machine_learning_workbench 0.1.0

data/lib/machine_learning_workbench/optimizer/natural_evolution_strategies/snes.rb

@@ -0,0 +1,40 @@
+
+module MachineLearningWorkbench::Optimizer::NaturalEvolutionStrategies
+  # Separable Natural Evolution Strategies
+  class SNES < Base
+
+    attr_reader :variances
+
+    def initialize_distribution mu_init: 0, sigma_init: 1
+      @mu = NMatrix.new([1, ndims], mu_init, dtype: :float64)
+      sigma_init = [sigma_init]*ndims unless sigma_init.kind_of? Enumerable
+      @variances = NMatrix.new([1,ndims], sigma_init, dtype: :float64)
+      @sigma = NMatrix.diagonal(variances, dtype: :float64)
+    end
+
+    def train picks: sorted_inds
+      g_mu = utils.dot(picks)
+      g_sigma = utils.dot(picks**2 - 1)
+      @mu += sigma.dot(g_mu.transpose).transpose * lrate
+      @variances *= (g_sigma * lrate / 2).exponential
+      @sigma = NMatrix.diagonal(variances, dtype: :float64)
+    end
+
+    # Estimate algorithm convergence as total variance
+    def convergence
+      variances.reduce :+
+    end
+
+    def save
+      [mu.to_consistent_a, variances.to_consistent_a]
+    end
+
+    def load data
+      raise ArgumentError unless data.size == 2
+      mu_ary, variances_ary = data
+      @mu = NMatrix[*mu_ary, dtype: :float64]
+      @variances = NMatrix[*variances_ary, dtype: :float64]
+      @sigma = NMatrix.diagonal(variances, dtype: :float64)
+    end
+  end
+end

data/lib/machine_learning_workbench/optimizer/natural_evolution_strategies/xnes.rb

@@ -0,0 +1,46 @@
+
+module MachineLearningWorkbench::Optimizer::NaturalEvolutionStrategies
+  # Exponential Natural Evolution Strategies
+  class XNES < Base
+    attr_reader :log_sigma
+
+    def initialize_distribution mu_init: 0, sigma_init: 1
+      @mu = NMatrix.new([1, ndims], mu_init, dtype: :float64)
+      sigma_init = [sigma_init]*ndims unless sigma_init.kind_of? Enumerable
+      @sigma = NMatrix.diag(sigma_init, dtype: :float64)
+      # Works with the log of sigma to avoid continuous decompositions (thanks Sun Yi)
+      log_sigma_init = sigma_init.map &Math.method(:log)
+      @log_sigma = NMatrix.diag(log_sigma_init, dtype: :float64)
+    end
+
+    def train picks: sorted_inds
+      g_mu = utils.dot(picks)
+      g_log_sigma = popsize.times.inject(NMatrix.zeros_like sigma) do |sum, i|
+        u = utils[i]
+        ind = picks.row(i)
+        ind_sq = ind.outer_flat(ind, &:*)
+        sum + (ind_sq - id) * u
+      end
+      @mu += sigma.dot(g_mu.transpose).transpose * lrate
+      @log_sigma += g_log_sigma * (lrate/2)
+      @sigma = log_sigma.exponential
+    end
+
+    # Estimate algorithm convergence as total variance
+    def convergence
+      sigma.trace
+    end
+
+    def save
+      [mu.to_consistent_a, log_sigma.to_consistent_a]
+    end
+
+    def load data
+      raise ArgumentError unless data.size == 2
+      mu_ary, log_sigma_ary = data
+      @mu = NMatrix[*mu_ary, dtype: :float64]
+      @log_sigma = NMatrix[*log_sigma_ary, dtype: :float64]
+      @sigma = log_sigma.exponential
+    end
+  end
+end

data/lib/machine_learning_workbench/tools.rb

@@ -0,0 +1,4 @@
+require_relative 'tools/execution'
+require_relative 'tools/normalization'
+require_relative 'tools/imaging'
+require_relative 'tools/verification'

data/lib/machine_learning_workbench/tools/execution.rb

@@ -0,0 +1,18 @@
+module MachineLearningWorkbench::Tools
+  module Execution
+    $fork_pids ||= []
+
+    # Execute block in a fork. Be sure to check also `#kill_forks`
+    def self.in_fork &block
+      raise ArgumentError "Need block to be executed in fork" unless block
+      pid = fork(&block)
+      Process.detach pid
+      $fork_pids << pid
+    end
+
+    # Call this in an `ensure` block after using `in_fork`
+    def self.kill_forks
+      $fork_pids&.each { |pid| Process.kill 'KILL', pid }
+    end
+  end
+end

data/lib/machine_learning_workbench/tools/imaging.rb

@@ -0,0 +1,48 @@
+module MachineLearningWorkbench::Tools
+  module Imaging
+    Forkable = MachineLearningWorkbench::Tools::Execution
+    Norm = MachineLearningWorkbench::Tools::Normalization
+
+    # Create RMagick::Image from NMatrix data
+    def self.nmat_to_img nmat, shape: nil
+      shape ||= nmat.shape
+      shape = [1, shape] if shape.kind_of?(Integer) || shape.size == 1
+      # `Image::constitute` requires Float pixels to be in [0,1]
+      pixels = Norm.feature_scaling nmat.round(4), to: [0,1]
+      Magick::Image.constitute *shape, "I", pixels.to_flat_a
+    end
+
+    # Create PNG file from NMatrix data
+    def self.nmat_to_png nmat, fname, shape: nil
+      nmat_to_img(nmat, shape: shape).write fname
+    end
+
+    # Show a NMatrix as image in a RMagick window
+    # @param disp_size the size of the image to display
+    # @param shape the true shape of the image (NMatrix could be flattened)
+    # @param in_fork [bool] whether to execute the display in fork (and continue running)
+    def self.display nmat, disp_size: [300, 300], shape: nil, in_fork: true
+      img = nmat_to_img(nmat, shape: shape).resize(*disp_size)
+      if in_fork
+        MachineLearningWorkbench::Tools::Execution.in_fork { img.display }
+      else
+        img.display
+      end
+    end
+
+    # Create NMatrix from png by filename.
+    # @param fname the file name
+    # @param scale optional rescaling of the image
+    # @param flat [bool] whether to return a flat array
+    # @param dtype dtype for the NMatrix, leave `nil` for automatic detection
+    def self.nmat_from_png fname, scale: nil, flat: false, dtype: nil
+      img = Magick::ImageList.new(fname).first
+      img.scale!(scale) if scale
+      shape = [img.columns, img.rows]
+      pixels = img.export_pixels(0, 0, *shape, 'I') # 'I' for intensity
+      raise "Sanity check" unless shape.reduce(:*)==pixels.size
+      return pixels.to_nm(nil, dtype) if flat
+      NMatrix.new shape, pixels, dtype: dtype
+    end
+  end
+end

data/lib/machine_learning_workbench/tools/normalization.rb

@@ -0,0 +1,22 @@
+module MachineLearningWorkbench::Tools
+  module Normalization
+    def self.feature_scaling nmat, from: nil, to: [0,1]
+      from ||= nmat.minmax
+      old_min, old_max = from
+      new_min, new_max = to
+      res = (nmat-old_min)*(new_max-new_min)/(old_max-old_min)+new_min
+    end
+
+    # @param per_column [bool] wheather to compute stats per-column or matrix-wise
+    def self.z_score nmat, per_column: true
+      raise NotImplementedError unless per_column
+      means = nmat.mean
+      stddevs = nmat.std
+      # address edge case of zero variance
+      stddevs.map! { |v| v.zero? ? 1 : v }
+      mean_mat = means.repeat nmat.rows, 0
+      stddev_mat = stddevs.repeat nmat.rows, 0
+      ret = (nmat - mean_mat) / stddev_mat
+    end
+  end
+end

data/lib/machine_learning_workbench/tools/verification.rb

@@ -0,0 +1,11 @@
+module MachineLearningWorkbench::Tools
+  module Verification
+    def self.in_range! nmat, vrange
+      vmin, vmax = vrange.to_a
+      nmat.each_with_indices do |v, *idxs|
+        nmat[*idxs] = vmin if v < vmin
+        nmat[*idxs] = vmax if v > vmax
+      end
+    end
+  end
+end

data/machine_learning_workbench.gemspec

@@ -0,0 +1,36 @@
+
+lib = File.expand_path("../lib", __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+
+Gem::Specification.new do |spec|
+  spec.name          = "machine_learning_workbench"
+  spec.version       = `git describe`
+  spec.authors       = ["Giuseppe Cuccu"]
+  spec.email         = ["giuseppe.cuccu@gmail.com"]
+
+  spec.summary       = %q{Workbench for practical machine learning in Ruby.}
+  spec.description   = %q{This workbench holds a collection of machine learning methods in Ruby. Rather than specializing on a single task or method, this gem aims at providing an encompassing framework for any machine learning application.}
+  spec.homepage      = "https://github.com/giuse/machine_learning_workbench"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0").reject do |f|
+    f.match(%r{^(test|spec|features)/})
+  end
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_dependency "nmatrix-atlas", "~> 0.2"
+
+  spec.add_development_dependency "bundler", "~> 1.16"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.0"
+  spec.add_development_dependency "pry", "~> 0.10"
+  spec.add_development_dependency "pry-nav", "~> 0.2"
+  spec.add_development_dependency "pry-rescue", "~> 1.4"
+  spec.add_development_dependency "pry-stack_explorer", "~> 0.4"
+
+  # currently under trial
+  spec.add_development_dependency "rmagick"
+  spec.add_development_dependency "parallel"
+end

metadata

@@ -0,0 +1,216 @@
+--- !ruby/object:Gem::Specification
+name: machine_learning_workbench
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Giuseppe Cuccu
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2018-03-06 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: nmatrix-atlas
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.2'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.2'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.16'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.16'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: pry
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.10'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.10'
+- !ruby/object:Gem::Dependency
+  name: pry-nav
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.2'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.2'
+- !ruby/object:Gem::Dependency
+  name: pry-rescue
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+- !ruby/object:Gem::Dependency
+  name: pry-stack_explorer
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.4'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.4'
+- !ruby/object:Gem::Dependency
+  name: rmagick
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: parallel
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: This workbench holds a collection of machine learning methods in Ruby.
+  Rather than specializing on a single task or method, this gem aims at providing
+  an encompassing framework for any machine learning application.
+email:
+- giuseppe.cuccu@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".codeclimate.yml"
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- lib/machine_learning_workbench.rb
+- lib/machine_learning_workbench/compressor.rb
+- lib/machine_learning_workbench/compressor/vector_quantization.rb
+- lib/machine_learning_workbench/monkey.rb
+- lib/machine_learning_workbench/neural_network.rb
+- lib/machine_learning_workbench/neural_network/base.rb
+- lib/machine_learning_workbench/neural_network/feed_forward.rb
+- lib/machine_learning_workbench/neural_network/recurrent.rb
+- lib/machine_learning_workbench/optimizer.rb
+- lib/machine_learning_workbench/optimizer/natural_evolution_strategies/base.rb
+- lib/machine_learning_workbench/optimizer/natural_evolution_strategies/bdnes.rb
+- lib/machine_learning_workbench/optimizer/natural_evolution_strategies/snes.rb
+- lib/machine_learning_workbench/optimizer/natural_evolution_strategies/xnes.rb
+- lib/machine_learning_workbench/tools.rb
+- lib/machine_learning_workbench/tools/execution.rb
+- lib/machine_learning_workbench/tools/imaging.rb
+- lib/machine_learning_workbench/tools/normalization.rb
+- lib/machine_learning_workbench/tools/verification.rb
+- machine_learning_workbench.gemspec
+homepage: https://github.com/giuse/machine_learning_workbench
+licenses:
+- MIT
+metadata: {}
+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: 2.6.11
+signing_key: 
+specification_version: 4
+summary: Workbench for practical machine learning in Ruby.
+test_files: []