rumale 0.20.2 → 0.22.2
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- checksums.yaml +4 -4
- data/.github/workflows/build.yml +23 -0
- data/.rubocop.yml +10 -0
- data/CHANGELOG.md +26 -0
- data/Gemfile +5 -2
- data/README.md +17 -14
- data/lib/rumale.rb +3 -0
- data/lib/rumale/clustering/snn.rb +1 -1
- data/lib/rumale/decomposition/pca.rb +1 -1
- data/lib/rumale/ensemble/stacking_classifier.rb +214 -0
- data/lib/rumale/ensemble/stacking_regressor.rb +163 -0
- data/lib/rumale/evaluation_measure/roc_auc.rb +3 -0
- data/lib/rumale/feature_extraction/feature_hasher.rb +1 -1
- data/lib/rumale/feature_extraction/hash_vectorizer.rb +1 -1
- data/lib/rumale/kernel_machine/kernel_svc.rb +4 -3
- data/lib/rumale/linear_model/base_sgd.rb +1 -1
- data/lib/rumale/linear_model/elastic_net.rb +2 -2
- data/lib/rumale/linear_model/lasso.rb +2 -2
- data/lib/rumale/linear_model/linear_regression.rb +3 -3
- data/lib/rumale/linear_model/logistic_regression.rb +123 -35
- data/lib/rumale/linear_model/ridge.rb +3 -3
- data/lib/rumale/linear_model/svc.rb +6 -5
- data/lib/rumale/linear_model/svr.rb +6 -5
- data/lib/rumale/metric_learning/mlkr.rb +161 -0
- data/lib/rumale/metric_learning/neighbourhood_component_analysis.rb +19 -48
- data/lib/rumale/pairwise_metric.rb +1 -1
- data/lib/rumale/pipeline/pipeline.rb +1 -1
- data/lib/rumale/tree/base_decision_tree.rb +2 -9
- data/lib/rumale/tree/gradient_tree_regressor.rb +3 -10
- data/lib/rumale/validation.rb +1 -1
- data/lib/rumale/version.rb +1 -1
- data/rumale.gemspec +2 -1
- metadata +25 -8
- data/.coveralls.yml +0 -1
checksums.yaml
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SHA256:
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metadata.gz:
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data.tar.gz: adc58efa3b46d9fc1a87ddb2a4df32472507d61f21a3a0eb07026068cc5e41af166fb0a0f8ae23f1b23aec649b22835a50edbed79d35255e8cc231b82b31eb8c
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name: build
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on: [push, pull_request]
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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ruby: [ '2.5', '2.6', '2.7' ]
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steps:
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- uses: actions/checkout@v2
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- name: Install BLAS and LAPACK
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run: sudo apt-get install -y libopenblas-dev liblapacke-dev
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- name: Set up Ruby ${{ matrix.ruby }}
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uses: actions/setup-ruby@v1
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with:
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ruby-version: ${{ matrix.ruby }}
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- name: Build and test with Rake
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run: |
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gem install bundler
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bundle install --jobs 4 --retry 3
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bundle exec rake
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data/.rubocop.yml
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require:
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- rubocop-performance
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- rubocop-rake
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- rubocop-rspec
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IgnoredPatterns: ['(\A|\s)#']
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Enabled: false
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Enabled: false
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RSpec/MultipleExpectations:
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Enabled: false
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data/CHANGELOG.md
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# 0.22.2
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- Add classifier and regressor classes for stacking method.
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- [StackingClassifier](https://yoshoku.github.io/rumale/doc/Rumale/Ensemble/StackingClassifier.html)
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- [StackingRegressor](https://yoshoku.github.io/rumale/doc/Rumale/Ensemble/StackingRegressor.html)
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- Refactor some codes with Rubocop.
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# 0.22.1
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- Add transfomer class for [MLKR](https://yoshoku.github.io/rumale/doc/Rumale/MetricLearning/MLKR.html), that implements Metric Learning for Kernel Regression.
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- Refactor NeighbourhoodComponentAnalysis.
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- Update API documentation.
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# 0.22.0
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## Breaking change
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- Add lbfgsb.rb gem to runtime dependencies. Rumale uses lbfgsb gem for optimization.
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This eliminates the need to require the mopti gem when using [NeighbourhoodComponentAnalysis](https://yoshoku.github.io/rumale/doc/Rumale/MetricLearning/NeighbourhoodComponentAnalysis.html).
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- Add lbfgs solver to [LogisticRegression](https://yoshoku.github.io/rumale/doc/Rumale/LinearModel/LogisticRegression.html) and make it the default solver.
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# 0.21.0
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## Breaking change
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- Change the default value of max_iter argument on LinearModel estimators to 1000.
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# 0.20.3
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- Fix to use automatic solver of PCA in NeighbourhoodComponentAnalysis.
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- Refactor some codes with Rubocop.
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- Update README.
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# 0.20.2
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- Add cross-validator class for time-series data.
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- [TimeSeriesSplit](https://yoshoku.github.io/rumale/doc/Rumale/ModelSelection/TimeSeriesSplit.html)
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data/Gemfile
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@@ -3,11 +3,14 @@ source 'https://rubygems.org'
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# Specify your gem's dependencies in rumale.gemspec
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gemspec
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gem 'coveralls', '~> 0.8'
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gem 'mmh3', '>= 1.0'
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gem 'mopti', '>= 0.1.0'
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gem 'numo-linalg', '>= 0.1.4'
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gem 'parallel', '>= 1.17.0'
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gem 'rake', '~> 12.0'
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gem 'rake-compiler', '~> 1.0'
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gem 'rspec', '~> 3.0'
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gem 'rubocop', '~> 1.0'
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gem 'rubocop-performance', '~> 1.8'
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gem 'rubocop-rake', '~> 0.5'
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gem 'rubocop-rspec', '~> 2.0'
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gem 'simplecov', '~> 0.19'
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data/README.md
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![Rumale](https://dl.dropboxusercontent.com/s/joxruk2720ur66o/rumale_header_400.png)
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[![Build Status](https://
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[![Coverage Status](https://coveralls.io/repos/github/yoshoku/rumale/badge.svg?branch=master)](https://coveralls.io/github/yoshoku/rumale?branch=master)
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[![Build Status](https://github.com/yoshoku/rumale/workflows/build/badge.svg)](https://github.com/yoshoku/rumale/actions?query=workflow%3Abuild)
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[![Gem Version](https://badge.fury.io/rb/rumale.svg)](https://badge.fury.io/rb/rumale)
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[![BSD 2-Clause License](https://img.shields.io/badge/License-BSD%202--Clause-orange.svg)](https://github.com/yoshoku/rumale/blob/
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[![BSD 2-Clause License](https://img.shields.io/badge/License-BSD%202--Clause-orange.svg)](https://github.com/yoshoku/rumale/blob/main/LICENSE.txt)
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[![Documentation](https://img.shields.io/badge/api-reference-blue.svg)](https://yoshoku.github.io/rumale/doc/)
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Rumale (**Ru**by **ma**chine **le**arning) is a machine learning library in Ruby.
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samples, labels = Rumale::Dataset.load_libsvm_file('pendigits')
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# Define the estimator to be evaluated.
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-
lr = Rumale::LinearModel::LogisticRegression.new
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lr = Rumale::LinearModel::LogisticRegression.new
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# Define the evaluation measure, splitting strategy, and cross validation.
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ev = Rumale::EvaluationMeasure::
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ev = Rumale::EvaluationMeasure::Accuracy.new
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kf = Rumale::ModelSelection::StratifiedKFold.new(n_splits: 5, shuffle: true, random_seed: 1)
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cv = Rumale::ModelSelection::CrossValidation.new(estimator: lr, splitter: kf, evaluator: ev)
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report = cv.perform(samples, labels)
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# Output result.
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-
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puts
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mean_accuracy = report[:test_score].sum / kf.n_splits
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puts "5-CV mean accuracy: %.1f%%" % (100.0 * mean_accuracy)
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```
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Execution of the above scripts result in the following.
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```bash
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$ ruby cross_validation.rb
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-
5-CV mean
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5-CV mean accuracy: 95.4%
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```
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### Example 3. Pipeline
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# Load dataset.
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samples, labels = Rumale::Dataset.load_libsvm_file('pendigits')
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# Construct pipeline with kernel approximation and
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rbf = Rumale::KernelApproximation::RBF.new(gamma:
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pipeline = Rumale::Pipeline::Pipeline.new(steps: { trns: rbf, clsf:
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# Construct pipeline with kernel approximation and LogisticRegression.
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rbf = Rumale::KernelApproximation::RBF.new(gamma: 1e-4, n_components: 800, random_seed: 1)
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lr = Rumale::LinearModel::LogisticRegression.new(reg_param: 1e-3)
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pipeline = Rumale::Pipeline::Pipeline.new(steps: { trns: rbf, clsf: lr })
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# Define the splitting strategy and cross validation.
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kf = Rumale::ModelSelection::StratifiedKFold.new(n_splits: 5, shuffle: true, random_seed: 1)
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report = cv.perform(samples, labels)
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# Output result.
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mean_accuracy = report[:test_score].
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mean_accuracy = report[:test_score].sum / kf.n_splits
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puts("5-CV mean accuracy: %.1f %%" % (mean_accuracy * 100.0))
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```
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estimator = Rumale::Ensemble::RandomForestClassifier.new(n_jobs: -1, random_seed: 1)
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```
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## Novelties
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* [Rumale SHOP](https://suzuri.jp/yoshoku)
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## Contributing
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Bug reports and pull requests are welcome on GitHub at https://github.com/yoshoku/rumale.
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## Code of Conduct
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Everyone interacting in the Rumale project’s codebases, issue trackers,
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chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/yoshoku/Rumale/blob/
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chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/yoshoku/Rumale/blob/main/CODE_OF_CONDUCT.md).
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data/lib/rumale.rb
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require 'rumale/ensemble/random_forest_regressor'
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require 'rumale/ensemble/extra_trees_classifier'
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require 'rumale/ensemble/extra_trees_regressor'
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require 'rumale/ensemble/stacking_classifier'
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require 'rumale/ensemble/stacking_regressor'
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require 'rumale/clustering/k_means'
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require 'rumale/clustering/mini_batch_k_means'
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require 'rumale/clustering/k_medoids'
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require 'rumale/manifold/mds'
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require 'rumale/metric_learning/fisher_discriminant_analysis'
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require 'rumale/metric_learning/neighbourhood_component_analysis'
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require 'rumale/metric_learning/mlkr'
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require 'rumale/neural_network/adam'
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require 'rumale/neural_network/base_mlp'
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require 'rumale/neural_network/mlp_regressor'
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# @param x [Numo::DFloat] (shape: [n_samples, n_features]) The samples to be used for cluster analysis.
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# If the metric is 'precomputed', x must be a square distance matrix (shape: [n_samples, n_samples]).
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# @return [Numo::Int32] (shape: [n_samples]) Predicted cluster label per sample.
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def fit_predict(x)
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def fit_predict(x) # rubocop:disable Lint/UselessMethodDefinition
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super
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end
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@params[:solver] = if solver == 'auto'
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load_linalg? ? 'evd' : 'fpt'
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else
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solver != 'evd' ? 'fpt' : 'evd'
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solver != 'evd' ? 'fpt' : 'evd' # rubocop:disable Style/NegatedIfElseCondition
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end
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@params[:n_components] = n_components
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@params[:max_iter] = max_iter
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# frozen_string_literal: true
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require 'rumale/base/base_estimator'
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require 'rumale/base/classifier'
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module Rumale
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module Ensemble
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# StackingClassifier is a class that implements classifier with stacking method.
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#
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# @example
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# estimators = {
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# lgr: Rumale::LinearModel::LogisticRegression.new(reg_param: 1e-2, random_seed: 1),
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# mlp: Rumele::NeuralNetwork::MLPClassifier.new(hidden_units: [256], random_seed: 1),
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# rnd: Rumale::Ensemble::RandomForestClassifier.new(random_seed: 1)
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# }
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# meta_estimator = Rumale::LinearModel::LogisticRegression.new(random_seed: 1)
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# classifier = Rumale::Ensemble::StackedClassifier.new(
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# estimators: estimators, meta_estimator: meta_estimator, random_seed: 1
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# )
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# classifier.fit(training_samples, traininig_labels)
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# results = classifier.predict(testing_samples)
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#
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# *Reference*
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# - Zhou, Z-H., "Ensemble Mehotds - Foundations and Algorithms," CRC Press Taylor and Francis Group, Chapman and Hall/CRC, 2012.
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class StackingClassifier
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include Base::BaseEstimator
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include Base::Classifier
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# Return the base classifiers.
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# @return [Hash<Symbol,Classifier>]
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attr_reader :estimators
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# Return the meta classifier.
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# @return [Classifier]
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attr_reader :meta_estimator
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# Return the class labels.
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# @return [Numo::Int32] (size: n_classes)
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attr_reader :classes
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# Return the method used by each base classifier.
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# @return [Hash<Symbol,Symbol>]
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attr_reader :stack_method
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# Create a new classifier with stacking method.
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#
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# @param estimators [Hash<Symbol,Classifier>] The base classifiers for extracting meta features.
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# @param meta_estimator [Classifier/Nil] The meta classifier that predicts class label.
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# If nil is given, LogisticRegression is used.
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# @param n_splits [Integer] The number of folds for cross validation with stratified k-fold on meta feature extraction in training phase.
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# @param shuffle [Boolean] The flag indicating whether to shuffle the dataset on cross validation.
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# @param stack_method [String] The method name of base classifier for using meta feature extraction.
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53
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+
# If 'auto' is given, it searches the callable method in the order 'predict_proba', 'decision_function', and 'predict'
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54
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+
# on each classifier.
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55
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+
# @param passthrough [Boolean] The flag indicating whether to concatenate the original features and meta features when training the meta classifier.
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56
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+
# @param random_seed [Integer/Nil] The seed value using to initialize the random generator on cross validation.
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57
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+
def initialize(estimators:, meta_estimator: nil, n_splits: 5, shuffle: true, stack_method: 'auto', passthrough: false, random_seed: nil)
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58
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+
check_params_type(Hash, estimators: estimators)
|
59
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+
check_params_numeric(n_splits: n_splits)
|
60
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+
check_params_string(stack_method: stack_method)
|
61
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+
check_params_boolean(shuffle: shuffle, passthrough: passthrough)
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62
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+
check_params_numeric_or_nil(random_seed: random_seed)
|
63
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+
@estimators = estimators
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64
|
+
@meta_estimator = meta_estimator || Rumale::LinearModel::LogisticRegression.new
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65
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+
@classes = nil
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66
|
+
@stack_method = nil
|
67
|
+
@output_size = nil
|
68
|
+
@params = {}
|
69
|
+
@params[:n_splits] = n_splits
|
70
|
+
@params[:shuffle] = shuffle
|
71
|
+
@params[:stack_method] = stack_method
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72
|
+
@params[:passthrough] = passthrough
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73
|
+
@params[:random_seed] = random_seed || srand
|
74
|
+
end
|
75
|
+
|
76
|
+
# Fit the model with given training data.
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77
|
+
#
|
78
|
+
# @param x [Numo::DFloat] (shape: [n_samples, n_features]) The training data to be used for fitting the model.
|
79
|
+
# @param y [Numo::Int32] (shape: [n_samples]) The labels to be used for fitting the model.
|
80
|
+
# @return [StackedClassifier] The learned classifier itself.
|
81
|
+
def fit(x, y)
|
82
|
+
x = check_convert_sample_array(x)
|
83
|
+
y = check_convert_label_array(y)
|
84
|
+
check_sample_label_size(x, y)
|
85
|
+
|
86
|
+
n_samples, n_features = x.shape
|
87
|
+
|
88
|
+
@encoder = Rumale::Preprocessing::LabelEncoder.new
|
89
|
+
y_encoded = @encoder.fit_transform(y)
|
90
|
+
@classes = Numo::NArray[*@encoder.classes]
|
91
|
+
|
92
|
+
# training base classifiers with all training data.
|
93
|
+
@estimators.each_key { |name| @estimators[name].fit(x, y_encoded) }
|
94
|
+
|
95
|
+
# detecting feature extraction method and its size of output for each base classifier.
|
96
|
+
@stack_method = detect_stack_method
|
97
|
+
@output_size = detect_output_size(n_features)
|
98
|
+
|
99
|
+
# extracting meta features with base classifiers.
|
100
|
+
n_components = @output_size.values.inject(:+)
|
101
|
+
z = Numo::DFloat.zeros(n_samples, n_components)
|
102
|
+
|
103
|
+
kf = Rumale::ModelSelection::StratifiedKFold.new(
|
104
|
+
n_splits: @params[:n_splits], shuffle: @params[:shuffle], random_seed: @params[:random_seed]
|
105
|
+
)
|
106
|
+
|
107
|
+
kf.split(x, y_encoded).each do |train_ids, valid_ids|
|
108
|
+
x_train = x[train_ids, true]
|
109
|
+
y_train = y_encoded[train_ids]
|
110
|
+
x_valid = x[valid_ids, true]
|
111
|
+
f_start = 0
|
112
|
+
@estimators.each_key do |name|
|
113
|
+
est_fold = Marshal.load(Marshal.dump(@estimators[name]))
|
114
|
+
f_last = f_start + @output_size[name]
|
115
|
+
f_position = @output_size[name] == 1 ? f_start : f_start...f_last
|
116
|
+
z[valid_ids, f_position] = est_fold.fit(x_train, y_train).public_send(@stack_method[name], x_valid)
|
117
|
+
f_start = f_last
|
118
|
+
end
|
119
|
+
end
|
120
|
+
|
121
|
+
# concatenating original features.
|
122
|
+
z = Numo::NArray.hstack([z, x]) if @params[:passthrough]
|
123
|
+
|
124
|
+
# training meta classifier.
|
125
|
+
@meta_estimator.fit(z, y_encoded)
|
126
|
+
|
127
|
+
self
|
128
|
+
end
|
129
|
+
|
130
|
+
# Calculate confidence scores for samples.
|
131
|
+
#
|
132
|
+
# @param x [Numo::DFloat] (shape: [n_samples, n_features]) The samples to compute the scores.
|
133
|
+
# @return [Numo::DFloat] (shape: [n_samples, n_classes]) The confidence score per sample.
|
134
|
+
def decision_function(x)
|
135
|
+
x = check_convert_sample_array(x)
|
136
|
+
z = transform(x)
|
137
|
+
@meta_estimator.decision_function(z)
|
138
|
+
end
|
139
|
+
|
140
|
+
# Predict class labels for samples.
|
141
|
+
#
|
142
|
+
# @param x [Numo::DFloat] (shape: [n_samples, n_features]) The samples to predict the labels.
|
143
|
+
# @return [Numo::Int32] (shape: [n_samples]) The predicted class label per sample.
|
144
|
+
def predict(x)
|
145
|
+
x = check_convert_sample_array(x)
|
146
|
+
z = transform(x)
|
147
|
+
Numo::Int32.cast(@encoder.inverse_transform(@meta_estimator.predict(z)))
|
148
|
+
end
|
149
|
+
|
150
|
+
# Predict probability for samples.
|
151
|
+
#
|
152
|
+
# @param x [Numo::DFloat] (shape: [n_samples, n_features]) The samples to predict the probailities.
|
153
|
+
# @return [Numo::DFloat] (shape: [n_samples, n_classes]) The predicted probability of each class per sample.
|
154
|
+
def predict_proba(x)
|
155
|
+
x = check_convert_sample_array(x)
|
156
|
+
z = transform(x)
|
157
|
+
@meta_estimator.predict_proba(z)
|
158
|
+
end
|
159
|
+
|
160
|
+
# Transform the given data with the learned model.
|
161
|
+
#
|
162
|
+
# @param x [Numo::DFloat] (shape: [n_samples, n_features]) The samples to be transformed with the learned model.
|
163
|
+
# @return [Numo::DFloat] (shape: [n_samples, n_components]) The meta features for samples.
|
164
|
+
def transform(x)
|
165
|
+
x = check_convert_sample_array(x)
|
166
|
+
n_samples = x.shape[0]
|
167
|
+
n_components = @output_size.values.inject(:+)
|
168
|
+
z = Numo::DFloat.zeros(n_samples, n_components)
|
169
|
+
f_start = 0
|
170
|
+
@estimators.each_key do |name|
|
171
|
+
f_last = f_start + @output_size[name]
|
172
|
+
f_position = @output_size[name] == 1 ? f_start : f_start...f_last
|
173
|
+
z[true, f_position] = @estimators[name].public_send(@stack_method[name], x)
|
174
|
+
f_start = f_last
|
175
|
+
end
|
176
|
+
z = Numo::NArray.hstack([z, x]) if @params[:passthrough]
|
177
|
+
z
|
178
|
+
end
|
179
|
+
|
180
|
+
# Fit the model with training data, and then transform them with the learned model.
|
181
|
+
#
|
182
|
+
# @param x [Numo::DFloat] (shape: [n_samples, n_features]) The training data to be used for fitting the model.
|
183
|
+
# @param y [Numo::Int32] (shape: [n_samples]) The labels to be used for fitting the model.
|
184
|
+
# @return [Numo::DFloat] (shape: [n_samples, n_components]) The meta features for training data.
|
185
|
+
def fit_transform(x, y)
|
186
|
+
x = check_convert_sample_array(x)
|
187
|
+
y = check_convert_label_array(y)
|
188
|
+
fit(x, y).transform(x)
|
189
|
+
end
|
190
|
+
|
191
|
+
private
|
192
|
+
|
193
|
+
STACK_METHODS = %i[predict_proba decision_function predict].freeze
|
194
|
+
|
195
|
+
private_constant :STACK_METHODS
|
196
|
+
|
197
|
+
def detect_stack_method
|
198
|
+
if @params[:stack_method] == 'auto'
|
199
|
+
@estimators.each_key.with_object({}) { |name, obj| obj[name] = STACK_METHODS.detect { |m| @estimators[name].respond_to?(m) } }
|
200
|
+
else
|
201
|
+
@estimators.each_key.with_object({}) { |name, obj| obj[name] = @params[:stack_method].to_sym }
|
202
|
+
end
|
203
|
+
end
|
204
|
+
|
205
|
+
def detect_output_size(n_features)
|
206
|
+
x_dummy = Numo::DFloat.new(2, n_features).rand
|
207
|
+
@estimators.each_key.with_object({}) do |name, obj|
|
208
|
+
output_dummy = @estimators[name].public_send(@stack_method[name], x_dummy)
|
209
|
+
obj[name] = output_dummy.ndim == 1 ? 1 : output_dummy.shape[1]
|
210
|
+
end
|
211
|
+
end
|
212
|
+
end
|
213
|
+
end
|
214
|
+
end
|