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.gdbscan |
Generalized DBSCAN
Generalized DBSCAN is an abstraction of the original DBSCAN idea,
that allows the use of arbitrary "neighborhood" and "core point" predicates.
|
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.kmeans.initialization |
Initialization strategies for k-means.
|
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.itemsetmining |
Algorithms for frequent itemset mining such as APRIORI.
|
de.lmu.ifi.dbs.elki.algorithm.outlier.lof |
LOF family of outlier detection algorithms
|
de.lmu.ifi.dbs.elki.database |
ELKI database layer - loading, storing, indexing and accessing data
|
de.lmu.ifi.dbs.elki.database.datastore.memory |
Memory data store implementation for ELKI.
|
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.distance.similarityfunction.kernel |
Kernel functions.
|
de.lmu.ifi.dbs.elki.index.preprocessed.fastoptics |
Preprocessed index used by the FastOPTICS algorithm.
|
de.lmu.ifi.dbs.elki.index.tree.metrical.covertree |
Cover-tree variations.
|
de.lmu.ifi.dbs.elki.index.tree.spatial.kd |
K-d-tree and variants
|
de.lmu.ifi.dbs.elki.result |
Result types, representation and handling
|
de.lmu.ifi.dbs.elki.result.outlier |
Outlier result classes
|
de.lmu.ifi.dbs.elki.visualization.gui |
Package to provide a visualization GUI
|
tutorial.clustering |
Classes from the tutorial on implementing a custom k-means variation
|
Modifier and Type | Method and Description |
---|---|
protected ArrayModifiableDBIDs |
SNNClustering.findSNNNeighbors(SimilarityQuery<O> snnInstance,
DBIDRef queryObject)
Returns the shared nearest neighbors of the specified query object in the
given database.
|
static ArrayModifiableDBIDs[] |
ClusteringAlgorithmUtil.partitionsFromIntegerLabels(DBIDs ids,
IntegerDataStore assignment,
int k)
Collect clusters from their [0;k-1] integer labels.
|
Modifier and Type | Method and Description |
---|---|
protected int |
GriDBSCAN.Instance.expandCluster(DBIDRef seed,
int clusterid,
WritableIntegerDataStore clusterids,
ModifiableDoubleDBIDList neighbors,
ArrayModifiableDBIDs activeSet,
RangeQuery<V> rq,
FiniteProgress pprog)
Set-based expand cluster implementation.
|
protected void |
DBSCAN.expandCluster(Relation<O> relation,
RangeQuery<O> rangeQuery,
DBIDRef startObjectID,
ArrayModifiableDBIDs seeds,
FiniteProgress objprog,
IndefiniteProgress clusprog)
DBSCAN-function expandCluster.
|
protected int |
GriDBSCAN.Instance.processCorePoint(DBIDRef seed,
DoubleDBIDList newneighbors,
int clusterid,
WritableIntegerDataStore clusterids,
ArrayModifiableDBIDs activeSet)
Process a single core point.
|
private void |
DBSCAN.processNeighbors(DoubleDBIDListIter neighbor,
ModifiableDBIDs currentCluster,
ArrayModifiableDBIDs seeds)
Process a single core point.
|
Modifier and Type | Field and Description |
---|---|
private ArrayModifiableDBIDs |
HiCO.Instance.clusterOrder
Cluster order.
|
private ArrayModifiableDBIDs |
HiCO.Instance.tmpIds
Temporary ids.
|
Modifier and Type | Method and Description |
---|---|
protected int |
GeneralizedDBSCAN.Instance.expandCluster(DBIDRef seed,
int clusterid,
WritableIntegerDataStore clusterids,
T neighbors,
ArrayModifiableDBIDs activeSet,
FiniteProgress progress)
Set-based expand cluster implementation.
|
protected int |
GeneralizedDBSCAN.Instance.processCorePoint(DBIDRef seed,
T newneighbors,
int clusterid,
WritableIntegerDataStore clusterids,
ArrayModifiableDBIDs activeSet)
Process a single core point.
|
Modifier and Type | Method and Description |
---|---|
protected static <O> void |
MiniMax.initializeMatrices(MatrixParadigm mat,
ArrayModifiableDBIDs prots,
DistanceQuery<O> dq)
Initializes the inter-cluster distance matrix of possible merges
|
Modifier and Type | Field and Description |
---|---|
protected ArrayModifiableDBIDs |
AbstractCutDendrogram.Instance.cluster_leads
Cluster lead objects
|
Modifier and Type | Method and Description |
---|---|
private void |
ClustersWithNoiseExtraction.Instance.mergeClusters(WritableDataStore<ArrayModifiableDBIDs> clusters,
DBIDRef it,
DBIDRef succ)
Merge two clusters
|
Modifier and Type | Field and Description |
---|---|
(package private) ArrayModifiableDBIDs |
CLARANS.Assignment.medoids
Medoids
|
Modifier and Type | Method and Description |
---|---|
protected ArrayModifiableDBIDs |
KMedoidsPAM.initialMedoids(DistanceQuery<V> distQ,
DBIDs ids)
Choose the initial medoids.
|
Modifier and Type | Method and Description |
---|---|
protected void |
KMedoidsFastPAM.Instance.findBestSwaps(DBIDArrayIter m,
ArrayModifiableDBIDs bestids,
double[] best,
double[] cost)
Find the best swaps.
|
protected double |
KMedoidsFastPAM.Instance.run(ArrayModifiableDBIDs medoids,
int maxiter)
Run the PAM optimization phase.
|
protected double |
KMedoidsFastPAM1.Instance.run(ArrayModifiableDBIDs medoids,
int maxiter)
Run the PAM optimization phase.
|
protected double |
KMedoidsPAM.Instance.run(ArrayModifiableDBIDs medoids,
int maxiter)
Run the PAM optimization phase.
|
protected double |
KMedoidsPAMReynolds.Instance.run(ArrayModifiableDBIDs medoids,
int maxiter)
Run the PAM optimization phase.
|
protected void |
KMedoidsFastPAM.run(DistanceQuery<V> distQ,
DBIDs ids,
ArrayModifiableDBIDs medoids,
WritableIntegerDataStore assignment) |
protected void |
KMedoidsFastPAM1.run(DistanceQuery<V> distQ,
DBIDs ids,
ArrayModifiableDBIDs medoids,
WritableIntegerDataStore assignment) |
protected void |
KMedoidsPAM.run(DistanceQuery<V> distQ,
DBIDs ids,
ArrayModifiableDBIDs medoids,
WritableIntegerDataStore assignment)
Run the main algorithm.
|
protected void |
KMedoidsPAMReynolds.run(DistanceQuery<V> distQ,
DBIDs ids,
ArrayModifiableDBIDs medoids,
WritableIntegerDataStore assignment) |
protected void |
KMedoidsFastPAM1.Instance.updateAssignment(ArrayModifiableDBIDs medoids,
DBIDArrayIter miter,
DBIDRef h,
int m)
Update an existing cluster assignment.
|
Modifier and Type | Method and Description |
---|---|
(package private) static void |
KMeansPlusPlusInitialMeans.chooseRemaining(DBIDs ids,
DistanceQuery<?> distQ,
int k,
ArrayModifiableDBIDs means,
WritableDoubleDataStore weights,
double weightsum,
java.util.Random random)
Choose remaining means, weighted by distance.
|
private static void |
LABInitialMeans.shuffle(ArrayModifiableDBIDs ids,
int ssize,
int end,
java.util.Random random)
Partial Fisher-Yates shuffle.
|
Modifier and Type | Field and Description |
---|---|
(package private) ArrayModifiableDBIDs |
OPTICSList.Instance.candidates
Current list of candidates.
|
protected ArrayModifiableDBIDs |
GeneralizedOPTICS.Instance.candidates
Current list of candidates.
|
(package private) ArrayModifiableDBIDs |
ClusterOrder.ids
Cluster order.
|
Modifier and Type | Method and Description |
---|---|
ArrayModifiableDBIDs |
ClusterOrder.order(DBIDs ids)
Use the cluster order to sort the given collection ids.
|
Modifier and Type | Method and Description |
---|---|
void |
OPTICSList.Instance.findBest(ArrayModifiableDBIDs candidates,
DBIDArrayMIter it,
DBIDVar out)
Find the minimum in the candidates array.
|
Constructor and Description |
---|
ClusterOrder(java.lang.String name,
java.lang.String shortname,
ArrayModifiableDBIDs ids,
WritableDoubleDataStore reachability,
WritableDBIDDataStore predecessor)
Constructor
|
CorrelationClusterOrder(java.lang.String name,
java.lang.String shortname,
ArrayModifiableDBIDs ids,
WritableDoubleDataStore reachability,
WritableDBIDDataStore predecessor,
WritableIntegerDataStore corrdim)
Constructor.
|
Modifier and Type | Field and Description |
---|---|
private ArrayModifiableDBIDs |
DiSH.Instance.clusterOrder
Cluster order.
|
private ArrayModifiableDBIDs |
HiSC.Instance.clusterOrder
Cluster order.
|
private ArrayModifiableDBIDs |
DiSH.Instance.tmpIds
Temporary ids.
|
Modifier and Type | Method and Description |
---|---|
private it.unimi.dsi.fastutil.objects.Object2ObjectOpenCustomHashMap<long[],java.util.List<ArrayModifiableDBIDs>> |
DiSH.extractClusters(Relation<V> relation,
DiSH.DiSHClusterOrder clusterOrder)
Extracts the clusters from the cluster order.
|
private Pair<long[],ArrayModifiableDBIDs> |
DiSH.findParent(Relation<V> relation,
Pair<long[],ArrayModifiableDBIDs> child,
it.unimi.dsi.fastutil.objects.Object2ObjectMap<long[],java.util.List<ArrayModifiableDBIDs>> clustersMap)
Returns the parent of the specified cluster
|
Modifier and Type | Method and Description |
---|---|
protected DBIDs |
DOC.findNeighbors(DBIDRef q,
long[] nD,
ArrayModifiableDBIDs S,
Relation<V> relation)
Find the neighbors of point q in the given subspace
|
protected Cluster<SubspaceModel> |
DOC.runDOC(Database database,
Relation<V> relation,
ArrayModifiableDBIDs S,
int d,
int n,
int m,
int r,
int minClusterSize)
Performs a single run of DOC, finding a single cluster.
|
protected Cluster<SubspaceModel> |
FastDOC.runDOC(Database database,
Relation<V> relation,
ArrayModifiableDBIDs S,
int d,
int n,
int m,
int r,
int minClusterSize)
Performs a single run of FastDOC, finding a single cluster.
|
Modifier and Type | Method and Description |
---|---|
private void |
DiSH.checkClusters(Relation<V> relation,
it.unimi.dsi.fastutil.objects.Object2ObjectMap<long[],java.util.List<ArrayModifiableDBIDs>> clustersMap)
Removes the clusters with size < minpts from the cluster map and adds them
to their parents.
|
private Pair<long[],ArrayModifiableDBIDs> |
DiSH.findParent(Relation<V> relation,
Pair<long[],ArrayModifiableDBIDs> child,
it.unimi.dsi.fastutil.objects.Object2ObjectMap<long[],java.util.List<ArrayModifiableDBIDs>> clustersMap)
Returns the parent of the specified cluster
|
private Pair<long[],ArrayModifiableDBIDs> |
DiSH.findParent(Relation<V> relation,
Pair<long[],ArrayModifiableDBIDs> child,
it.unimi.dsi.fastutil.objects.Object2ObjectMap<long[],java.util.List<ArrayModifiableDBIDs>> clustersMap)
Returns the parent of the specified cluster
|
private void |
DiSH.logClusterSizes(java.lang.String m,
int dimensionality,
it.unimi.dsi.fastutil.objects.Object2ObjectOpenCustomHashMap<long[],java.util.List<ArrayModifiableDBIDs>> clustersMap)
Log cluster sizes in verbose mode.
|
private java.util.List<Cluster<SubspaceModel>> |
DiSH.sortClusters(Relation<V> relation,
it.unimi.dsi.fastutil.objects.Object2ObjectMap<long[],java.util.List<ArrayModifiableDBIDs>> clustersMap)
Returns a sorted list of the clusters w.r.t. the subspace dimensionality in
descending order.
|
Constructor and Description |
---|
DiSHClusterOrder(java.lang.String name,
java.lang.String shortname,
ArrayModifiableDBIDs ids,
WritableDoubleDataStore reachability,
WritableDBIDDataStore predecessor,
WritableIntegerDataStore corrdim,
WritableDataStore<long[]> commonPreferenceVectors)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
protected java.util.List<SparseItemset> |
APRIORI.buildFrequentTwoItemsets(java.util.List<OneItemset> oneitems,
Relation<BitVector> relation,
int dim,
int needed,
DBIDs ids,
ArrayModifiableDBIDs survivors)
Build the 2-itemsets.
|
protected java.util.List<? extends Itemset> |
APRIORI.frequentItemsets(java.util.List<? extends Itemset> candidates,
Relation<BitVector> relation,
int needed,
DBIDs ids,
ArrayModifiableDBIDs survivors,
int length)
Returns the frequent BitSets out of the given BitSets with respect to the
given database.
|
protected java.util.List<SparseItemset> |
APRIORI.frequentItemsetsSparse(java.util.List<SparseItemset> candidates,
Relation<BitVector> relation,
int needed,
DBIDs ids,
ArrayModifiableDBIDs survivors,
int length)
Returns the frequent BitSets out of the given BitSets with respect to the
given database.
|
Modifier and Type | Method and Description |
---|---|
private ArrayModifiableDBIDs |
OnlineLOF.LOFKNNListener.mergeIDs(java.util.List<? extends DoubleDBIDList> queryResults,
DBIDs... ids)
Merges the ids of the query result with the specified ids.
|
Modifier and Type | Method and Description |
---|---|
private void |
ALOCI.ALOCIQuadTree.bulkLoad(double[] lmin,
double[] lmax,
java.util.List<ALOCI.Node> children,
ArrayModifiableDBIDs ids,
int start,
int end,
int dim,
int level,
int code)
Bulk load the tree
|
Modifier and Type | Method and Description |
---|---|
static ArrayModifiableDBIDs |
DatabaseUtil.getObjectsByLabelMatch(Database database,
java.util.regex.Pattern name_pattern)
Find object by matching their labels.
|
Modifier and Type | Field and Description |
---|---|
private ArrayModifiableDBIDs |
ArrayDBIDStore.data
Data array
|
Modifier and Type | Method and Description |
---|---|
ArrayModifiableDBIDs |
DBIDFactory.newArray()
Make a new (modifiable) array of DBIDs.
|
static ArrayModifiableDBIDs |
DBIDUtil.newArray()
Make a new (modifiable) array of DBIDs.
|
ArrayModifiableDBIDs |
DBIDFactory.newArray(DBIDs existing)
Make a new (modifiable) array of DBIDs.
|
static ArrayModifiableDBIDs |
DBIDUtil.newArray(DBIDs existing)
Make a new (modifiable) array of DBIDs.
|
ArrayModifiableDBIDs |
DBIDFactory.newArray(int size)
Make a new (modifiable) array of DBIDs.
|
static ArrayModifiableDBIDs |
DBIDUtil.newArray(int size)
Make a new (modifiable) array of DBIDs.
|
Modifier and Type | Method and Description |
---|---|
private static void |
QuickSelectDBIDs.insertionSort(ArrayModifiableDBIDs data,
java.util.Comparator<? super DBIDRef> comparator,
int start,
int end,
DBIDArrayIter iter1,
DBIDArrayIter iter2)
Sort a small array using repetitive insertion sort.
|
static int |
QuickSelectDBIDs.median(ArrayModifiableDBIDs data,
java.util.Comparator<? super DBIDRef> comparator)
Compute the median of an array efficiently using the QuickSelect method.
|
static int |
QuickSelectDBIDs.median(ArrayModifiableDBIDs data,
java.util.Comparator<? super DBIDRef> comparator,
int begin,
int end)
Compute the median of an array efficiently using the QuickSelect method.
|
static int |
QuickSelectDBIDs.quantile(ArrayModifiableDBIDs data,
java.util.Comparator<? super DBIDRef> comparator,
double quant)
Compute the median of an array efficiently using the QuickSelect method.
|
static int |
QuickSelectDBIDs.quantile(ArrayModifiableDBIDs data,
java.util.Comparator<? super DBIDRef> comparator,
int begin,
int end,
double quant)
Compute the median of an array efficiently using the QuickSelect method.
|
static void |
QuickSelectDBIDs.quickSelect(ArrayModifiableDBIDs data,
java.util.Comparator<? super DBIDRef> comparator,
int rank)
QuickSelect is essentially quicksort, except that we only "sort" that half
of the array that we are interested in.
|
static void |
QuickSelectDBIDs.quickSelect(ArrayModifiableDBIDs data,
java.util.Comparator<? super DBIDRef> comparator,
int start,
int end,
int rank)
QuickSelect is essentially quicksort, except that we only "sort" that half
of the array that we are interested in.
|
static void |
DBIDUtil.randomShuffle(ArrayModifiableDBIDs ids,
java.util.Random random)
Produce a random shuffling of the given DBID array.
|
static void |
DBIDUtil.randomShuffle(ArrayModifiableDBIDs ids,
RandomFactory rnd)
Produce a random shuffling of the given DBID array.
|
static void |
DBIDUtil.randomShuffle(ArrayModifiableDBIDs ids,
java.util.Random random,
int limit)
Produce a random shuffling of the given DBID array.
|
Modifier and Type | Class and Description |
---|---|
(package private) class |
ArrayModifiableIntegerDBIDs
Class using a primitive int[] array as storage.
|
Modifier and Type | Method and Description |
---|---|
ArrayModifiableDBIDs |
AbstractIntegerDBIDFactory.newArray() |
ArrayModifiableDBIDs |
AbstractIntegerDBIDFactory.newArray(DBIDs existing) |
ArrayModifiableDBIDs |
AbstractIntegerDBIDFactory.newArray(int size) |
Modifier and Type | Field and Description |
---|---|
(package private) ArrayModifiableDBIDs |
KernelMatrix.SortedArrayMap.ids |
Modifier and Type | Method and Description |
---|---|
int |
RandomProjectedNeighborsAndDensities.splitByDistance(ArrayModifiableDBIDs ind,
int begin,
int end,
DoubleDataStore tpro,
java.util.Random rand)
Split the data set by distances.
|
int |
RandomProjectedNeighborsAndDensities.splitRandomly(ArrayModifiableDBIDs ind,
int begin,
int end,
DoubleDataStore tpro,
java.util.Random rand)
Split the data set randomly.
|
void |
RandomProjectedNeighborsAndDensities.splitupNoSort(ArrayModifiableDBIDs ind,
int begin,
int end,
int dim,
java.util.Random rand)
Recursively splits entire point set until the set is below a threshold
|
Modifier and Type | Field and Description |
---|---|
(package private) ArrayModifiableDBIDs |
SimplifiedCoverTree.Node.singletons
Objects in this node.
|
Modifier and Type | Field and Description |
---|---|
(package private) ArrayModifiableDBIDs |
MinimalisticMemoryKDTree.sorted
The actual "tree" as a sorted array.
|
Modifier and Type | Method and Description |
---|---|
ArrayModifiableDBIDs |
OrderingResult.order(DBIDs ids)
Sort the given ids according to this ordering and return an iterator.
|
ArrayModifiableDBIDs |
OrderingFromDataStore.order(DBIDs ids) |
Modifier and Type | Method and Description |
---|---|
ArrayModifiableDBIDs |
OrderingFromRelation.order(DBIDs ids) |
Modifier and Type | Field and Description |
---|---|
(package private) ArrayModifiableDBIDs |
SelectionTableWindow.dbids
The DBIDs to display
|
Modifier and Type | Method and Description |
---|---|
protected ArrayModifiableDBIDs |
SameSizeKMeansAlgorithm.initialAssignment(java.util.List<ModifiableDBIDs> clusters,
WritableDataStore<SameSizeKMeansAlgorithm.Meta> metas,
DBIDs ids) |
Modifier and Type | Method and Description |
---|---|
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.