[scikit-learn] clustering on big dataset

Manuel Castejón Limas manuel.castejon at gmail.com
Wed Feb 7 12:01:37 EST 2018

Hope this helps!



author="Ciampi, Antonio

and Lechevallier, Yves

and Limas, Manuel Castej{\'o}n

and Marcos, Ana Gonz{\'a}lez",

title="Hierarchical clustering of subpopulations with a dissimilarity based
on the likelihood ratio statistic: application to clustering massive data

journal="Pattern Analysis and Applications",







abstract="The problem of clustering subpopulations on the basis of samples
is considered within a statistical framework: a distribution for the
variables is assumed for each subpopulation and the dissimilarity between
any two populations is defined as the likelihood ratio statistic which
compares the hypothesis that the two subpopulations differ in the parameter
of their distributions to the hypothesis that they do not. A general
algorithm for the construction of a hierarchical classification is
described which has the important property of not having inversions in the
dendrogram. The essential elements of the algorithm are specified for the
case of well-known distributions (normal, multinomial and Poisson) and an
outline of the general parametric case is also discussed. Several
applications are discussed, the main one being a novel approach to dealing
with massive data in the context of a two-step approach. After clustering
the data in a reasonable number of `bins' by a fast algorithm such as
k-Means, we apply a version of our algorithm to the resulting bins.
Multivariate normality for the means calculated on each bin is assumed:
this is justified by the central limit theorem and the assumption that each
bin contains a large number of units, an assumption generally justified
when dealing with truly massive data such as currently found in modern data
analysis. However, no assumption is made about the data generating





2018-01-04 12:55 GMT+01:00 Joel Nothman <joel.nothman at gmail.com>:

> Can you use nearest neighbors with a KD tree to build a distance matrix
> that is sparse, in that distances to all but the nearest neighbors of a
> point are (near-)infinite? Yes, this again has an additional parameter
> (neighborhood size), just as BIRCH has its threshold. I suspect you will
> not be able to improve on having another, approximating, parameter. You do
> not need to set n_clusters to a fixed value for BIRCH. You only need to
> provide another clusterer, which has its own parameters, although you
> should be able to experiment with different "global clusterers".
> On 4 January 2018 at 11:04, Shiheng Duan <shiduan at ucdavis.edu> wrote:
>> Yes, it is an efficient method, still, we need to specify the number of
>> clusters or the threshold. Is there another way to run hierarchy clustering
>> on the big dataset? The main problem is the distance matrix.
>> Thanks.
>> On Tue, Jan 2, 2018 at 6:02 AM, Olivier Grisel <olivier.grisel at ensta.org>
>> wrote:
>>> Have you had a look at BIRCH?
>>> http://scikit-learn.org/stable/modules/clustering.html#birch
>>> --
>>> Olivier
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