@Override
public void process(final DAVOptions options) {
final String[] args = getOriginalArgs();
final UseModality<DAVOptions> executed;
final int maxSplitIndex = splitPlan.getMaxSplitIndex();
final ProgressLogger logger = new ProgressLogger(LOGGER);
logger.expectedUpdates = maxSplitIndex;
logger.itemsName = "splits";
logger.priority = Level.INFO;
logger.start("Parallel split processing");
final SplitParallelRegion region = new SplitParallelRegion(maxSplitIndex, args, logger);
try {
getParallelTeam().execute(region);
} catch (Exception e) {
LOGGER.error("An exception occurred.", e);
}
logger.stop();
/** Time the duration of the sequence: */
timeService.setModelId(modelId);
timeService.stop();
executed = region.getExecuted();
if (executed != null && executed instanceof SequenceMode) {
// if we executed SequenceMode
final SequenceMode sequenceMode = (SequenceMode) executed;
if (evaluateStatistics) {
final String label = sequenceMode.getValue("label");
final String statsFilename = sequenceMode.getValue("predictions-filename");
if (statsFilename != null && label != null) {
// and the sequence defined the variables "predictions-filename" and "label"
try {
final List<String> statsModeArgs =
new ObjectArrayList<String>(
new String[] {
"--mode",
"stats",
"--predictions",
statsFilename,
"--submission-file",
labelPrefix(label) + "-maqcii-submission.txt",
"--label",
label,
"--model-id",
modelId,
"--dataset-name",
options.datasetName,
"--other-measures",
"prec,rec,F-1,MCC,binary-auc"
});
if (options.adjustSignalToFloorValue) {
statsModeArgs.add("--floor");
statsModeArgs.add(Double.toString(options.signalFloorValue));
}
// extract survival options if any
// TODO: clean this up - we should not be checking for "%survival%"
final String survivalFileName = sequenceMode.getValue("survival");
if (StringUtils.isNotBlank(survivalFileName)
&& !"%survival%".equals(survivalFileName)) {
statsModeArgs.add("--survival");
statsModeArgs.add(survivalFileName);
}
LOGGER.debug("Estimating statistics: " + statsModeArgs);
// we create a new DAVMode here since we want to use the old StatsMode code
// which is no longer exposed by DiscoverAndValidate (BDVal main method)
final DAVMode statsMode = new DAVMode();
statsMode.registerMode("stats", StatsMode.class);
final DAVOptions statsModeOptions = new DAVOptions();
statsMode.process(
statsModeArgs.toArray(new String[statsModeArgs.size()]), statsModeOptions);
} catch (Exception e) {
LOGGER.error("Error executing --mode stats for all splits", e);
}
}
}
}
}
/**
* For a specific sub-set of blocks (child nodes), find a 'base' subset of parents for which the
* block's logLikelihood is not -Infinity
*
* @param candidateParentsPerNode
* @param chosenArcsPerNode
* @param setOfBlocks
* @return
*/
protected double getOutOfMinusInfinity(
Int2ObjectOpenHashMap<IntOpenHashSet> candidateParentsPerNode,
Int2ObjectOpenHashMap<ObjectOpenHashSet<Arc>> chosenArcsPerNode,
IntOpenHashSet setOfBlocks,
TIntDoubleHashMap logLPerNode) {
double totalLogL = 0;
ProgressLogger pl = new ProgressLogger(LOGGER, ProgressLogger.TEN_SECONDS, "blocks");
pl.start("Begin initializing, to avoid zero likelihood, using set-cover heuristic");
pl.expectedUpdates = setOfBlocks.size();
int nArcs = 0;
for (int v : setOfBlocks) {
pl.update();
IntOpenHashSet vParents = candidateParentsPerNode.get(v);
Int2ObjectOpenHashMap<IntOpenHashSet> parentActions =
new Int2ObjectOpenHashMap<IntOpenHashSet>();
Int2ObjectOpenHashMap<IntArrayList> cPlusV = auxiliary.getCplusOnline(v);
Int2ObjectOpenHashMap<IntArrayList> cMinusV = auxiliary.getCminusOnline(v);
if (cPlusV != null) {
IntSet actions = cPlusV.keySet();
// Heuristic: first add the parents that participate in A+ for
// most actions
for (int action : actions) {
for (int u : cPlusV.get(action)) {
if (!parentActions.containsKey(u)) {
parentActions.put(u, new IntOpenHashSet());
}
parentActions.get(u).add(action);
}
}
}
KeepMaximum km = new KeepMaximum();
km.addAllKey2Listsize(parentActions);
IntOpenHashSet baseSetOfParents = new IntOpenHashSet();
double logL = Double.NEGATIVE_INFINITY;
while (logL == Double.NEGATIVE_INFINITY && (km.getMaximumKey() != -1)) {
int u = km.getMaximumKey();
if (baseSetOfParents.contains(u)) {
throw new IllegalStateException("Attempted to add twice the same parent");
}
baseSetOfParents.add(u);
logL = blockLogLikelihood(v, cPlusV, cMinusV, baseSetOfParents);
IntOpenHashSet uActions = parentActions.get(u);
for (int parent : vParents) {
parentActions.get(parent).removeAll(uActions);
}
vParents.remove(u);
parentActions.remove(u);
km.reset();
km.addAllKey2Listsize(parentActions);
}
// keep track of the likelihood
totalLogL += logL;
if (logLPerNode != null) {
logLPerNode.put(v, logL);
}
chosenArcsPerNode.put(v, new ObjectOpenHashSet<Arc>());
for (int u : baseSetOfParents) {
nArcs++;
chosenArcsPerNode.get(v).add(new Arc(u, v));
}
}
pl.stop("Done initialization. Added " + nArcs + " arcs, logLikelihood=" + totalLogL);
return totalLogL;
}