SimpleSVM.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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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"
#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);
  };
}