flexible-clustering-tree 0.12

easy interface for ensemble clustering

flexible-clustering-tree
========================

--------------

What's this?
============

In the context of **clustering** task, ``flexible-clustering-tree``
provides you **easy** and **controllable** clustering framework.

.. figure:: https://user-images.githubusercontent.com/1772712/47308081-9980cd00-d66b-11e8-98c0-a275db021cd7.gif
:alt:

Background
==========

Let's suppose, you have huge data. You'd like to observe data as easy as
possible.

Hierarchical clustering is a way to see clustering tree. However,
hierarchical clustering tends to fall into local optimization.

So, you need other clustering method. But at the same time, you wanna
observe your data with tree structure style.

here, ``flexible-clustering-tree`` could give you simple way from data
into tree viewer(d3 based)

You could set any kinds of clustering algorithm such as Kmeans, DBSCAN,
Spectral-Clustering.

Multi feature and Multi clustering
----------------------------------

During making a tree, you might want use various kind of clustering
algorithm. For example, you use Kmeans for the 1st later of a tree, and
DBSCAN for the 2nd layer of a tree.

And you might also use various kind of feature type depending on a layer
of a tree. For example, in the context of document clustering, "title"
of news for the 1st layer, and "whole text" for the 2nd layer.

The example below, this is a clustering tree of 20-news data set.

- 1st layer(red highlight) is done with HDBSCAN clustering, and feature
is dense vector of ``Subject`` text, which is converted by word2vec
model.
- 2nd layer(blue highlight) is done with Kmeans, and feature is sparse
vector of whole text(BOW).

You could design your clustering tree as you want!

.. figure:: https://user-images.githubusercontent.com/1772712/47308468-abaf3b00-d66c-11e8-9a08-26facc39e80e.png
:alt:

Both are possible ``flexible-clustering-tree``!

Contribution
============

- Easy interface(scikit-learn way) from data(feature matrix) into a
tree viewer
- Possible to make various clustering algorithms ensemble
- Possible to set various feature types

How to use?
===========

.. code:: python

from flexible_clustering_tree import FeatureMatrixObject, MultiFeatureMatrixObject
from flexible_clustering_tree import ClusteringOperator, MultiClusteringOperator
from flexible_clustering_tree import FlexibleClustering

# set feature matrix
f_obj_1st = FeatureMatrixObject(0, numpy.random.rand(500, 600))
f_obj_2nd = FeatureMatrixObject(1, numpy.random.rand(500, 300))
f_obj_3rd = FeatureMatrixObject(2, numpy.random.rand(500, 50))
dict_index2label = {i: "label-{}".format(i) for i in range(0, 500)}
multi_feature_matrix = MultiFeatureMatrixObject(
[f_obj_1st, f_obj_2nd, f_obj_3rd],
dict_index2label=dict_index2label
)

# set clustering operation
from sklearn.cluster.k_means_ import KMeans
from hdbscan.hdbscan_ import HDBSCAN
c_operation_1st = ClusteringOperator(0, 10, KMeans(10))
c_operation_2nd = ClusteringOperator(1, 5, KMeans(5))
multi_clustering = MultiClusteringOperator([c_operation_1st, c_operation_2nd])

# run flexible clustering
clustering_runner = FlexibleClustering(max_depth=3)
index2cluster_no = clustering_runner.fit_transform(multi_feature_matrix, multi_clustering)
html = clustering_runner.clustering_tree.to_html()

# output to html
with codecs.open("out.html", "w", "utf-8") as f:
f.write(html)

You could see examples at ``/examples``.

setup
=====

.. code:: bash

pip install flexible_clustering_tree

or close this repository

.. code:: bash

python setup.py install

For Developers
==============

Environment
-----------

- Python >= 3.x

Dev/Test environment by Docker
------------------------------

You build dev/test environment with Docker container. Here is simple
procedure,

1. build docker image
2. start docker container
3. run test in the container

.. code:: bash

$ cd tests
$ docker-compose build
$ docker-compose up
$ docker run --name test-container -v `pwd`:/codes/flexible-clustering-tree/ -dt tests_dev_env
$ docker exec -it test-container python /codes/flexible-clustering-tree/setup.py test

If you're using pycharm professional edition, you could call a
docker-compose file as Python interpreter.