Examples with BootstrapSampler edu.cmu.tetrad.data.BootstrapSampler used on opensource projects

Example 1 with BootstrapSampler

use of edu.cmu.tetrad.data.BootstrapSampler in project tetrad by cmu-phil.

the class StabilitySelection method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    DataSet _dataSet = (DataSet) dataSet;
    double percentageB = parameters.getDouble("percentSubsampleSize");
    int numSubsamples = parameters.getInt("numSubsamples");
    Map<Edge, Integer> counts = new HashMap<>();
    List<Graph> graphs = new ArrayList<>();
    final ForkJoinPool pool = ForkJoinPoolInstance.getInstance().getPool();
    class StabilityAction extends RecursiveAction {

        private int chunk;

        private int from;

        private int to;

        private StabilityAction(int chunk, int from, int to) {
            this.chunk = chunk;
            this.from = from;
            this.to = to;
        }

        @Override
        protected void compute() {
            if (to - from <= chunk) {
                for (int s = from; s < to; s++) {
                    BootstrapSampler sampler = new BootstrapSampler();
                    sampler.setWithoutReplacements(true);
                    DataSet sample = sampler.sample(_dataSet, (int) (percentageB * _dataSet.getNumRows()));
                    Graph graph = algorithm.search(sample, parameters);
                    graphs.add(graph);
                }
            } else {
                final int mid = (to + from) / 2;
                StabilityAction left = new StabilityAction(chunk, from, mid);
                StabilityAction right = new StabilityAction(chunk, mid, to);
                left.fork();
                right.compute();
                left.join();
            }
        }
    }
    final int chunk = 2;
    pool.invoke(new StabilityAction(chunk, 0, numSubsamples));
    // }
    for (Graph graph : graphs) {
        for (Edge edge : graph.getEdges()) {
            increment(edge, counts);
        }
    }
    initialGraph = new EdgeListGraph(dataSet.getVariables());
    double percentStability = parameters.getDouble("percentStability");
    for (Edge edge : counts.keySet()) {
        if (counts.get(edge) > percentStability * numSubsamples) {
            initialGraph.addEdge(edge);
        }
    }
    return initialGraph;
}