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

Example 1 with ChoiceGenerator

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

the class LTestSsys1 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[][] 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;
        }
    }
    double[][] gene = new double[ntimes][ngenes];
    double[][] deriv = new double[ntimes][ngenes];
    double[] sum = new double[ngenes];
    double baseLevel = 15.0;
    NumberFormat nf = NumberFormatUtil.getInstance().getNumberFormat();
    double min = 1000.0;
    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 (gene[j][g] < min) {
                min = gene[j][g];
            }
            if (j != 0) {
                deriv[j][g] = (gene[j][g] - gene[j - 1][g]) / 10.0;
            }
        }
    /*  DEBUG Prints
            System.out.println("At time " + j);
            for(int g = 0; g < ngenes; g++) {
              String expression = nf.format(gene[j][g]);
              System.out.print(expression + " ");
            }
            System.out.println();
            */
    }
    System.out.println("minimum value = " + min);
    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(Math.log(gene[t][regs[0]] + baseLevel));
                String g1 = nf.format(Math.log(gene[t][regs[1]] + baseLevel));
                String g2 = nf.format(Math.log(gene[t][regs[2]] + baseLevel));
                String g3 = nf.format(Math.log(gene[t][regs[3]] + baseLevel));
                String g4 = nf.format(Math.log(gene[t][regs[4]] + baseLevel));
                if (deriv[t][g] > 0.35) {
                    System.out.println("lnamlnb+" + g0 + "gmh0+" + g1 + "gmh1+" + g2 + "gmh2+" + g3 + "gmh3+" + g4 + "gmh4 > 0");
                } else if (deriv[t][g] < -0.35) {
                    System.out.println("lnamlnb+" + g0 + "gmh0+" + g1 + "gmh1+" + g2 + "gmh2+" + g3 + "gmh3+" + g4 + "gmh4 < 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 2 with ChoiceGenerator

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

the class TestChoiceGenerator method testChoiceGeneratorCounts.

/**
 * Tests to make sure the ChoiceGenerator is output the correct number of choices
 * for various values of and b.
 */
@Test
public void testChoiceGeneratorCounts() {
    for (int a = 0; a <= 20; a++) {
        for (int b = 0; b <= a; b++) {
            ChoiceGenerator generator = new ChoiceGenerator(a, b);
            int n = 0;
            while ((generator.next()) != null) {
                n++;
            }
            long numerator = 1;
            long denominator = 1;
            for (int k = a; k - b > 0; k--) {
                numerator *= k;
                denominator *= k - b;
            }
            long numChoices = numerator / denominator;
            if (n != numChoices) {
                fail("a = " + a + " b = " + b + " numChoices = " + numChoices + " n = " + n);
            }
        }
    }
}

Example 3 with ChoiceGenerator

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

the class Fges2 method calculateArrowsForward.

// Calculates the new arrows for an a->b edge.
private void calculateArrowsForward(Node a, Node b) {
    if (mode == Mode.heuristicSpeedup && !effectEdgesGraph.isAdjacentTo(a, b))
        return;
    if (adjacencies != null && !adjacencies.isAdjacentTo(a, b))
        return;
    this.neighbors.put(b, getNeighbors(b));
    if (a == b)
        throw new IllegalArgumentException();
    if (existsKnowledge()) {
        if (getKnowledge().isForbidden(a.getName(), b.getName())) {
            return;
        }
    }
    Set<Node> naYX = getNaYX(a, b);
    if (!isClique(naYX))
        return;
    List<Node> TNeighbors = getTNeighbors(a, b);
    Set<Set<Node>> previousCliques = new HashSet<>();
    previousCliques.add(new HashSet<Node>());
    Set<Set<Node>> newCliques = new HashSet<>();
    FOR: for (int i = 0; i <= TNeighbors.size(); i++) {
        final ChoiceGenerator gen = new ChoiceGenerator(TNeighbors.size(), i);
        int[] choice;
        while ((choice = gen.next()) != null) {
            Set<Node> T = GraphUtils.asSet(choice, TNeighbors);
            Set<Node> union = new HashSet<>(naYX);
            union.addAll(T);
            boolean foundAPreviousClique = false;
            for (Set<Node> clique : previousCliques) {
                if (union.containsAll(clique)) {
                    foundAPreviousClique = true;
                    break;
                }
            }
            if (!foundAPreviousClique) {
                break FOR;
            }
            if (!isClique(union))
                continue;
            newCliques.add(union);
            double bump = insertEval(a, b, T, naYX, hashIndices);
            if (Double.isNaN(bump)) {
                bump = Double.MIN_VALUE;
            }
            if (bump > 0 || Double.isNaN(bump)) {
                addArrow(a, b, naYX, T, bump);
            }
        // if (mode == Mode.heuristicSpeedup && union.isEmpty() && score.isEffectEdge(bump) &&
        // !effectEdgesGraph.isAdjacentTo(a, b) && graph.getParents(b).isEmpty()) {
        // effectEdgesGraph.addUndirectedEdge(a, b);
        // }
        }
        previousCliques = newCliques;
        newCliques = new HashSet<>();
    }
}

Example 4 with ChoiceGenerator

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

the class FgesMb method calculateArrowsForward.

// Calculates the new arrows for an a->b edge.
private void calculateArrowsForward(Node a, Node b) {
    if (mode == Mode.heuristicSpeedup && !effectEdgesGraph.isAdjacentTo(a, b)) {
        return;
    }
    if (adjacencies != null && !adjacencies.isAdjacentTo(a, b)) {
        return;
    }
    this.neighbors.put(b, getNeighbors(b));
    if (existsKnowledge()) {
        if (getKnowledge().isForbidden(a.getName(), b.getName())) {
            return;
        }
    }
    Set<Node> naYX = getNaYX(a, b);
    if (!GraphUtils.isClique(naYX, this.graph)) {
        return;
    }
    List<Node> TNeighbors = getTNeighbors(a, b);
    int _maxIndegree = maxIndegree == -1 ? 1000 : maxIndegree;
    final int _max = Math.min(TNeighbors.size(), _maxIndegree - graph.getIndegree(b));
    Set<Set<Node>> previousCliques = new HashSet<>();
    previousCliques.add(new HashSet<Node>());
    Set<Set<Node>> newCliques = new HashSet<>();
    FOR: for (int i = 0; i <= _max; i++) {
        final ChoiceGenerator gen = new ChoiceGenerator(TNeighbors.size(), i);
        int[] choice;
        while ((choice = gen.next()) != null) {
            if (Thread.currentThread().isInterrupted()) {
                break;
            }
            Set<Node> T = GraphUtils.asSet(choice, TNeighbors);
            Set<Node> union = new HashSet<>(naYX);
            union.addAll(T);
            boolean foundAPreviousClique = false;
            for (Set<Node> clique : previousCliques) {
                if (union.containsAll(clique)) {
                    foundAPreviousClique = true;
                    break;
                }
            }
            if (!foundAPreviousClique) {
                break FOR;
            }
            if (!GraphUtils.isClique(union, this.graph)) {
                continue;
            }
            newCliques.add(union);
            double bump = insertEval(a, b, T, naYX, hashIndices);
            if (bump > 0.0) {
                addArrow(a, b, naYX, T, bump);
            }
        // if (mode == Mode.heuristicSpeedup && union.isEmpty() && score.isEffectEdge(bump) &&
        // !effectEdgesGraph.isAdjacentTo(a, b) && graph.getParents(b).isEmpty()) {
        // effectEdgesGraph.addUndirectedEdge(a, b);
        // }
        }
        previousCliques = newCliques;
        newCliques = new HashSet<>();
    }
}

Example 5 with ChoiceGenerator

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

the class GFciMax method search.

// ========================PUBLIC METHODS==========================//
public Graph search() {
    long time1 = System.currentTimeMillis();
    List<Node> nodes = getIndependenceTest().getVariables();
    logger.log("info", "Starting FCI algorithm.");
    logger.log("info", "Independence test = " + getIndependenceTest() + ".");
    this.graph = new EdgeListGraphSingleConnections(nodes);
    Fges fges = new Fges(score);
    fges.setKnowledge(getKnowledge());
    fges.setVerbose(verbose);
    fges.setNumPatternsToStore(0);
    fges.setFaithfulnessAssumed(faithfulnessAssumed);
    fges.setMaxDegree(maxDegree);
    fges.setOut(out);
    graph = fges.search();
    Graph fgesGraph = new EdgeListGraphSingleConnections(graph);
    sepsets = new SepsetsGreedy(fgesGraph, independenceTest, null, maxDegree);
    graph.reorientAllWith(Endpoint.CIRCLE);
    for (Node b : nodes) {
        List<Node> adjacentNodes = fgesGraph.getAdjacentNodes(b);
        if (adjacentNodes.size() < 2) {
            continue;
        }
        ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
        int[] combination;
        while ((combination = cg.next()) != null) {
            Node a = adjacentNodes.get(combination[0]);
            Node c = adjacentNodes.get(combination[1]);
            if (graph.isAdjacentTo(a, c) && fgesGraph.isAdjacentTo(a, c)) {
                if (sepsets.getSepset(a, c) != null) {
                    graph.removeEdge(a, c);
                }
            }
        }
    }
    // modifiedR0(fgesGraph);
    sepsets = new SepsetsMinScore(fgesGraph, independenceTest, maxDegree);
    addColliders(graph, fgesGraph);
    FciOrient fciOrient = new FciOrient(sepsets);
    fciOrient.setVerbose(verbose);
    fciOrient.setOut(out);
    fciOrient.setKnowledge(getKnowledge());
    fciOrient.setCompleteRuleSetUsed(completeRuleSetUsed);
    fciOrient.setMaxPathLength(maxPathLength);
    fciOrient.doFinalOrientation(graph);
    GraphUtils.replaceNodes(graph, independenceTest.getVariables());
    long time2 = System.currentTimeMillis();
    elapsedTime = time2 - time1;
    return graph;
}