brains 0.1.0-java

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data/.gitignore

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

data/.rspec

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+--format documentation
+--color

data/.travis.yml

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+sudo: false
+language: ruby
+rvm:
+  - 2.3.1
+before_install: gem install bundler -v 1.12.3

data/CODE_OF_CONDUCT.md

@@ -0,0 +1,49 @@
+# 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 joseph.dayo@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

@@ -0,0 +1,4 @@
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in brains.gemspec
+gemspec

data/LICENSE.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2016 Joseph Emmanuel Dayo
+
+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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+# Brains
+
+A Feedforward neural network toolkit for JRuby. Easily add machine learning features
+to your ruby application using this Gem. Though there are faster native C implementations
+this java backend provides a balance of performance and ease of use.
+
+## Installation
+
+Do note that this gem requires JRuby as it uses a java backend to run the neural network
+computations.
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'brains'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install brains
+
+## Usage
+
+The brains gem contains facilities for training and using the feedforward neural network
+
+Training (XOR example)
+--------
+
+Initialize the neural net backend
+
+```ruby
+require 'brains'
+
+
+# Build a 3 layer network: 4 input neurons, 4 hidden neurons, 3 output neurons
+# Bias neurons are automatically added to input + hidden layers; no need to specify these
+# 5 = 4 in one hidden layer + 1 output neuron (input neurons not counted)
+
+nn = Brains::Net.create(2, 1, 5, { neurons_per_layer: 4 })
+nn.randomize_weights
+```
+
+Consider that we want to train the neural network to handle XOR computations
+
+```
+A    B   A XOR B
+1    1      0
+1    0      1
+0    1      1
+0    0      0
+```
+
+First we build the training data. This is an array of arrays with each item
+in the following format:
+
+```
+[
+[[input1, input2, input3....], [expected1, expected2, expected3 ...]]
+[[input1, input2, input3....], [expected1, expected2, expected3 ...]]
+]
+```
+
+```ruby
+training_data = [
+  [[0.9, 0.9], [0.1]],
+  [[0.9, 0.1], [0.9]],
+  [[0.1, 0.9], [0.9]],
+  [[0.1, 0.1], [0.1]],
+]
+```
+Note that we map 1 = 0.9 and 0 = 0.1 since using absolute 1 and 0s might cause
+issues with certain neural networks. There are other techniques to "normalize"
+input, but this is beyond the scope of this example.
+
+Start training on the data by calling optimize. Here we use 0.01 as the expected
+MSE error before terminating and 1000 as the max epochs.
+
+```ruby
+result = nn.optimize(training_data, 0.01, 1_000 ) { |i, error|
+  puts "#{i} #{error}"
+}
+```
+
+To test the neural network you can call the feed method.
+
+nn.feed( [test_input1, test_input2, .....]) => [output1, output2, ...]
+
+Check if the network is trained. There are more advanced and proper techniques to check if
+a network is sufficiently trained, but this is beyond the scope of this example.
+
+```ruby
+# test on untrained data
+test_data = [
+  [0.9, 0.9],
+  [0.9, 0.1],
+  [0.1, 0.9],
+  [0.1, 0.1]
+]
+
+results = test_data.collect { |item|
+  nn.feed(item)
+}
+
+p results
+
+[[0.19717958808009528], [0.7983320405281495], [0.8386219299757574], [0.16609147896733775]]
+```
+
+Using the test data we can see the correlation and the neural network function now approximates
+the xor function with the desired error:
+
+```
+[0.9, 0.9] => [0.19717958808009528]
+[0.9, 0.1] => [0.7983320405281495]
+[0.1, 0.9] => [0.8386219299757574]
+[0.1, 0.1] => [0.16609147896733775]
+```
+
+Saving brain state
+==================
+
+Save the neuron state at any time to a string using to_json
+
+```ruby
+saved_state = nn.to_json
+```
+
+You can then save it to a file. You can then load it back using load()
+
+```ruby
+  nn = Brains::Net.load(saved_state)
+```
+
+For other samples please take a look at the example folder.
+
+Java Neural Network backend is based on:
+
+https://github.com/jedld/brains
+
+You can compile the java source code as brains.jar and use it directly with this gem.
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/brains. 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

@@ -0,0 +1,6 @@
+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec

data/bin/console

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "brains"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start

data/bin/setup

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/brains.gemspec

@@ -0,0 +1,34 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'brains/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "brains"
+  spec.version       = Brains::VERSION
+  spec.authors       = ["Joseph Emmanuel Dayo"]
+  spec.email         = ["joseph.dayo@gmail.com"]
+
+  spec.summary       = %q{A feedforward neural network library for JRuby}
+  spec.description   = %q{A feedforward neural network library for JRuby}
+  spec.homepage      = "https://github.com/jedld/brains-jruby"
+  spec.license       = "MIT"
+  spec.platform      = "java"
+
+  # Prevent pushing this gem to RubyGems.org. To allow pushes either set the 'allowed_push_host'
+  # to allow pushing to a single host or delete this section to allow pushing to any host.
+  if spec.respond_to?(:metadata)
+    spec.metadata['allowed_push_host'] = "https://rubygems.org"
+  else
+    raise "RubyGems 2.0 or newer is required to protect against public gem pushes."
+  end
+
+  spec.files         = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.12"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.0"
+end

data/example/iris.rb

@@ -0,0 +1,100 @@
+#!/usr/bin/env ruby
+
+require 'brains'
+
+# This neural network will predict the species of an iris based on sepal and petal size
+# Dataset: http://en.wikipedia.org/wiki/Iris_flower_data_set
+
+rows = File.readlines("iris.data").map {|l| l.chomp.split(',') }
+
+rows.shuffle!
+
+label_encodings = {
+  "Iris-setosa"     => [1, 0, 0],
+  "Iris-versicolor" => [0, 1, 0],
+  "Iris-virginica"  => [0, 0 ,1]
+}
+
+x_data = rows.map {|row| row[0,4].map(&:to_f) }
+y_data = rows.map {|row| label_encodings[row[4]] }
+
+# Normalize data values before feeding into network
+normalize = -> (val, high, low) {  (val - low) / (high - low) } # maps input to float between 0 and 1
+
+columns = (0..3).map do |i|
+  x_data.map {|row| row[i] }
+end
+
+x_data.map! do |row|
+  row.map.with_index do |val, j|
+    max, min = columns[j].max, columns[j].min
+    normalize.(val, max, min)
+  end
+end
+
+x_train = x_data.slice(0, 100)
+y_train = y_data.slice(0, 100)
+
+x_test = x_data.slice(100, 50)
+y_test = y_data.slice(100, 50)
+
+test_cases = []
+x_train.each_with_index do |x, index|
+  test_cases << [x, y_train[index] ]
+end
+
+validation_cases = []
+x_test.each_with_index do |x, index|
+  test_cases << [x, y_test[index] ]
+end
+
+# Build a 3 layer network: 4 input neurons, 4 hidden neurons, 3 output neurons
+# Bias neurons are automatically added to input + hidden layers; no need to specify these
+nn = Brains::Net.create(4, 3, 7, { neurons_per_layer: 4 })
+nn.randomize_weights
+
+prediction_success = -> (actual, ideal) {
+  predicted = (0..2).max_by {|i| actual[i] }
+  ideal[predicted] == 1
+}
+
+mse = -> (actual, ideal) {
+  errors = actual.zip(ideal).map {|a, i| a - i }
+  (errors.inject(0) {|sum, err| sum += err**2}) / errors.length.to_f
+}
+
+error_rate = -> (errors, total) { ((errors / total.to_f) * 100).round }
+
+run_test = -> (nn, inputs, expected_outputs) {
+  success, failure, errsum = 0,0,0
+  inputs.each.with_index do |input, i|
+    output = nn.feed input
+    prediction_success.(output, expected_outputs[i]) ? success += 1 : failure += 1
+    errsum += mse.(output, expected_outputs[i])
+  end
+  [success, failure, errsum / inputs.length.to_f]
+}
+
+puts "Testing the untrained network..."
+
+success, failure, avg_mse = run_test.(nn, x_test, y_test)
+
+puts "Untrained classification success: #{success}, failure: #{failure} (classification error: #{error_rate.(failure, x_test.length)}%, mse: #{(avg_mse * 100).round(2)}%)"
+
+
+puts "\nTraining the network...\n\n"
+
+t1 = Time.now
+result = nn.optimize(test_cases, 0.01, 1_000 ) { |i, error|
+  puts "#{i} #{error}"
+}
+
+# puts result
+puts "\nDone training the network: #{result[:iterations]} iterations, #{(result[:error] * 100).round(2)}% mse, #{(Time.now - t1).round(1)}s"
+
+
+puts "\nTesting the trained network..."
+
+success, failure, avg_mse = run_test.(nn, x_test, y_test)
+
+puts "Trained classification success: #{success}, failure: #{failure} (classification error: #{error_rate.(failure, x_test.length)}%, mse: #{(avg_mse * 100).round(2)}%)"

data/example/xor.rb

@@ -0,0 +1,64 @@
+#!/usr/bin/env ruby
+
+require 'brains'
+
+
+# Build a 3 layer network: 4 input neurons, 4 hidden neurons, 3 output neurons
+# Bias neurons are automatically added to input + hidden layers; no need to specify these
+# 5 = 4 in one hidden layer + 1 output neuron (input neurons not counted)
+
+nn = Brains::Net.create(2, 1, 5, { neurons_per_layer: 4 })
+nn.randomize_weights
+
+# A    B   A XOR B
+# 1    1      0
+# 1    0      1
+# 0    1      1
+# 0    0      0
+
+training_data = [
+  [[0.9, 0.9], [0.1]],
+  [[0.9, 0.1], [0.9]],
+  [[0.1, 0.9], [0.9]],
+  [[0.1, 0.1], [0.1]],
+]
+
+# test on untrained data
+test_data = [
+  [0.9, 0.9],
+  [0.9, 0.1],
+  [0.1, 0.9],
+  [0.1, 0.1]
+]
+
+results = test_data.collect { |item|
+  nn.feed(item)
+}
+
+p results
+
+result = nn.optimize(training_data, 0.01, 1_000 ) { |i, error|
+  puts "#{i} #{error}"
+}
+
+puts "after training"
+
+results = test_data.collect { |item|
+  nn.feed(item)
+}
+
+
+p results
+
+state = nn.to_json
+puts state
+
+nn2 = Brains::Net.load(state)
+
+results2 = test_data.collect { |item|
+  nn2.feed(item)
+}
+
+puts "use saved state"
+
+p results2

data/iris.data

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data/lib/brains.rb

@@ -0,0 +1,13 @@
+require "brains/version"
+require "brains/brains.jar"
+require "brains/gson.jar"
+require "brains/commons-lang3.jar"
+require "brains/commons-cli.jar"
+require "brains/net"
+require "json"
+
+module Brains
+  class Config
+    attr_accessor :neurons_per_layer, :input_neurons, :output_neurons
+  end
+end

data/lib/brains/net.rb

@@ -0,0 +1,105 @@
+require 'java'
+
+module Brains
+  class Net
+    attr_accessor :nn, :config
+
+    def self.create(input, output, total, opts = {})
+      config = com.dayosoft.nn.NeuralNet::Config.new(input, output, total)
+      config.bias = opts[:bias] || 1.0
+      config.outputBias = opts[:output_bias] || 1.0
+      config.learningRate = opts[:learning_rate] || 0.1
+      config.neuronsPerLayer = opts[:neurons_per_layer] || 5
+      config.momentumFactor = opts[:momentum_factor] || 0.5
+      config.activationFunctionType = opt_to_func(opts[:activation_function] || :htan)
+      config.outputActivationFunctionType = opt_to_func(opts[:activation_function] || :sigmoid)
+      config.errorFormula = opt_to_error_func(opts[:activation_function] || :mean_squared)
+      nn = com.dayosoft.nn.NeuralNet.new(config);
+
+      Brains::Net.new.set_nn(nn).set_config(config)
+    end
+
+    def self.load(json_string)
+      nn = com.dayosoft.nn.NeuralNet::loadStateFromJsonString(nil, json_string)
+      config = nn.getConfig
+
+      Brains::Net.new.set_nn(nn).set_config(config)
+    end
+
+    def randomize_weights(min = -1, max = 1)
+      @nn.randomizeWeights(min, max)
+    end
+
+    def dump_weights
+      @nn.dumpWeights.to_a.map(&:to_a)
+    end
+
+    def dump_biases
+      @nn.dumpWeights.to_a.map(&:to_a)
+    end
+
+    def optimize(test_cases, target_error = 0.01, max_epoch = 1_000_000_000, is_batch = false, &callback)
+      inputs = []
+      outputs = []
+
+      test_cases.each do |item|
+        inputs << item[0].to_java(Java::double)
+        outputs << item[1].to_java(Java::double)
+      end
+
+      result = @nn.optimize(java.util.ArrayList.new(inputs), java.util.ArrayList.new(outputs), target_error, max_epoch, is_batch, callback)
+      { iterations: result.first, error: result.second }
+    end
+
+    def feed(input)
+      output = @nn.feed(input.to_java(Java::double)).to_a
+    end
+
+    def to_json
+      @nn.saveStateToJson
+    end
+
+    def set_nn(nn)
+      @nn = nn
+      self
+    end
+
+    def set_config(config)
+      @config = config
+      self
+    end
+
+    protected
+
+    def initialize
+    end
+
+    private
+
+    def self.opt_to_func(func)
+      case func
+      when :htan
+        com.dayosoft.nn.Neuron::HTAN
+      when :sigmoid
+        com.dayosoft.nn.Neuron::SIGMOID
+      when :softmax
+        com.dayosoft.nn.Neuron::SOFTMAX
+      when :rectifier
+        com.dayosoft.nn.Neuron::RECTIFIER
+      else
+        raise "invalid activation function #{func}"
+      end
+    end
+
+    def self.opt_to_error_func(func)
+      case func
+      when :mean_squared
+        com.dayosoft.nn.NeuralNet::Config::MEAN_SQUARED
+      when :cross_entropy
+        com.dayosoft.nn.NeuralNet::Config::CROSS_ENTROPY
+      else
+        raise "Invalid Error Function #{func}"
+      end
+    end
+  end
+end

data/lib/brains/version.rb

@@ -0,0 +1,3 @@
+module Brains
+  VERSION = "0.1.0"
+end

metadata

@@ -0,0 +1,108 @@
+--- !ruby/object:Gem::Specification
+name: brains
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: java
+authors:
+- Joseph Emmanuel Dayo
+autorequire:
+bindir: exe
+cert_chain: []
+date: 2017-02-23 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.12'
+  name: bundler
+  prerelease: false
+  type: :development
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.12'
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  name: rake
+  prerelease: false
+  type: :development
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  name: rspec
+  prerelease: false
+  type: :development
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+description: A feedforward neural network library for JRuby
+email:
+- joseph.dayo@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- CODE_OF_CONDUCT.md
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- brains.gemspec
+- example/iris.rb
+- example/xor.rb
+- iris.data
+- lib/brains.rb
+- lib/brains/brains.jar
+- lib/brains/commons-cli.jar
+- lib/brains/commons-lang3.jar
+- lib/brains/gson.jar
+- lib/brains/net.rb
+- lib/brains/version.rb
+homepage: https://github.com/jedld/brains-jruby
+licenses:
+- MIT
+metadata:
+  allowed_push_host: https://rubygems.org
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project:
+rubygems_version: 2.4.8
+signing_key:
+specification_version: 4
+summary: A feedforward neural network library for JRuby
+test_files: []