SimpleSVM.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
 
#include <svm.h>
 
#include <map>
#include <vector>
#include <utility> // for "pair"
#include <tuple>
 
namespace OpenMS
{
  class OPENMS_DLLAPI SimpleSVM :
    public DefaultParamHandler
  {
 
  public:
    typedef std::map<String, std::vector<double> > PredictorMap;
 
    typedef std::map<String, std::pair<double, double> > ScaleMap;
 
    struct Prediction
    {
      double outcome;
 
      std::map<double, double> probabilities;
    };
 
    SimpleSVM();
 
    ~SimpleSVM() override;
 
    void setup(PredictorMap& predictors, const std::map<Size, double>& outcomes, bool classification = true);
 
    void predict(std::vector<Prediction>& predictions,
                 std::vector<Size> indexes = std::vector<Size>()) const;
 
    void predict(PredictorMap& predictors, std::vector<Prediction>& predictions) const;
 
    void getFeatureWeights(std::map<String, double>& feature_weights) const;
 
    void writeXvalResults(const String& path) const;
 
    const ScaleMap& getScaling() const;
 
  protected:
    void clear_();
 
    typedef std::vector<std::vector<std::vector<double>>> SVMPerformance;
 
    std::vector<std::vector<struct svm_node> > nodes_;
 
    struct svm_problem data_;
 
    struct svm_parameter svm_params_;
 
    struct svm_model* model_;
 
    std::vector<String> predictor_names_;
 
    Size n_parts_;
 
    std::vector<double> log2_C_, log2_gamma_, log2_p_;
 
    ScaleMap scaling_;
 
    SVMPerformance performance_;
 
    static void printNull_(const char*) {}
 
    void scaleData_(PredictorMap& predictors);
 
    void convertData_(const PredictorMap& predictors);
 
    std::tuple<double, double, double> chooseBestParameters_(bool higher_better) const;
 
    void optimizeParameters_(bool classification);
  };
}