Package | Description |
---|---|
de.lmu.ifi.dbs.elki.algorithm.clustering |
Clustering algorithms
Clustering algorithms are supposed to implement the
Algorithm -Interface. |
de.lmu.ifi.dbs.elki.algorithm.clustering.correlation |
Correlation clustering algorithms
|
de.lmu.ifi.dbs.elki.algorithm.clustering.correlation.cash |
Helper classes for the
CASH
algorithm. |
de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical |
Hierarchical agglomerative clustering (HAC).
|
de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.extraction |
Extraction of partitional clusterings from hierarchical results.
|
de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans |
K-means clustering and variations
|
de.lmu.ifi.dbs.elki.algorithm.clustering.optics |
OPTICS family of clustering algorithms.
|
de.lmu.ifi.dbs.elki.algorithm.clustering.subspace |
Axis-parallel subspace clustering algorithms
The clustering algorithms in this package are instances of both, projected
clustering algorithms or subspace clustering algorithms according to the
classical but somewhat obsolete classification schema of clustering
algorithms for axis-parallel subspaces.
|
de.lmu.ifi.dbs.elki.algorithm.clustering.subspace.clique |
Helper classes for the
CLIQUE
algorithm. |
de.lmu.ifi.dbs.elki.algorithm.clustering.uncertain |
Clustering algorithms for uncertain data.
|
de.lmu.ifi.dbs.elki.algorithm.outlier |
Outlier detection algorithms
|
de.lmu.ifi.dbs.elki.algorithm.outlier.lof |
LOF family of outlier detection algorithms
|
de.lmu.ifi.dbs.elki.algorithm.statistics |
Statistical analysis algorithms.
|
de.lmu.ifi.dbs.elki.database.ids |
Database object identification and ID group handling API.
|
de.lmu.ifi.dbs.elki.database.ids.integer |
Integer-based DBID implementation --
do not use directly - always use
DBIDUtil . |
de.lmu.ifi.dbs.elki.index.preprocessed.preference |
Indexes storing preference vectors
|
de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.mktrees.mkapp | |
de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.mktrees.mkcop | |
de.lmu.ifi.dbs.elki.visualization.visualizers.pairsegments |
Visualizers for inspecting cluster differences using pair counting segments
|
tutorial.clustering |
Classes from the tutorial on implementing a custom k-means variation
|
Modifier and Type | Field and Description |
---|---|
protected ModifiableDBIDs |
SNNClustering.noise
Holds a set of noise.
|
protected ModifiableDBIDs |
DBSCAN.noise
Holds a set of noise.
|
protected ModifiableDBIDs |
SNNClustering.processedIDs
Holds a set of processed ids.
|
protected ModifiableDBIDs |
DBSCAN.processedIDs
Holds a set of processed ids.
|
Modifier and Type | Field and Description |
---|---|
(package private) it.unimi.dsi.fastutil.longs.Long2ObjectOpenHashMap<ModifiableDBIDs> |
GriDBSCAN.Instance.grid
Data grid partitioning.
|
protected java.util.List<ModifiableDBIDs> |
SNNClustering.resultList
Holds a list of clusters found.
|
protected java.util.List<ModifiableDBIDs> |
DBSCAN.resultList
Holds a list of clusters found.
|
Modifier and Type | Method and Description |
---|---|
protected void |
GriDBSCAN.Instance.mergeClusterInformation(ModifiableDBIDs cellids,
WritableIntegerDataStore temporary,
WritableDataStore<Assignment> clusterids)
Merge cluster information.
|
private void |
DBSCAN.processNeighbors(DoubleDBIDListIter neighbor,
ModifiableDBIDs currentCluster,
ArrayModifiableDBIDs seeds)
Process a single core point.
|
Modifier and Type | Field and Description |
---|---|
(package private) ModifiableDBIDs |
ORCLUS.ORCLUSCluster.objectIDs
The ids of the objects belonging to this cluster.
|
private ModifiableDBIDs |
CASH.processedIDs
Holds a set of processed ids.
|
Modifier and Type | Method and Description |
---|---|
private double[][] |
CASH.runDerivator(Relation<ParameterizationFunction> relation,
int dim,
CASHInterval interval,
ModifiableDBIDs ids)
Runs the derivator on the specified interval and assigns all points having
a distance less then the standard deviation of the derivator model to the
model to this model.
|
Modifier and Type | Field and Description |
---|---|
private ModifiableDBIDs |
CASHInterval.ids
Holds the ids of the objects associated with this interval.
|
Modifier and Type | Method and Description |
---|---|
ModifiableDBIDs |
CASHIntervalSplit.determineIDs(DBIDs superSetIDs,
HyperBoundingBox interval,
double d_min,
double d_max)
Determines the ids belonging to the given interval, i.e. the
parameterization functions falling within the interval.
|
ModifiableDBIDs |
CASHInterval.getIDs()
Returns the set of ids of the objects associated with this interval.
|
Constructor and Description |
---|
CASHInterval(double[] min,
double[] max,
CASHIntervalSplit split,
ModifiableDBIDs ids,
int maxSplitDimension,
int level,
double d_min,
double d_max)
Provides a unique interval represented by its id, a hyper bounding box and
a set of objects ids associated with this interval.
|
Modifier and Type | Method and Description |
---|---|
protected static int |
MiniMax.findMerge(int end,
MatrixParadigm mat,
DBIDArrayMIter prots,
PointerHierarchyRepresentationBuilder builder,
it.unimi.dsi.fastutil.ints.Int2ObjectOpenHashMap<ModifiableDBIDs> clusters,
DistanceQuery<?> dq)
Find the best merge.
|
protected int |
MiniMaxAnderberg.findMerge(int size,
MatrixParadigm mat,
DBIDArrayMIter prots,
PointerHierarchyRepresentationBuilder builder,
it.unimi.dsi.fastutil.ints.Int2ObjectOpenHashMap<ModifiableDBIDs> clusters,
double[] bestd,
int[] besti,
DistanceQuery<O> dq)
Perform the next merge step.
|
protected static void |
MiniMax.merge(int size,
MatrixParadigm mat,
DBIDArrayMIter prots,
PointerHierarchyRepresentationBuilder builder,
it.unimi.dsi.fastutil.ints.Int2ObjectOpenHashMap<ModifiableDBIDs> clusters,
DistanceQuery<?> dq,
int x,
int y)
Merges two clusters given by x, y, their points with smallest IDs, and y to
keep
|
protected void |
MiniMaxAnderberg.merge(int size,
MatrixParadigm mat,
DBIDArrayMIter prots,
PointerHierarchyRepresentationBuilder builder,
it.unimi.dsi.fastutil.ints.Int2ObjectOpenHashMap<ModifiableDBIDs> clusters,
DistanceQuery<O> dq,
double[] bestd,
int[] besti,
int x,
int y)
Execute the cluster merge
|
private void |
MiniMaxNNChain.nnChainCore(MatrixParadigm mat,
DBIDArrayMIter prots,
DistanceQuery<O> dq,
PointerHierarchyRepresentationBuilder builder,
it.unimi.dsi.fastutil.ints.Int2ObjectOpenHashMap<ModifiableDBIDs> clusters)
Uses NNChain as in "Modern hierarchical, agglomerative clustering
algorithms" by Daniel Müllner
|
protected static void |
MiniMax.updateEntry(MatrixParadigm mat,
DBIDArrayMIter prots,
it.unimi.dsi.fastutil.ints.Int2ObjectOpenHashMap<ModifiableDBIDs> clusters,
DistanceQuery<?> dq,
int x,
int y)
Update entry at x,y for distance matrix distances
|
private void |
MiniMaxAnderberg.updateMatrices(int size,
MatrixParadigm mat,
DBIDArrayMIter prots,
PointerHierarchyRepresentationBuilder builder,
it.unimi.dsi.fastutil.ints.Int2ObjectOpenHashMap<ModifiableDBIDs> clusters,
DistanceQuery<O> dq,
double[] bestd,
int[] besti,
int x,
int y)
Update the entries of the matrices that contain a distance to y, the newly
merged cluster.
|
protected static <O> void |
MiniMax.updateMatrices(int size,
MatrixParadigm mat,
DBIDArrayMIter prots,
PointerHierarchyRepresentationBuilder builder,
it.unimi.dsi.fastutil.ints.Int2ObjectOpenHashMap<ModifiableDBIDs> clusters,
DistanceQuery<O> dq,
int c)
Update the entries of the matrices that contain a distance to c, the newly
merged cluster.
|
Modifier and Type | Field and Description |
---|---|
protected ModifiableDBIDs |
HDBSCANHierarchyExtraction.TempCluster.members
New ids, not yet in child clusters.
|
protected ModifiableDBIDs |
SimplifiedHierarchyExtraction.TempCluster.newids
New ids, not yet in child clusters.
|
Modifier and Type | Field and Description |
---|---|
protected java.util.ArrayList<ModifiableDBIDs> |
AbstractCutDendrogram.Instance.cluster_dbids
Storage for cluster contents
|
Modifier and Type | Field and Description |
---|---|
protected java.util.List<ModifiableDBIDs> |
AbstractKMeans.Instance.clusters
Store the elements per cluster.
|
Modifier and Type | Method and Description |
---|---|
protected double |
KMedoidsPark.assignToNearestCluster(DBIDArrayIter miter,
double[] dsum,
java.util.List<? extends ModifiableDBIDs> clusters,
DistanceQuery<V> distQ)
Returns a list of clusters.
|
protected int |
KMedoidsPark.currentCluster(java.util.List<? extends ModifiableDBIDs> clusters,
DBIDRef id)
Find the current cluster assignment.
|
Modifier and Type | Field and Description |
---|---|
(package private) ModifiableDBIDs |
FastOPTICS.processed
processed points
|
(package private) ModifiableDBIDs |
OPTICSList.Instance.processedIDs
Holds a set of processed ids.
|
protected ModifiableDBIDs |
GeneralizedOPTICS.Instance.processedIDs
Holds a set of processed ids.
|
private ModifiableDBIDs |
OPTICSHeap.Instance.processedIDs
Holds a set of processed ids.
|
Modifier and Type | Field and Description |
---|---|
ModifiableDBIDs |
P3C.ClusterCandidate.ids
Objects contained in cluster.
|
(package private) ModifiableDBIDs |
PROCLUS.PROCLUSCluster.objectIDs
The ids of the objects belonging to this cluster.
|
Modifier and Type | Method and Description |
---|---|
private java.util.List<Pair<Subspace,ModifiableDBIDs>> |
CLIQUE.determineClusters(java.util.List<CLIQUESubspace> denseSubspaces)
Determines the clusters in the specified dense subspaces.
|
Modifier and Type | Method and Description |
---|---|
private void |
P3C.assignUnassigned(Relation<V> relation,
WritableDataStore<double[]> probClusterIGivenX,
java.util.List<MultivariateGaussianModel> models,
ModifiableDBIDs unassigned)
Assign unassigned objects to best candidate based on shortest Mahalanobis
distance.
|
private void |
P3C.computeFuzzyMembership(Relation<V> relation,
java.util.ArrayList<P3C.Signature> clusterCores,
ModifiableDBIDs unassigned,
WritableDataStore<double[]> probClusterIGivenX,
java.util.List<MultivariateGaussianModel> models,
int dim)
Computes a fuzzy membership with the weights based on which cluster cores
each data point is part of.
|
private void |
P3C.findOutliers(Relation<V> relation,
java.util.List<MultivariateGaussianModel> models,
java.util.ArrayList<P3C.ClusterCandidate> clusterCandidates,
ModifiableDBIDs noise)
Performs outlier detection by testing the Mahalanobis distance of each
point in a cluster against the critical value of the ChiSquared
distribution with as many degrees of freedom as the cluster has relevant
attributes.
|
Constructor and Description |
---|
PROCLUSCluster(ModifiableDBIDs objectIDs,
long[] dimensions,
double[] centroid)
Constructor.
|
Modifier and Type | Field and Description |
---|---|
private ModifiableDBIDs |
CLIQUEUnit.ids
The ids of the feature vectors this unit contains.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<Pair<Subspace,ModifiableDBIDs>> |
CLIQUESubspace.determineClusters()
Determines all clusters in this subspace by performing a depth-first search
algorithm to find connected dense units.
|
Modifier and Type | Method and Description |
---|---|
void |
CLIQUESubspace.dfs(CLIQUEUnit unit,
ModifiableDBIDs cluster,
CLIQUESubspace model)
Depth-first search algorithm to find connected dense units in this subspace
that build a cluster.
|
Constructor and Description |
---|
CLIQUEUnit(CLIQUEUnit prefix,
int newdim,
double min,
double max,
ModifiableDBIDs ids)
Creates a new k-dimensional unit for the given intervals.
|
Modifier and Type | Method and Description |
---|---|
protected boolean |
UKMeans.assignToNearestCluster(Relation<DiscreteUncertainObject> relation,
java.util.List<double[]> means,
java.util.List<? extends ModifiableDBIDs> clusters,
WritableIntegerDataStore assignment,
double[] varsum)
Returns a list of clusters.
|
protected java.util.List<double[]> |
UKMeans.means(java.util.List<? extends ModifiableDBIDs> clusters,
java.util.List<double[]> means,
Relation<DiscreteUncertainObject> database)
Returns the mean vectors of the given clusters in the given database.
|
protected boolean |
UKMeans.updateAssignment(DBIDIter iditer,
java.util.List<? extends ModifiableDBIDs> clusters,
WritableIntegerDataStore assignment,
int newA)
Update the cluster assignment.
|
Modifier and Type | Method and Description |
---|---|
private void |
DWOF.clusterData(DBIDs ids,
RangeQuery<O> rnnQuery,
WritableDoubleDataStore radii,
WritableDataStore<ModifiableDBIDs> labels)
This method applies a density based clustering algorithm.
|
private int |
DWOF.updateSizes(DBIDs ids,
WritableDataStore<ModifiableDBIDs> labels,
WritableIntegerDataStore newSizes)
This method updates each object's cluster size after the clustering step.
|
Modifier and Type | Method and Description |
---|---|
protected void |
INFLO.computeINFLO(Relation<O> relation,
ModifiableDBIDs pruned,
KNNQuery<O> knnq,
WritableDataStore<ModifiableDBIDs> rNNminuskNNs,
WritableDoubleDataStore inflos,
DoubleMinMax inflominmax)
Compute the final INFLO scores.
|
private void |
INFLO.computeNeighborhoods(Relation<O> relation,
DataStore<SetDBIDs> knns,
ModifiableDBIDs pruned,
WritableDataStore<ModifiableDBIDs> rNNminuskNNs)
Compute the reverse kNN minus the kNN.
|
Modifier and Type | Method and Description |
---|---|
protected void |
INFLO.computeINFLO(Relation<O> relation,
ModifiableDBIDs pruned,
KNNQuery<O> knnq,
WritableDataStore<ModifiableDBIDs> rNNminuskNNs,
WritableDoubleDataStore inflos,
DoubleMinMax inflominmax)
Compute the final INFLO scores.
|
private void |
INFLO.computeNeighborhoods(Relation<O> relation,
DataStore<SetDBIDs> knns,
ModifiableDBIDs pruned,
WritableDataStore<ModifiableDBIDs> rNNminuskNNs)
Compute the reverse kNN minus the kNN.
|
Modifier and Type | Method and Description |
---|---|
private void |
EvaluateRetrievalPerformance.findMatches(ModifiableDBIDs posn,
Relation<?> lrelation,
java.lang.Object label)
Find all matching objects.
|
Modifier and Type | Interface and Description |
---|---|
interface |
ArrayModifiableDBIDs
Array-oriented implementation of a modifiable DBID collection.
|
interface |
HashSetModifiableDBIDs
Set-oriented implementation of a modifiable DBID collection.
|
Modifier and Type | Method and Description |
---|---|
static ModifiableDBIDs |
DBIDUtil.difference(DBIDs ids1,
DBIDs ids2)
Returns the difference of the two specified collection of IDs.
|
static ModifiableDBIDs |
DBIDUtil.ensureModifiable(DBIDs ids)
Ensure modifiable.
|
private static ModifiableDBIDs |
DBIDUtil.internalIntersection(DBIDs first,
DBIDs second)
Compute the set intersection of two sets.
|
static ModifiableDBIDs |
DBIDUtil.intersection(DBIDs first,
DBIDs second)
Compute the set intersection of two sets.
|
static ModifiableDBIDs |
DBIDUtil.randomSample(DBIDs source,
int k,
int seed)
Produce a random sample of the given DBIDs.
|
static ModifiableDBIDs |
DBIDUtil.randomSample(DBIDs source,
int k,
java.lang.Long seed)
Produce a random sample of the given DBIDs.
|
static ModifiableDBIDs |
DBIDUtil.randomSample(DBIDs source,
int k,
java.util.Random random)
Produce a random sample of the given DBIDs.
|
static ModifiableDBIDs |
DBIDUtil.randomSample(DBIDs source,
int k,
RandomFactory rnd)
Produce a random sample of the given DBIDs.
|
static ModifiableDBIDs |
DBIDUtil.randomSampleExcept(DBIDs source,
DBIDRef except,
int k,
java.util.Random random)
Produce a random sample of the given DBIDs.
|
static ModifiableDBIDs |
DBIDUtil.randomSampleExcept(DBIDs source,
DBIDRef except,
int k,
RandomFactory rnd)
Produce a random sample of the given DBIDs.
|
static ModifiableDBIDs |
DBIDUtil.union(DBIDs ids1,
DBIDs ids2)
Returns the union of the two specified collection of IDs.
|
Modifier and Type | Class and Description |
---|---|
(package private) class |
ArrayModifiableIntegerDBIDs
Class using a primitive int[] array as storage.
|
(package private) class |
FastutilIntOpenHashSetModifiableDBIDs
Implementation using Fastutil IntSet.
|
Modifier and Type | Method and Description |
---|---|
private long[] |
DiSHPreferenceVectorIndex.determinePreferenceVector(Relation<V> relation,
ModifiableDBIDs[] neighborIDs,
java.lang.StringBuilder msg)
Determines the preference vector according to the specified neighbor ids.
|
private long[] |
DiSHPreferenceVectorIndex.determinePreferenceVectorByApriori(Relation<V> relation,
ModifiableDBIDs[] neighborIDs,
java.lang.StringBuilder msg)
Determines the preference vector with the apriori strategy.
|
private long[] |
DiSHPreferenceVectorIndex.determinePreferenceVectorByMaxIntersection(ModifiableDBIDs[] neighborIDs,
java.lang.StringBuilder msg)
Determines the preference vector with the max intersection strategy.
|
private int |
DiSHPreferenceVectorIndex.maxIntersection(java.util.Map<java.lang.Integer,ModifiableDBIDs> candidates,
ModifiableDBIDs set)
Returns the index of the set having the maximum intersection set with the
specified set contained in the specified map.
|
Modifier and Type | Method and Description |
---|---|
private int |
DiSHPreferenceVectorIndex.max(java.util.Map<java.lang.Integer,ModifiableDBIDs> candidates)
Returns the set with the maximum size contained in the specified map.
|
private int |
DiSHPreferenceVectorIndex.maxIntersection(java.util.Map<java.lang.Integer,ModifiableDBIDs> candidates,
ModifiableDBIDs set)
Returns the index of the set having the maximum intersection set with the
specified set contained in the specified map.
|
Modifier and Type | Method and Description |
---|---|
private void |
MkAppTree.leafEntryIDs(MkAppTreeNode<O> node,
ModifiableDBIDs result)
Determines the ids of the leaf entries stored in the specified subtree.
|
Modifier and Type | Method and Description |
---|---|
private void |
MkCoPTree.doReverseKNNQuery(int k,
DBIDRef q,
ModifiableDoubleDBIDList result,
ModifiableDBIDs candidates)
Performs a reverse knn query.
|
Modifier and Type | Field and Description |
---|---|
protected ModifiableDBIDs |
SegmentsStylingPolicy.unselectedObjects
Not selected IDs that will be drawn in default colors.
|
Modifier and Type | Method and Description |
---|---|
protected void |
SameSizeKMeansAlgorithm.transfer(WritableDataStore<SameSizeKMeansAlgorithm.Meta> metas,
SameSizeKMeansAlgorithm.Meta meta,
ModifiableDBIDs src,
ModifiableDBIDs dst,
DBIDRef id,
int dstnum)
Transfer a single element from one cluster to another.
|
Modifier and Type | Method and Description |
---|---|
protected ArrayModifiableDBIDs |
SameSizeKMeansAlgorithm.initialAssignment(java.util.List<ModifiableDBIDs> clusters,
WritableDataStore<SameSizeKMeansAlgorithm.Meta> metas,
DBIDs ids) |
protected double[][] |
SameSizeKMeansAlgorithm.refineResult(Relation<V> relation,
double[][] means,
java.util.List<ModifiableDBIDs> clusters,
WritableDataStore<SameSizeKMeansAlgorithm.Meta> metas,
ArrayModifiableDBIDs tids)
Perform k-means style iterations to improve the clustering result.
|
Copyright © 2019 ELKI Development Team. License information.