Example shifted

.gitignore

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+.pyc
+.project
+.idea
+.pydevproject
+*.pyc
+*.project
+*.idea
+*.pydevproject

README.md

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-# PyDeep 
-
-NEWS: In the following weeks there will be a lot of updates, see list of features below
-
-PyDeep is a machine learning / deep learning library with focus on unsupervised learning especially Restricted Boltzmann machines.
-
-So why another ML lib?
-
-- First of all, the library will contain code I produced during my research that allows to reproduce the results in corresponding publications.
-- If you simply want to use standard algorithms, use one of the big ML libs having GPU support, symbolic differentiation, etc. , this library is not meant to compete with those libraries!
-- The focus is on well documented and modular code that allows you to understand the functionality and thus modify the code easily.
-
-Feature list:
-- Centered Binary-Binary RBMs
-- CD and PCD sampling
-- Centered gradient
-- Calculate true partition function
-- Calculate Log-likelihood
-- Calculate reconstruction error
-- Visualization, profiling, misc. tools
-
-Being prepared for commit:
-- Centered Gaussian-Binary RBMs
-- Centered Gaussian-Binary RBMs with trainable variance
-- Centered Binary-Rectifier RBMs
-- Centered Rectifier-Binary RBMs
-- Centered RectRect RBM (RR-RBM)
-- Centered GaussianRectVariance RBM (GRV-RBM)
-- Centered RBMs with additional label units
-- Centered Softmax RBMs
-- unit tests
-- PCA
-- ZCA
-- Fast ICA
-- Annealed inportant sampling
-- Reverse annealed important sampling
-- MDP wrapper
-- Auto encoder
+Documentation: http://pydeep.readthedocs.io/en/latest/index.html
 
 
+Welcome
+
+PyDeep is a machine learning / deep learning library with focus on unsupervised learning.
+The library has a modular design, is well documented and purely written in Python/Numpy.
+This allows you to understand, use, modify, and debug the code easily. Furthermore,
+its extensive use of unittests assures a high level of reliability and correctness.
+
+News
+
+- The documentation is updated to restructured text
+- Documentation hosted
+- Next the unit tests will be added
+- Upcoming: Tutorials will be added
+- Upcoming: Auto encoders will be added
+- Upcoming: MDP integration will be added
+- Upcoming: Deep Boltzmann machines will be added
+- Upcoming: Feed Forward neural networks will be added
+
+Features
+
+        - Principal Component Analysis (PCA)
+
+        - Zero Phase Component Analysis (ZCA)
+
+        - Independent Component Analysis (ICA)
+
+        - centered BinaryBinary RBM (BB-RBM)
+
+        - centered GaussianBinary RBM (GB-RBM) with fixed variance
+
+        - centered GaussianBinaryVariance RBM (GB-RBM) with trainable variance
+
+        - centered BinaryBinaryLabel RBM (BBL-RBM)
+
+        - centered GaussianBinaryLabel RBM (GBL-RBM)
+
+        - centered BinaryRect RBM (BR-RBM)
+
+        - centered RectBinary RBM (RB-RBM)
+
+        - centered RectRect RBM (RR-RBM)
+
+        - centered GaussianRect RBM (GR-RBM)
+
+        - centered GaussianRectVariance RBM (GRV-RBM)
+
+        - Gibbs Sampling
+
+        - Persistent Gibbs Sampling
+
+        - Parallel Tempering Sampling
+
+        - Independent Parallel Tempering Sampling
+
+        - Annealed Importance Sampling (AIS)
+
+        - reverse Annealed Importance Sampling (AIS)
+
+        - Contrastive Divergence (CD)
+
+        - Persistent Contrastive Divergence (PCD)
+
+        - Tempering Sampling Contrastive Divergence (PT)
+
+        - Independent Tempering Sampling Contrastive Divergence (IPT)
+
+        - Exact Gradient (GD)
+
+
+Scientific use
+
+The library contains code I have written during my PhD research allowing you to reproduce
+the results described in the following publications.
+
+- `Gaussian-binary restricted Boltzmann machines for modeling natural image statistics. Melchior, J., Wang, N., & Wiskott, L.. (2017). PLOS ONE, 12(2), 1–24. <http://doi.org/10.1371/journal.pone.0171015>`_
+
+- `How to Center Deep Boltzmann Machines. Melchior, J., Fischer, A., & Wiskott, L.. (2016). Journal of Machine Learning Research, 17(99), 1–61. <http://jmlr.org/papers/v17/14-237.html>`_
+
+- `Gaussian-binary Restricted Boltzmann Machines on Modeling Natural Image statistics Wang, N., Melchior, J., & Wiskott, L.. (2014). (Vol. 1401.5900). arXiv.org e-Print archive. <http://arxiv.org/abs/1401.5900>`_
+
+- `How to Center Binary Restricted Boltzmann Machines (Vol. 1311.1354). Melchior, J., Fischer, A., Wang, N., & Wiskott, L.. (2013). arXiv.org e-Print archive. <http://arxiv.org/pdf/1311.1354.pdf>`_
+
+- `An Analysis of Gaussian-Binary Restricted Boltzmann Machines for Natural Images. Wang, N., Melchior, J., & Wiskott, L.. (2012). In Proc. 20th European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning, Apr 25–27, Bruges, Belgium (pp. 287–292). <https://www.ini.rub.de/PEOPLE/wiskott/Reprints/WangMelchiorEtAl-2012a-ProcESANN-RBMImages.pdf>`_
+
+- `Learning Natural Image Statistics with Gaussian-Binary Restricted Boltzmann Machines. Melchior, J, 29.05.2012. Master’s thesis, Applied Computer Science, Univ. of Bochum, Germany. <https://www.ini.rub.de/PEOPLE/wiskott/Reprints/Melchior-2012-MasterThesis-RBMs.pdf>`_
+
+IF you want to use PyDeep in your publication, you can cite it as follows.
+
+.. code-block:: latex
+
+   @misc{melchior2017pydeep,
+         title={PyDeep},
+         author={Melchior, Jan},
+         year={2017},
+         publisher={GitHub},
+         howpublished={\url{https://github.com/MelJan/PyDeep.git}},
+        }
+
+Contact:
+
+`Jan Melchior <https://www.ini.rub.de/the_institute/people/jan-melchior/>`_

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = PyDeep
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

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+# -*- coding: utf-8 -*-
+#
+# PyDeep documentation build configuration file, created by
+# sphinx-quickstart on Wed Apr  5 20:57:40 2017.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../'))
+
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.intersphinx','sphinx.ext.autosectionlabel']#,'autoapi.extension']
+
+# Document Python Code
+#autoapi_type = 'python'
+#autoapi_dirs = ['../pydeep']
+#autoapi_file_pattern = '*.py'
+#autoapi_options = ['members', 'private-members', 'special-members']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'PyDeep'
+copyright = u'2017, Jan Melchior'
+author = u'Jan Melchior'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = u'1.1.0'
+# The full version, including alpha/beta/rc tags.
+release = u'1.1.0'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+# language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+# todo_include_todos = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'default'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'PyDeepdoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'PyDeep.tex', u'PyDeep Documentation',
+     u'Jan Melchior', 'manual'),
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'pydeep', u'PyDeep Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'PyDeep', u'PyDeep Documentation',
+     author, 'PyDeep', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}