Examples with GeneralLinearOperator org.broadinstitute.hellbender.tools.coveragemodel.linalg.GeneralLinearOperator used on opensource projects

Example 1 with GeneralLinearOperator

use of org.broadinstitute.hellbender.tools.coveragemodel.linalg.GeneralLinearOperator in project gatk-protected by broadinstitute.

the class CoverageModelEMWorkspace method updateBiasCovariatesRegularized.

/**
     * E-step update of bias covariates w/ regularization (local implementation)
     *
     * @return a {@link SubroutineSignal} containing the update size (key: "error_norm")
     */
@UpdatesRDD
@EvaluatesRDD
@CachesRDD
private SubroutineSignal updateBiasCovariatesRegularized(final double admixingRatio) {
    mapWorkers(cb -> cb.cloneWithUpdatedCachesByTag(CoverageModelEMComputeBlock.CoverageModelICGCacheTag.E_STEP_W_REG));
    cacheWorkers("after E-step update of bias covariates w/ regularization");
    final INDArray W_tl_old = fetchFromWorkers(CoverageModelEMComputeBlock.CoverageModelICGCacheNode.W_tl, 0);
    final INDArray v_tl = fetchFromWorkers(CoverageModelEMComputeBlock.CoverageModelICGCacheNode.v_tl, 0);
    /* initialize the linear operators */
    final GeneralLinearOperator<INDArray> linop, precond;
    final ImmutablePair<GeneralLinearOperator<INDArray>, GeneralLinearOperator<INDArray>> ops = getBiasCovariatesRegularizedLinearOperators();
    linop = ops.left;
    precond = ops.right;
    /* initialize the iterative solver */
    final IterativeLinearSolverNDArray iterSolver = new IterativeLinearSolverNDArray(linop, v_tl, precond, config.getWAbsoluteTolerance(), config.getWRelativeTolerance(), config.getWMaxIterations(), x -> x.normmaxNumber().doubleValue(), /* norm */
    (x, y) -> x.mul(y).sumNumber().doubleValue(), /* inner product */
    true);
    /* solve */
    long startTime = System.nanoTime();
    final SubroutineSignal sig = iterSolver.solveUsingPreconditionedConjugateGradient(W_tl_old);
    linop.cleanupAfter();
    precond.cleanupAfter();
    long endTime = System.nanoTime();
    logger.debug("CG execution time for solving the regularized M-step update equation for bias covariates" + (double) (endTime - startTime) / 1000000 + " ms");
    /* check the exit status of the solver and push the new W to workers */
    final ExitStatus exitStatus = sig.get(StandardSubroutineSignals.EXIT_STATUS);
    if (exitStatus == ExitStatus.FAIL_MAX_ITERS) {
        logger.warn("CG iterations for M-step update of bias covariates did not converge. Increase maximum iterations" + " and/or decrease absolute/relative error tolerances");
    }
    final int iters = sig.<Integer>get(StandardSubroutineSignals.ITERATIONS);
    final INDArray W_tl_new = sig.get(StandardSubroutineSignals.SOLUTION);
    switch(config.getBiasCovariatesComputeNodeCommunicationPolicy()) {
        case BROADCAST_HASH_JOIN:
            pushToWorkers(mapINDArrayToBlocks(W_tl_new), (W, cb) -> cb.cloneWithUpdatedPrimitive(CoverageModelEMComputeBlock.CoverageModelICGCacheNode.W_tl, W.get(cb.getTargetSpaceBlock())));
            break;
        case RDD_JOIN:
            joinWithWorkersAndMap(chopINDArrayToBlocks(W_tl_new), p -> p._1.cloneWithUpdatedPrimitive(CoverageModelEMComputeBlock.CoverageModelICGCacheNode.W_tl, p._2));
            break;
        default:
            throw new GATKException.ShouldNeverReachHereException("Unknown communication policy for M-step update" + " of bias covariates");
    }
    /* update F[W] */
    updateFilteredBiasCovariates(W_tl_new);
    final double errorNormInfinity = CoverageModelEMWorkspaceMathUtils.getINDArrayNormInfinity(W_tl_new.sub(W_tl_old));
    /* send the signal to workers for consistency */
    final SubroutineSignal newSig = SubroutineSignal.builder().put(StandardSubroutineSignals.RESIDUAL_ERROR_NORM, errorNormInfinity).put(StandardSubroutineSignals.ITERATIONS, iters).build();
    mapWorkers(cb -> cb.cloneWithUpdatedSignal(newSig));
    return newSig;
}

Example 2 with GeneralLinearOperator

use of org.broadinstitute.hellbender.tools.coveragemodel.linalg.GeneralLinearOperator in project gatk by broadinstitute.

the class CoverageModelEMWorkspace method updateBiasCovariatesRegularized.

/**
     * E-step update of bias covariates w/ regularization (local implementation)
     *
     * @return a {@link SubroutineSignal} containing the update size (key: "error_norm")
     */
@UpdatesRDD
@EvaluatesRDD
@CachesRDD
private SubroutineSignal updateBiasCovariatesRegularized(final double admixingRatio) {
    mapWorkers(cb -> cb.cloneWithUpdatedCachesByTag(CoverageModelEMComputeBlock.CoverageModelICGCacheTag.E_STEP_W_REG));
    cacheWorkers("after E-step update of bias covariates w/ regularization");
    final INDArray W_tl_old = fetchFromWorkers(CoverageModelEMComputeBlock.CoverageModelICGCacheNode.W_tl, 0);
    final INDArray v_tl = fetchFromWorkers(CoverageModelEMComputeBlock.CoverageModelICGCacheNode.v_tl, 0);
    /* initialize the linear operators */
    final GeneralLinearOperator<INDArray> linop, precond;
    final ImmutablePair<GeneralLinearOperator<INDArray>, GeneralLinearOperator<INDArray>> ops = getBiasCovariatesRegularizedLinearOperators();
    linop = ops.left;
    precond = ops.right;
    /* initialize the iterative solver */
    final IterativeLinearSolverNDArray iterSolver = new IterativeLinearSolverNDArray(linop, v_tl, precond, config.getWAbsoluteTolerance(), config.getWRelativeTolerance(), config.getWMaxIterations(), x -> x.normmaxNumber().doubleValue(), /* norm */
    (x, y) -> x.mul(y).sumNumber().doubleValue(), /* inner product */
    true);
    /* solve */
    long startTime = System.nanoTime();
    final SubroutineSignal sig = iterSolver.solveUsingPreconditionedConjugateGradient(W_tl_old);
    linop.cleanupAfter();
    precond.cleanupAfter();
    long endTime = System.nanoTime();
    logger.debug("CG execution time for solving the regularized M-step update equation for bias covariates" + (double) (endTime - startTime) / 1000000 + " ms");
    /* check the exit status of the solver and push the new W to workers */
    final ExitStatus exitStatus = sig.get(StandardSubroutineSignals.EXIT_STATUS);
    if (exitStatus == ExitStatus.FAIL_MAX_ITERS) {
        logger.warn("CG iterations for M-step update of bias covariates did not converge. Increase maximum iterations" + " and/or decrease absolute/relative error tolerances");
    }
    final int iters = sig.<Integer>get(StandardSubroutineSignals.ITERATIONS);
    final INDArray W_tl_new = sig.get(StandardSubroutineSignals.SOLUTION);
    switch(config.getBiasCovariatesComputeNodeCommunicationPolicy()) {
        case BROADCAST_HASH_JOIN:
            pushToWorkers(mapINDArrayToBlocks(W_tl_new), (W, cb) -> cb.cloneWithUpdatedPrimitive(CoverageModelEMComputeBlock.CoverageModelICGCacheNode.W_tl, W.get(cb.getTargetSpaceBlock())));
            break;
        case RDD_JOIN:
            joinWithWorkersAndMap(chopINDArrayToBlocks(W_tl_new), p -> p._1.cloneWithUpdatedPrimitive(CoverageModelEMComputeBlock.CoverageModelICGCacheNode.W_tl, p._2));
            break;
        default:
            throw new GATKException.ShouldNeverReachHereException("Unknown communication policy for M-step update" + " of bias covariates");
    }
    /* update F[W] */
    updateFilteredBiasCovariates(W_tl_new);
    final double errorNormInfinity = CoverageModelEMWorkspaceMathUtils.getINDArrayNormInfinity(W_tl_new.sub(W_tl_old));
    /* send the signal to workers for consistency */
    final SubroutineSignal newSig = SubroutineSignal.builder().put(StandardSubroutineSignals.RESIDUAL_ERROR_NORM, errorNormInfinity).put(StandardSubroutineSignals.ITERATIONS, iters).build();
    mapWorkers(cb -> cb.cloneWithUpdatedSignal(newSig));
    return newSig;
}