sabina 0.1.0

checksums.yaml

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data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+/ex/

data/.rspec

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+--format documentation
+--color

data/.travis.yml

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+language: ruby
+
+rvm:
+  - 2.0.0
+  - 2.3.0
+
+before_install: gem install bundler -v 1.11.2
+
+bundler_args: --without development --jobs=2
+
+script: 
+  - bundle exec rspec
+
+branches:
+  only:
+    - master

data/CODE_OF_CONDUCT.md

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+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, and in the interest of
+fostering an open and welcoming community, we pledge to respect all people who
+contribute through reporting issues, posting feature requests, updating
+documentation, submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free
+experience for everyone, regardless of level of experience, gender, gender
+identity and expression, sexual orientation, disability, personal appearance,
+body size, race, ethnicity, age, religion, or nationality.
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery
+* Personal attacks
+* Trolling or insulting/derogatory comments
+* Public or private harassment
+* Publishing other's private information, such as physical or electronic
+  addresses, without explicit permission
+* Other unethical or unprofessional conduct
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+By adopting this Code of Conduct, project maintainers commit themselves to
+fairly and consistently applying these principles to every aspect of managing
+this project. Project maintainers who do not follow or enforce the Code of
+Conduct may be permanently removed from the project team.
+
+This code of conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting a project maintainer at seinosuke.3606@gmail.com. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. Maintainers are
+obligated to maintain confidentiality with regard to the reporter of an
+incident.
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 1.3.0, available at
+[http://contributor-covenant.org/version/1/3/0/][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/3/0/

data/Gemfile

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+source 'https://rubygems.org'
+
+gem 'rake'
+
+group :development do
+  gem 'pry'
+end
+
+group :test do
+  gem 'rspec', '~> 3.0'
+end
+
+gemspec

data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2016 seinosuke
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README.md

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+# Sabina
+
+Sabina is a machine learning library.  
+This gem provides tools for Multi-Layer Perceptrons and Auto-Encoders.  
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'sabina'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install sabina
+
+## Usage
+
+### MultilayerPerceptron
+
+Example of normal usage is shown below.  
+
+```ruby
+require 'sabina'
+
+DIM = 2
+K = 3
+LOOP_NUM = 100
+
+training_data = Sabina::MultilayerPerceptron.load_csv('training_data.csv')
+
+options = {
+  :layers => [
+    Sabina::Layer::MPInputLayer.new(DIM),
+    Sabina::Layer::MPHiddenLayer.new(8),
+    Sabina::Layer::MPOutputLayer.new(K)
+  ],
+  :mini_batch_size => 10,
+  :learning_rate => 0.01,
+  :training_data => training_data,
+}
+
+mp = Sabina::MultilayerPerceptron.new(options)
+
+LOOP_NUM.times do |t|
+  mp.learn
+  error = mp.error(training_data)
+  puts " error : #{error}"
+end
+```
+
+### AutoEncoder
+
+Example of normal usage is shown below. Use `SparseAutoEncoder` class when the number of input units is less than that of hidden units.
+
+```ruby
+require 'sabina'
+
+DIM = 2
+LOOP_NUM = 10
+
+original_data = Sabina::AutoEncoder.load_csv('training_data.csv')
+
+options = {
+  :layers => [
+    Sabina::Layer::AEInputLayer.new(DIM),
+    Sabina::Layer::AEHiddenLayer.new(8),
+    Sabina::Layer::AEOutputLayer.new(DIM)
+  ],
+  :mini_batch_size => 10,
+  :learning_rate => 0.01,
+  :training_data => original_data,
+}
+
+sae = Sabina::SparseAutoEncoder.new(options)
+
+LOOP_NUM.times do |t|
+  sae.learn
+  error = sae.error(original_data)
+  puts " error : #{error}"
+end
+```
+
+### About a training data CSV file format
+
+Examples of a CSV file are shown below.  
+
+```
+x0,x1,label
+0.8616722150185228,0.7958526101017311,0
+0.548524744634457,0.8355704092991548,1
+0.2430915120750876,0.6252296416575435,1
+0.968877668321639,0.7502385938940324,0
+...
+```
+
+This is a example for two-dimensional vector data. For example, if you want to input D-dimensional vector data, write `x0,x1,...,x(D-1),label` at the first line.
+The column of `label` is used for a cluster id. For example, if there are three clusters in training data, a number at the `label` column will be 0, 1 or 2.  
+  
+When you prepare a CSV file, load the file as shown below.
+
+```ruby
+training_data = Sabina::MultilayerPerceptron.load_csv('training_data.csv')
+```
+
+When you use a auto-encoder, load a CSV file as shown below.
+
+```ruby
+original_data = Sabina::AutoEncoder.load_csv('training_data.csv')
+```
+
+### Configuration
+
+You can set default values by using `Sabina.configure` method. These values could be overwritten by providing an argument.  
+
+```ruby
+Sabina.configure do |config|
+  config.layers = [
+    Sabina::Layer::MPInputLayer.new(2),
+    Sabina::Layer::MPHiddenLayer.new(8),
+    Sabina::Layer::MPOutputLayer.new(3)
+  ]
+  config.mini_batch_size = 10
+  config.learning_rate = 0.01
+  config.training_data = Sabina::MultilayerPerceptron.load_csv('training_data.csv')
+end
+
+options = {
+  :mini_batch_size => 20
+}
+
+mp_01 = Sabina::MultilayerPerceptron.new
+mp_02 = Sabina::MultilayerPerceptron.new(options)
+
+mp_01.mini_batch_size # => 10
+mp_02.mini_batch_size # => 20
+```
+
+### Your own layer class
+You can create your own layer class. In the following example below, a rectified linear function is set as an activation function. `@f_` is differentiation of `@f`.
+
+```ruby
+class MyHiddenLayer < Sabina::Layer::BaseLayer
+  def initialize(size)
+    super
+    # f(x) = max(0, x)
+    @f = ->(x){ x > 0.0 ? x : 0.0 }
+    @f_ = ->(x){ x > 0.0 ? 1.0 : 0.0 }
+  end
+end
+
+options = {
+  :layers => [
+    Sabina::Layer::MPInputLayer.new(DIM),
+    MyHiddenLayer.new(16),
+    MyHiddenLayer.new(8),
+    Sabina::Layer::MPOutputLayer.new(K)
+  ],
+  :mini_batch_size => 10,
+  :learning_rate => 0.01,
+  :training_data => training_data,
+}
+```
+
+## Examples
+
+These examples require gnuplot version 5.0 or later.
+
+### examples/example_mp_01/
+
+Run [examples/example_mp_01/main.rb](https://github.com/seinosuke/sabina/blob/master/examples/example_mp_01/main.rb).  
+
+![mp_learning_process.gif](https://github.com/seinosuke/sabina/blob/master/examples/example_mp_01/mp_learning_process.gif)
+
+### examples/example_mp_02/
+
+Run [examples/example_mp_02/main.rb](https://github.com/seinosuke/sabina/blob/master/examples/example_mp_02/main.rb).  
+
+![mp_learning_process.gif](https://github.com/seinosuke/sabina/blob/master/examples/example_mp_02/mp_learning_process.gif)
+
+### examples/example_ae_01/
+
+Run [examples/example_ae_01/main.rb](https://github.com/seinosuke/sabina/blob/master/examples/example_ae_01/main.rb).  
+
+![ae_learning_process.gif](https://github.com/seinosuke/sabina/blob/master/examples/example_ae_01/mp_learning_process.gif)
+
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/seinosuke/sabina. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
+
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](http://opensource.org/licenses/MIT).
+

data/Rakefile

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+require "bundler/gem_tasks"
+
+require "rspec/core/rake_task"
+RSpec::Core::RakeTask.new(:spec)

data/examples/example_ae_01/main.rb

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+$LOAD_PATH.unshift File.expand_path('../../../lib', __FILE__)
+require 'open3'
+require 'sabina'
+
+DIM = 2
+LOOP_NUM = 100
+xrange = [-2.2, 2.2]
+yrange = [-2.2, 2.2]
+
+original_data = Sabina::AutoEncoder.load_csv('training_data.csv')
+
+options = {
+  :layers => [
+    Sabina::Layer::AEInputLayer.new(DIM),
+    Sabina::Layer::AEHiddenLayer.new(20),
+    Sabina::Layer::AEOutputLayer.new(DIM)
+  ],
+  :mini_batch_size => 10,
+  :learning_rate => 0.0002,
+  :training_data => original_data,
+}
+
+# Use a sparse autoencoder
+# because the number of input units is less than that of hidden units.
+sae = Sabina::SparseAutoEncoder.new(options)
+
+
+
+##################################################
+# Make a chart of original data.
+##################################################
+Open3.popen3('gnuplot') do |gp_in, gp_out, gp_err|
+  output_file = "./ae_original_data.png"
+  gp_in.puts "set colorsequence classic"
+  gp_in.puts "set terminal png size 480, 450"
+  gp_in.puts "set output '#{output_file}'"
+  gp_in.puts "set label 2 center at screen 0.5,0.9 'Original Data' font 'Helvetica,22'"
+  gp_in.puts "set tmargin 3.2"
+  gp_in.puts "set xlabel 'x0'"
+  gp_in.puts "set ylabel 'x1'"
+  gp_in.puts "set size square"
+  gp_in.puts xrange.tap { |f, t| break "set xrange [#{f}:#{t}]" }
+  gp_in.puts yrange.tap { |f, t| break "set yrange [#{f}:#{t}]" }
+  plot = "plot "
+
+  plot << "'-' notitle pt 1 ps 1 lc 1,\\\n"
+  plot.gsub!(/,\\\n\z/, "\n")
+
+  original_data.each do |data|
+    data[:x].tap { |x, y| plot << "#{x}, #{y}\n" }
+  end
+  plot << "e\n"
+
+  gp_in.puts plot
+  puts output_file
+  gp_in.puts "set output"
+  gp_in.puts "exit"
+  gp_in.close
+end
+
+
+##################################################
+# Make a GIF of the learning process.
+##################################################
+Open3.popen3('gnuplot') do |gp_in, gp_out, gp_err|
+  output_file = "./ae_learning_process.gif"
+  gp_in.puts "set colorsequence classic"
+  gp_in.puts "set terminal gif animate delay 10 optimize size 880, 450"
+  gp_in.puts "set output '#{output_file}'"
+  gp_in.puts "set tmargin 3.2"
+  gp_in.puts "set size square"
+  gp_in.puts xrange.tap { |f, t| break "set xrange [#{f}:#{t}]" }
+  gp_in.puts yrange.tap { |f, t| break "set yrange [#{f}:#{t}]" }
+  gp_in.puts "set xlabel 'x0'"
+  gp_in.puts "set ylabel 'x1'"
+  log = []
+  x_mat = Matrix.columns( original_data.map { |data| data[:x] } )
+
+  LOOP_NUM.times do |t|
+    sae.learn
+    log << sae.error(original_data)
+    gp_in.puts "set multiplot layout 1, 2"
+
+    ##################################################
+    # Original Data
+    ##################################################
+    gp_in.puts "set label 2 center at screen 0.28,0.9 'Original Data' font 'Helvetica,22'"
+    plot = "plot "
+    plot << "'-' notitle pt 1 ps 1 lc 1,\\\n"
+    plot.gsub!(/,\\\n\z/, "\n")
+
+    original_data.each do |data|
+      data[:x].tap { |x, y| plot << "#{x}, #{y}\n" }
+    end
+    plot << "e\n"
+    gp_in.puts plot
+
+    ##################################################
+    # Decoded Data
+    ##################################################
+    gp_in.puts "set label 2 center at screen 0.79,0.9 'Decoded Data' font 'Helvetica,22'"
+    plot = "plot "
+    plot << "'-' notitle pt 1 ps 1 lc 1,\\\n"
+    plot.gsub!(/,\\\n\z/, "\n")
+
+    decoded_data = sae.propagate_forward(x_mat).t.to_a
+    decoded_data.each do |data|
+      data.tap { |x, y| plot << "#{x}, #{y}\n" }
+    end
+    plot << "e\n"
+    gp_in.puts plot
+
+    # progress bar
+    puts " error : #{log.last}"
+    puts " [#{("*"*(t / (LOOP_NUM / 10))).ljust(10, " ")}]"
+    print "\e[2A"; STDOUT.flush;
+  end
+
+  gp_in.puts "set output"
+  puts output_file
+  gp_in.puts "exit"
+  gp_in.close
+end