Examples with ChoiceGenerator edu.cmu.tetrad.util.ChoiceGenerator used on opensource projects

Example 86 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class GraphUtils method getAmbiguousTriplesFromGraph.

/**
 * @return A list of triples of the form <X, Y, Z>, where <X, Y, Z> is a
 * definite noncollider in the given graph.
 */
public static List<Triple> getAmbiguousTriplesFromGraph(Node node, Graph graph) {
    List<Triple> ambiguousTriples = new ArrayList<>();
    List<Node> adj = graph.getAdjacentNodes(node);
    if (adj.size() < 2) {
        return new LinkedList<>();
    }
    ChoiceGenerator gen = new ChoiceGenerator(adj.size(), 2);
    int[] choice;
    while ((choice = gen.next()) != null) {
        Node x = adj.get(choice[0]);
        Node z = adj.get(choice[1]);
        if (graph.isAmbiguousTriple(x, node, z)) {
            ambiguousTriples.add(new Triple(x, node, z));
        }
    }
    return ambiguousTriples;
}

Example 87 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class GraphUtils method getCollidersFromGraph.

/**
 * @return A list of triples of the form X*->Y<-*Z.
 */
public static List<Triple> getCollidersFromGraph(Node node, Graph graph) {
    List<Triple> colliders = new ArrayList<>();
    List<Node> adj = graph.getAdjacentNodes(node);
    if (adj.size() < 2) {
        return new LinkedList<>();
    }
    ChoiceGenerator gen = new ChoiceGenerator(adj.size(), 2);
    int[] choice;
    while ((choice = gen.next()) != null) {
        Node x = adj.get(choice[0]);
        Node z = adj.get(choice[1]);
        Endpoint endpt1 = graph.getEdge(x, node).getProximalEndpoint(node);
        Endpoint endpt2 = graph.getEdge(z, node).getProximalEndpoint(node);
        if (endpt1 == Endpoint.ARROW && endpt2 == Endpoint.ARROW) {
            colliders.add(new Triple(x, node, z));
        }
    }
    return colliders;
}

Example 88 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class CcdMax method maxPSepset.

private Pair maxPSepset(Node i, Node k, Graph graph) {
    double _p = Double.POSITIVE_INFINITY;
    List<Node> _v = null;
    List<Node> adji = graph.getAdjacentNodes(i);
    List<Node> adjk = graph.getAdjacentNodes(k);
    adji.remove(k);
    adjk.remove(i);
    for (int d = 0; d <= Math.min((depth == -1 ? 1000 : depth), Math.max(adji.size(), adjk.size())); d++) {
        if (d <= adji.size()) {
            ChoiceGenerator gen = new ChoiceGenerator(adji.size(), d);
            int[] choice;
            while ((choice = gen.next()) != null) {
                List<Node> v2 = GraphUtils.asList(choice, adji);
                if (isForbidden(i, k, v2))
                    continue;
                try {
                    getIndependenceTest().isIndependent(i, k, v2);
                    double p2 = getIndependenceTest().getScore();
                    if (p2 < _p) {
                        _p = p2;
                        _v = v2;
                    }
                } catch (Exception e) {
                    e.printStackTrace();
                    return new Pair(null, Double.POSITIVE_INFINITY);
                }
            }
        }
        if (d <= adjk.size()) {
            ChoiceGenerator gen = new ChoiceGenerator(adjk.size(), d);
            int[] choice;
            while ((choice = gen.next()) != null) {
                List<Node> v2 = GraphUtils.asList(choice, adjk);
                try {
                    getIndependenceTest().isIndependent(i, k, v2);
                    double p2 = getIndependenceTest().getScore();
                    if (p2 < _p) {
                        _p = p2;
                        _v = v2;
                    }
                } catch (Exception e) {
                    e.printStackTrace();
                    return new Pair(null, Double.POSITIVE_INFINITY);
                }
            }
        }
    }
    return new Pair(_v, _p);
}

Example 89 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class LTestQnet3 method main.

public static void main(String[] argv) {
    String fileName = argv[0];
    InputStream s;
    StringTokenizer st;
    int ngenes = 5;
    int ntimes = 400;
    int nrecords = 5;
    int nchips = 4;
    // double[] chisq = {3.84, 5.99, 7.81, 9.49, 11.1, 12.6, 14.1, 15.5,
    // 16.9, 18.3, 19.7, 21.0, 22.4, 23.7, 25.0, 26.3,
    // 27.6, 28.9, 30.1, 31.4, 32.7, 33.9, 35.2, 36.4,
    // 37.7, 38.9, 40.1, 41.3, 42.6, 43.8};
    double[][] cases = new double[4][2004];
    try {
        s = new FileInputStream(fileName);
    } catch (IOException e) {
        System.out.println("Cannot open file " + fileName);
        return;
    }
    // DataInputStream in = new DataInputStream(s);
    BufferedReader in = new BufferedReader(new InputStreamReader(s));
    for (int k = 0; k < nrecords; k++) {
        try {
            st = new StringTokenizer(in.readLine());
            if (k == 0) {
                continue;
            }
            // int ichip = Integer.parseInt(st.nextToken("\t"));
            for (int j = 0; j < ntimes * ngenes; j++) {
                cases[k - 1][j] = Double.parseDouble(st.nextToken("\t"));
            }
        } catch (IOException e) {
            System.out.println("Read error in " + fileName);
            return;
        }
    }
    // System.out.println("Read " + cases[0][0] + " " + cases[1][0] + " " +
    // cases[2][0] + " " + cases[3][0]);
    double[][] gene = new double[ntimes][ngenes];
    double[][] deriv = new double[ntimes][ngenes];
    double[] sum = new double[ngenes];
    for (int j = 0; j < ntimes; j++) {
        for (int g = 0; g < ngenes; g++) {
            int icol = j * ngenes + g;
            sum[g] = 0.0;
            for (int c = 0; c < nchips; c++) // sum[g] += cases[c][icol]*cases[c][icol];
            {
                sum[g] += cases[c][icol];
            }
            gene[j][g] = sum[g];
            if (j != 0) {
                deriv[j][g] = (gene[j][g] - gene[j - 1][g]) / 10.0;
            }
        }
    /*
            if(j != 0) {
              System.out.println();
              for(int k = 0; k < ngenes; k++)
                System.out.print(deriv[j][k] + " ");
              System.out.println();
            }
            */
    }
    NumberFormat nf = NumberFormatUtil.getInstance().getNumberFormat();
    for (int g = 0; g < ngenes; g++) {
        System.out.println("For gene " + g);
        int k = 5;
        ChoiceGenerator cg = new ChoiceGenerator(ngenes, k);
        int[] regs = new int[k];
        while ((regs = cg.next()) != null) {
            System.out.println("Sets of " + k + " regulators are:");
            System.out.println(regs[0] + " " + regs[1] + " " + regs[2] + " " + regs[3] + " " + regs[4]);
            for (int t = 1; t < ntimes; t++) {
                String g0 = nf.format(gene[t][regs[0]]);
                String g1 = nf.format(gene[t][regs[1]]);
                String g2 = nf.format(gene[t][regs[2]]);
                String g3 = nf.format(gene[t][regs[3]]);
                String g4 = nf.format(gene[t][regs[4]]);
                if (deriv[t][g] > 0.3) {
                    System.out.println(g0 + "a0+" + g1 + "a1+" + g2 + "a2+" + g3 + "a3+" + g4 + "a4+b > 0");
                } else if (deriv[t][g] < -0.3) {
                    System.out.println(g0 + "a0+" + g1 + "a1+" + g2 + "a2+" + g3 + "a3+" + g4 + "a4+b< 0");
                }
            }
        }
    }
/*
        double[] p = new double[ngenes];
        for(int g = 0; g < ngenes; g++) {
          for(int j = 0; j < ntimes; j++)
            if(gene[j][g] > 0) p[g]++;
          p[g] /= ntimes;
          //System.out.println(" gene " + g + " p = " + p[g]);
        }
        */
}

Example 90 with ChoiceGenerator

use of edu.cmu.tetrad.util.ChoiceGenerator in project tetrad by cmu-phil.

the class ItkPredictorSearch method predictor.

public void predictor(int gene) {
    SortedSet[][] S = new TreeSet[nrows][nrows];
    Gene[] G = new Gene[ngenes];
    System.out.println("For gene " + names[gene] + ":");
    for (int i = 0; i < nrows; i++) {
        for (int j = 0; j < nrows; j++) {
            S[i][j] = new TreeSet();
        }
    }
    for (int k = 0; k < ngenes; k++) {
        G[k] = new Gene(k);
    }
    // Consider all pairs of rows of the expression matrix.
    ChoiceGenerator cg = new ChoiceGenerator(ngenes, 2);
    int[] rows;
    while ((rows = cg.next()) != null) {
        // Exclude row pairs in which the given gene was perturbed.
        if (expression[rows[0]][gene] == -1 || expression[rows[0]][gene] == 2 || expression[rows[1]][gene] == -1 || expression[rows[1]][gene] == 2) {
            continue;
        }
        // differ between the two rows (perturbations).
        if (!differByPerturbation(gene, rows[0], rows[1])) {
            continue;
        }
        // between the two perturbations.
        for (int gother = 0; gother < ngenes; gother++) {
            if (gother == gene) {
                // Don't test this gene
                continue;
            }
            // Exclude genes which do not differ between the two rows
            if (!differByPerturbation(gother, rows[0], rows[1])) {
                continue;
            }
            S[rows[0]][rows[1]].add(G[gother]);
        }
        System.out.print("sem" + rows[0] + rows[1] + " = ");
        for (Iterator it = S[rows[0]][rows[1]].iterator(); it.hasNext(); ) {
            System.out.print(((Gene) it.next()).getIndex());
        }
        System.out.println();
    }
    int sum = 0;
    for (int i = 0; i < nrows; i++) {
        for (int j = 0; j < nrows; j++) {
            sum += S[i][j].size();
        }
    }
    if (sum == 0) {
        System.out.println("Insufficient perturbations for gene " + names[gene]);
        System.out.println();
        return;
    }
    System.out.println("Smin:");
    SortedSet[] minCover;
    minCover = minCoveringSet(S);
    for (SortedSet<Gene> aMinCover : minCover) {
        display(aMinCover);
        inferFunction(gene, aMinCover);
    }
    System.out.println();
}