Jenetics：正确使用编解码器与列 Genotype

Question

目前我正在研究 Jenetics (link to jenetics) 实现以优化粒子加速器束线。我的健身函数调用加速器检测器，定义如下：

private double fitness(final DoubleChromosome chromosomes) {
    // private double fitness(final Genotype<DoubleGene> chromosomes) {
    // Convert genes to a format the device scanner can understand
    // we will inject a 1:n Set<List<Double>>
    final Set<List<Double>> trimValues = new HashSet<>();

    final List<Double> valueList = new ArrayList<>();
    for (final DoubleGene chromosome : chromosomes) {
        valueList.add(Double.valueOf(chromosome.doubleValue()));
    }
    trimValues.add(valueList);

    ....
    more code specific to application
    }

Jenetics 的流引擎在特定方法中初始化：

public void initAlgorithm(final Object scanParameters) throws Exception {
    if (scanParameters != null) {
        /// See constructor of EvolvingImagesWorker
        _geneticScanParameters = (GeneticScanParameters) scanParameters;
    }

    if (_geneticScanParameters.getTrimParameterSets() != null) {

        final int chromosomeCount = _geneticScanParameters.getTrimParameterSets().size();
        if (chromosomeCount > 0) {
            ISeq<DoubleChromosome> chromosomeSet = ISeq.empty();

            // create an ISeq of genes
            for (final TrimParameterValueSet valueSet : _geneticScanParameters.getTrimParameterSets()) {
                final double minValue = valueSet.getMinValue();
                final double maxValue = valueSet.getMaxValue();
                final double initialValue = (maxValue + minValue) / 2;

                final DoubleGene doubleGene = DoubleGene.of(initialValue, minValue, maxValue);
                final DoubleChromosome doubleChromosome = DoubleChromosome.of(doubleGene.newInstance());
                chromosomeSet = chromosomeSet.append(doubleChromosome.newInstance());
            }
            Codec<DoubleChromosome, DoubleGene> codec = null;
            try {
                final Genotype<DoubleGene> genotype = Genotype.of(chromosomeSet);
                codec = Codec.of(genotype.newInstance(), //
                        gt -> (DoubleChromosome) gt.getChromosome());
            } catch (final IllegalArgumentException ex) {
                MessageLogger.logError(getClass(), Thread.currentThread(), ex);
                throw ex;
            }

            _scannerEngine = Engine.builder(this::fitness, codec) //
                    .executor(Executors.newSingleThreadExecutor()) // without this command, engine will be executed
                                                                   // in
                                                                   // parallel threads
                    .populationSize(_geneticScanParameters.getPopulationSize()) //
                    .optimize(_geneticScanParameters.getOptimizationStrategy()) //
                    .offspringFraction(_geneticScanParameters.getOffspringSize()) //
                    .survivorsSelector(new RouletteWheelSelector<>()) //
                    .offspringSelector(new TournamentSelector<>(_geneticScanParameters.getTournamentSizeLimit())) //
                    .alterers( //
                            new Mutator<>(_geneticScanParameters.getMutator()), //
                            new MeanAlterer<>(_geneticScanParameters.getMeanAlterer()) //
                    ) //
                    .build();
        } else {
            throw new IllegalStateException(ERROR_INITSCANNER_NO_SETTING_DEVICE);
        }
    }
    }

其中：

private Engine<DoubleGene, Double> _scannerEngine = null;

我想做的是调用适应度函数，这样我就可以在适应度函数中使用基因型来访问基因值（我发送到加速器的设置）。我已经尝试如下定义 fitness() ：

private double fitness(final Genotype<DoubleChromosome> genotype) {
...
}

但是这个调用会导致编译错误。

Answer 1

我看过你的代码，我想你想做这样的事情：

class Foo {

    // Your parameter class.
    class TrimParameterSet {
        double min, max;
    }

    static double fitness(final double[] values) {
        // Your fitness function.
        return 0;
    }

    public static void main(final String[] args) {
        final List<TrimParameterSet> valueSets = ...;

        final DoubleRange[] ranges = valueSets.stream()
            .map(p -> DoubleRange.of(p.min, p.max))
            .toArray(DoubleRange[]::new);

        final Codec<double[], DoubleGene> codec = Codecs.ofVector(ranges);
        final Engine<DoubleGene, Double> engine = Engine.builder(Foo::fitness, codec)
            .build();

        // ...
    }
}

您的适应度函数的 double[] 数组具有不同的范围，根据您 TrimParameterSet class 中定义的范围。如果你想定义一个直接适应度函数，你必须定义一个基因型作为参数类型。

double fitness(Genotype<DoubleGene> gt) {...}

Answer 2

由于评论功能不允许我完成记录我的最终实现，这里是实际代码：

ISeq<DoubleChromosome> chromosomeSet = ISeq.empty();

// create an ISeq of genes
for (loop criteria) {
    final DoubleGene doubleGene = DoubleGene.of(initialValue, minValue, maxValue);
    final DoubleChromosome doubleChromosome = DoubleChromosome.of(doubleGene.newInstance());
    chromosomeSet = chromosomeSet.append(doubleChromosome.newInstance());
}
_genotype = Genotype.of(chromosomeSet);

_scannerEngine = Engine.builder(this::fitness, _genotype)
                     ... // engine settings
                     .build();

double fitness(Genotype<DoubleGene> gt) {...}

Jenetics：正确使用编解码器与列 Genotype

Jenetics: proper usage of codec with column Genotype

java

frameworks

genetic-algorithm

genetic-programming

jenetics