feel i'm making the progress in a wrong way.Thanks in anticipation.
K-means clustering can be used for online learning, you just need to select the number of clusters a priori. Also, I think you shouldn't normalize your data, because cosine already provides values in the range [0:1]. Your Min-Max normalization could lead to information loss.
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Looks like I can't use this similarity metric for with sklearn KDTree, for example, but I need because I am using measuring words vectors similarity. What is fast robust customization algorithm for this case? I know about Local Sensitivity Hashing, but it should tunned & tested up a lot to find params.
The ranking your would get with cosine similarity is equivalent to the rank order of the euclidean distance when you normalize all the data points first. So you can use a KD tree to the the k nearest neighbors with KDTrees, but you will need to recompute what the cosine similarity is.
The cosine similarity is not a distance metric as normally presented, but it can be transformed into one. If done, you can then use other structures like Ball Trees to do accelerated nn with cosine similarity directly. I've implemented this in the JSAT library, if you were interested in a Java implementation.
According to the table at the end of this page, cosine support eoth k-d-tree should be possible: ELKI supports cosine with the R-tree, and you can derive bounding rectangles for the k-d-tree, too; and the k-d-tree supports at least five metrics in that table. So I do not see why it shouldn't work.
Indexing support in sklearn often is not very complete (albeit improving), unfortunately; so don't take that as a reference.
While the k-d-tree can theoretically support Cosine by
transforming the data such that Cosine becomes Euclidean distance
working with the bounding boxes and the minimum angle to the bounding box (that appears to be what ELKI is doing for the R-tree)
You should be aware that the k-d-tree does not work very well with high-dimensional data, and cosine is mostly popular for very high-dimensional data. A k-d-tree always only looks at one dimension. If you want all d dimension to be used once, you need O(2^d) data points. For high d, there is no way all attributes are used.
The R-tree is slightly better here because it uses bounding boxes; these shrink with every split in all dimensions, so the pruning does get better. But this also means it needs a lot of memory for such data, and the tree construction may suffer from the same problem.
So in essence, don't use either for high dimensional data.
But also don't assume that Cosine does magically improve your results, in particular for high-d data. It's very much overrated. As above transformation indicates, there cannot be a systematic benefit of Cosine over Euclidean: Cosine is a special case of Euclidean.
For sparse data, inverted lists (c.f. Lucene, Xapian, Solr, ...) are the way to index for cosine.
In a lot of articles in my field, this sentence has been repeated: " The 2 matrices has been normalized to have the same average sum-of-squares (computed across all subjects and all voxels for each modality)". Suppose that we have two matrices that the rows define different subjects and the columns are features (voxels). In these articles, no much explanation can be found for normalization method. Does anybody knows how I should normalize data to have "same average sum-of-squares"? I don't understand it at all. Thanks
For a start normalization in this context is also known as features scaling, which pretty much sums it up. You scale your features, your data to get rid of variances and range of values which would disturb your algorithm and your results in the end.
https://en.wikipedia.org/wiki/Feature_scaling
In data processing, normalization is quite useful (depending on the application). E.g. in distance based machine learning algorithms you should normalize your features in order to get a proportional contribution to the outcome of your algorithm, independent of the range of value the features comprise.
To do so, you can use different statistical measurements, like the
Sum of squares:
SUM_i(Xi-Xbar)²
Other than that you could use the variance or the standard deviation of your data.
https://www.westgard.com/lesson35.htm#4
Those statistical terms can then be used to normalize your data, to improve e.g. the clustering quality of your algorithm. Which term to use and which method highly depends on the algorithms and data you're using and what you're aiming at.
Here is a paper which compares some of the approaches you could choose from for clustering:
http://maxwellsci.com/print/rjaset/v6-3299-3303.pdf
I hope this can help you a little.
I am using mahout recommenditembased algorithm. What are the differences between all the --similarity Classes available? How to know what is the best choice for my application? These are my choices:
SIMILARITY_COOCCURRENCE
SIMILARITY_LOGLIKELIHOOD
SIMILARITY_TANIMOTO_COEFFICIENT
SIMILARITY_CITY_BLOCK
SIMILARITY_COSINE
SIMILARITY_PEARSON_CORRELATION
SIMILARITY_EUCLIDEAN_DISTANCE
What does it mean each one?
I'm not familiar with all of them, but I can help with some.
Cooccurrence is how often two items occur with the same user. http://en.wikipedia.org/wiki/Co-occurrence
Log-Likelihood is the log of the probability that the item will be recommended given the characteristics you are recommending on. http://en.wikipedia.org/wiki/Log-likelihood
Not sure about tanimoto
City block is the distance between two instances if you assume you can only move around like you're in a checkboard style city. http://en.wikipedia.org/wiki/Taxicab_geometry
Cosine similarity is the cosine of the angle between the two feature vectors. http://en.wikipedia.org/wiki/Cosine_similarity
Pearson Correlation is covariance of the features normalized by their standard deviation. http://en.wikipedia.org/wiki/Pearson_correlation_coefficient
Euclidean distance is the standard straight line distance between two points. http://en.wikipedia.org/wiki/Euclidean_distance
To determine which is the best for you application you most likely need to have some intuition about your data and what it means. If your data is continuous value features than something like euclidean distance or pearson correlation makes sense. If you have more discrete values than something along the lines of city block or cosine similarity may make more sense.
Another option is to set up a cross-validation experiment where you see how well each similarity metric works to predict the desired output values and select the metric that works the best from the cross-validation results.
Tanimoto and Jaccard are similars, is a statistic used for comparing the similarity and diversity of sample sets.
https://en.wikipedia.org/wiki/Jaccard_index
I 've used a part of reuters 21578 dataset and mahout k-means for clustering.To be more specific I extracted only the texts that has a unique value for category 'topics'.So I ve been left with 9494 texts that belong to one among 66 categories. I ve used seqdirectory to create sequence files from texts and then seq2sparse to crate the vectors. Then I run k-means with cosine distance measure (I ve tried tanimoto and euclidean too, with no better luck), cd=0.1 and k=66 (same as the number of categories). So I tried to evaluate the results with silhouette measure using custom Java code and the matlab implementation of silhouette (just to be sure that there is no error in my code) and I get that the average silhouette of the clustering is 0.0405. Knowing that the best clustering could give an average silhouette value close to 1, I see that the clustering result I get is no good at all.
So is this due to Mahout or the quality of catgorization on reuters dataset is low?
PS: I m using Mahout 0.7
PS2: Sorry for my bad English..
I've never actually worked with Mahout, so I cannot say what it does by default, but you might consider checking what sort of distance metric it uses by default. For example, if the metric is Euclidean distance on unnormalized document word counts, you can expect very poor quality cluster quality, as document length will dominate any meaningful comparison between documents. On the other hand, something like cosine distance on normalized, or tf-idf weighted word counts can do much better.
One other thing to look at is the distribution of topics in the Reuters 21578. It is very skewed towards a few topics such as "acq" or "earn", while others are used only handfuls of times. This can it difficult to achieve good external clustering metrics.
If I use a similarity based algorithm such as pearson correlation score to compare two feature vectors
and I want to know those dimensions/feature fields which are very much dissimilar amongst the feature set then what is the algorithm to be used? I am using Mahout which is a machine learning library for Java
Well, it would just be the dimension in which the two vectors differed most -- in which the absolute value of the difference of the vectors' values in the dimension was largest. Is that really all you mean or are you looking for something subtler?