SimpleSVM.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser $
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#pragma once

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>

#include <svm.h>

#include <map>
#include <vector>
#include <utility> // for "pair"

namespace OpenMS
{
  class OPENMS_DLLAPI SimpleSVM :
    public DefaultParamHandler
  {

  public:
    typedef std::map<String, std::vector<double> > PredictorMap;

    struct Prediction
    {
      Int label;

      std::map<Int, double> probabilities;
    };

    SimpleSVM();

    ~SimpleSVM() override;

    void setup(PredictorMap& predictors, const std::map<Size, Int>& labels);

    void predict(std::vector<Prediction>& predictions,
                 std::vector<Size> indexes = std::vector<Size>()) const;

    void getFeatureWeights(std::map<String, double>& feature_weights) const;

    void writeXvalResults(const String& path) const;

  protected:
    typedef 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_;

    SVMPerformance performance_;

    static void printNull_(const char*) {}

    void scaleData_(PredictorMap& predictors) const;

    void convertData_(const PredictorMap& predictors);

    std::pair<double, double> chooseBestParameters_() const;

    void optimizeParameters_();
  };
}