This is an old blog post, see the newer version in this post

  • In a previous notebook, we tried to reproduce the learning strategy specified in the framework of the SparseNet algorithm from Bruno Olshausen. It allows to efficiently code natural image patches by constraining the code to be sparse. We have shown that:

    • one can denoise an image using the learned dictionary
    • that the dictionaries are qualitatively the same,
    • that the efficiency is roughly similar but best when the learning and the coding are set to Orthogonal Matching Pursuit,
  • However, the dictionaries are qualitatively not the same as the one from the original paper, and this is certainly due to the lack of control in the competition during the learning phase.

  • Herein, we re-implement the cooperation mechanism in the dictionary learning routine - this will be then proposed to the main code.
  • the goal of this notebooks is to illustrate a PR to sklearn
In [1]:
import matplotlib.pyplot as plt
%matplotlib inline
%config InlineBackend.figure_format='svg'
import numpy as np
np.set_printoptions(precision=4, suppress=True)
import pandas as pd
import seaborn as sns
%load_ext autoreload
%autoreload 2
/usr/local/lib/python3.5/site-packages/matplotlib/__init__.py:872: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.
  warnings.warn(self.msg_depr % (key, alt_key))
/usr/local/lib/python3.5/site-packages/matplotlib/__init__.py:872: UserWarning: axes.color_cycle is deprecated and replaced with axes.prop_cycle; please use the latter.
  warnings.warn(self.msg_depr % (key, alt_key))
In [2]:
from shl_scripts import SHL
DEBUG_DOWNSCALE, verbose = 1, 100
DEBUG_DOWNSCALE, verbose = 10, 0
DEBUG_DOWNSCALE, verbose = 100, 100
DEBUG_DOWNSCALE, verbose = 1, 0
np.logspace(-3, 0, int(15/(DEBUG_DOWNSCALE)**.3), base=10, endpoint=False)

#shl = SHL(DEBUG_DOWNSCALE=DEBUG_DOWNSCALE, verbose=verbose, eta_homeo=0.001)
#dico = shl.learn_dico()
Out[2]:
array([ 0.001 ,  0.0016,  0.0025,  0.004 ,  0.0063,  0.01  ,  0.0158,
        0.0251,  0.0398,  0.0631,  0.1   ,  0.1585,  0.2512,  0.3981,
        0.631 ])
In [3]:
from shl_scripts import SHL
database = '/Users/lolo/pool/science/BICV/SHL_scripts/database/'
DEBUG_DOWNSCALE, verbose = 1, 100
DEBUG_DOWNSCALE, verbose = 100, 0
DEBUG_DOWNSCALE, verbose = 100, 100
DEBUG_DOWNSCALE, verbose = 1, 0
shl = SHL(database=database, DEBUG_DOWNSCALE=DEBUG_DOWNSCALE, verbose=verbose, eta_homeo=0.)
dico = shl.learn_dico()
fig, ax = shl.show_dico(dico, title='no_homeo')
fig.show()
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T

a quick diagnostic

An assumption in the existing code is the way that the norm of the filters is controlled. Here, sklearn simply assumes that $ || V_k ||_2 = 1$, $\forall k$ (with $0 <= k < n_{components}$). This may be a problem as a dictionary element with a high variance may be more likely to be selected again, and therefore that the learning will concentrate only on a small sub-set of elements.

In [4]:
data = shl.get_data()
print(shl.max_patches)
dico.set_params(transform_algorithm='omp', transform_n_nonzero_coefs=int(shl.n_components/10))
code = dico.transform(data)
1000
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T
In [5]:
n_components, n_samples = code.shape
Z = np.mean(code**2)
fig = plt.figure(figsize=(12, 4))
ax = fig.add_subplot(111)
ax.bar(np.arange(shl.n_components), np.mean(code**2/Z, axis=0))#, yerr=np.std(code**2/Z, axis=0))
ax.set_title('Variance of coefficients')
ax.set_ylabel('Variance')
ax.set_xlabel('#')
ax.axis('tight')
fig.show()

Worst, this distribution has heavy tails, showing that a small sub-set dominate: this is best shown by showing the correding histogram oif mean variance values:

In [6]:
fig = plt.figure(figsize=(6, 4))
ax = fig.add_subplot(111)
data = pd.DataFrame(np.mean(code**2, axis=0)/np.mean(code**2), columns=['Variance'])
with sns.axes_style("white"):
    ax = sns.distplot(data['Variance'],  kde_kws={'clip':(0., 5.)})
ax.set_title('distribution of the mean variance of coefficients')
ax.set_ylabel('pdf')
fig.show()

A strategy used by Olshausen in it's original paper is to include a gain vector which will be used during the learning to control the norm of the dictionary elements. In turn, this will control how these elements learn and allow for a more equilibrated learning. Let's try to implement thatin sklearn's code.

contributing code to sklearn (1)

The learning code in sklearn is concentrated in one file (sklearn/decomposition/dict_learning.py) that we will modify to use in our extended version of the learning.

  • set-up variables

     cd ~/pool/libs/
     github_user='bicv'
     lib='scikit-learn'
     project='sparsenet'
     git clone https://github.com/$github_user/$lib
     cd $lib
  • creating a new branch for his project

    git branches
    git remote add $github_user https://github.com/$github_user/$lib
    
    git checkout -b $project
  • installing the library in dev mode:

     pip uninstall $lib
     pip install -e .
  • making the one line change to moviepy's code and test it with the minimum working example above:

     mvim sklearn/decomposition/dict_learning.py

More details on MiniBatchDictionaryLearning:

great, let's try that new version of the algorithm

What differs from the original algorithm is mainly

Note that we did not need to modify the OMP routine as it uses the gram matrix.

In [7]:
from shl_scripts import SHL
shl = SHL(database=database, DEBUG_DOWNSCALE=DEBUG_DOWNSCALE, verbose=verbose, eta_homeo=0.01)
dico = shl.learn_dico()
fig, ax = shl.show_dico(dico)
fig.show()
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T

This dictionary looks better and similar to that of Olshausen.

Let's now check the mean variance of the different components (remember it is the same coding algorithm):

In [8]:
data = shl.get_data()
dico.set_params(transform_algorithm='omp', transform_n_nonzero_coefs=shl.transform_n_nonzero_coefs)
code = dico.transform(data)
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T
In [9]:
n_components, n_samples = code.shape
Z = np.mean(code**2)
fig = plt.figure(figsize=(12, 4))
ax = fig.add_subplot(111)
ax.bar(np.arange(shl.n_components), np.mean(code**2/Z, axis=0))
ax.set_title('Variance of coefficients')
ax.set_ylabel('Variance')
ax.set_xlabel('#')
ax.axis('tight')
fig.show()
In [10]:
fig = plt.figure(figsize=(6, 4))
ax = fig.add_subplot(111)
data = pd.DataFrame(np.mean(code**2, axis=0)/np.mean(code**2), columns=['Variance'])
with sns.axes_style("white"):
    ax = sns.distplot(data['Variance'],  kde_kws={'clip':(0., 5.)})
ax.set_title('distribution of the mean variance of coefficients')
ax.set_ylabel('pdf')
fig.show()

contributing code to sklearn (2)

Works as expected! Let's try to do a pull request

  • publishing results

    git status
    git commit -am" making dictionary learning closer to the SparseNet algorithm \n The dictionary learning algorithm was assuming that the norm of the filters was equal to one. By using a heuristic to control for the norm of the filters, we allow for a more equilibrated learning. The implementation is a simplification of the one used in the original paper from Olshausen."
    git push $github_user $project
  • confirm the pull request

    open https://github.com/$github_user/$lib
  • come back to the master branch

    git checkout master

scanning some parameters

Let's explore the dictionaries obtained when modifyng some of the parameters of the OMP algorithm.

In [11]:
from shl_scripts import SHL
DEBUG_DOWNSCALE, verbose = 1, 0

for gain_rate in np.logspace(-3.5, 0, int(15/(DEBUG_DOWNSCALE)**.3), base=10, endpoint=False):
    shl = SHL(database=database, DEBUG_DOWNSCALE=DEBUG_DOWNSCALE, eta_homeo=gain_rate, verbose=verbose)
    dico = shl.learn_dico()
    fig, ax = shl.show_dico(dico, title='gain_rate={}'.format(gain_rate))
    fig.show()
    data = shl.get_data()
    dico.set_params(transform_algorithm='omp', transform_n_nonzero_coefs=shl.transform_n_nonzero_coefs)
    code = dico.transform(data)
    n_components, n_samples = code.shape
    Z = np.mean(code**2)
    fig = plt.figure(figsize=(12, 4))
    ax = fig.add_subplot(111)
    ax.bar(np.arange(shl.n_components), np.mean(code**2, axis=0)/Z)
    ax.set_title('Variance of coefficients - gain {}'.format(gain_rate))
    ax.set_ylabel('Variance')
    ax.set_xlabel('#')      
    ax.axis('tight')
    fig.show()
    fig = plt.figure(figsize=(6, 4))
    ax = fig.add_subplot(111)
    data = pd.DataFrame(np.mean(code**2, axis=0)/np.mean(code**2), columns=['Variance'])
    with sns.axes_style("white"):
        ax = sns.distplot(data['Variance'],  kde_kws={'clip':(0., 5.)})
    ax.set_title('distribution of the mean variance of coefficients - gain {}'.format(gain_rate))
    ax.set_ylabel('pdf')
    fig.show()
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T
/usr/local/lib/python3.5/site-packages/matplotlib/pyplot.py:516: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  max_open_warning, RuntimeWarning)
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T
/usr/local/lib/python3.5/site-packages/matplotlib/pyplot.py:516: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  max_open_warning, RuntimeWarning)
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T
/usr/local/lib/python3.5/site-packages/matplotlib/pyplot.py:516: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  max_open_warning, RuntimeWarning)
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T
/usr/local/lib/python3.5/site-packages/matplotlib/pyplot.py:516: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  max_open_warning, RuntimeWarning)
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T
/usr/local/lib/python3.5/site-packages/matplotlib/pyplot.py:516: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  max_open_warning, RuntimeWarning)
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T
/usr/local/lib/python3.5/site-packages/matplotlib/pyplot.py:516: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  max_open_warning, RuntimeWarning)
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T
/usr/local/lib/python3.5/site-packages/matplotlib/pyplot.py:516: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  max_open_warning, RuntimeWarning)
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T
/usr/local/lib/python3.5/site-packages/matplotlib/pyplot.py:516: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  max_open_warning, RuntimeWarning)
/Users/lolo/pool/libs/numbers/scikit-learn-sparsenet/sklearn/decomposition/dict_learning.py:152: RuntimeWarning:  Orthogonal matching pursuit ended prematurely due to linear
dependence in the dictionary. The requested precision might not have been met.

  copy_Xy=copy_cov).T
/usr/local/lib/python3.5/site-packages/matplotlib/pyplot.py:516: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  max_open_warning, RuntimeWarning)