Data Mining and Knowledge Discovery 2, 169–194 (1998)

°
c 1998 Kluwer Academic Publishers. Manufactured in The Netherlands.

Density-Based Clustering in Spatial Databases:

The Algorithm GDBSCAN and Its Applications
JÖRG SANDER [email protected]
MARTIN ESTER [email protected]
HANS-PETER KRIEGEL [email protected]
XIAOWEI XU [email protected]
Institute for Computer Science, University of Munich, Oettingenstr. 67, D-80538 München, Germany

Editor: Usama Fayyad

Received February 21, 1997; Revised December 1997 and March 1998; Accepted April 1998

Abstract. The clustering algorithm DBSCAN relies on a density-based notion of clusters and is designed to
discover clusters of arbitrary shape as well as to distinguish noise. In this paper, we generalize this algorithm in two
important directions. The generalized algorithm—called GDBSCAN—can cluster point objects as well as spatially
extended objects according to both, their spatial and their nonspatial attributes. In addition, four applications using
2D points (astronomy), 3D points (biology), 5D points (earth science) and 2D polygons (geography) are presented,
demonstrating the applicability of GDBSCAN to real-world problems.

Keywords: clustering algorithms, spatial databases, efficiency, applications

1. Introduction

Spatial Database Systems (SDBS) (Gueting 1994) are database systems for the management
of spatial data, i.e., point objects or spatially extended objects in a 2D or 3D space or in
some high-dimensional vector space. While a lot of research has been conducted on knowl-
edge discovery in relational databases in the last years, only a few methods for knowledge
discovery in spatial databases have been proposed in the literature. Knowledge discovery
becomes more and more important in spatial databases since increasingly large amount of
data obtained from satellite images, X-ray crystallography or other automatic equipment
are stored in spatial databases.
Data mining is a step in the KDD process consisting of the application of data analysis and
discovery algorithms that, under acceptable computational efficiency limitations, produce
a particular enumeration of patterns over the data (Fayyad et al., 1996). Clustering, i.e.,
grouping the objects of a database into meaningful subclasses, is one of the major data
mining methods (Matheus et al., 1993). There has been a lot of research on clustering
algorithms for decades but the application to large spatial databases introduces the following
new requirements:

1. Minimal requirements of domain knowledge to determine the input parameters, because

appropriate values are often not known in advance when dealing with large databases.
170 SANDER ET AL.

2. Discovery of clusters with arbitrary shape, because the shape of clusters in spatial
databases may be nonconvex, spherical, drawn-out, linear, elongated etc.
3. Good efficiency on large databases, i.e., on databases of significantly more than just a
few thousand objects.

Ester et al. (1996) present the density-based clustering algorithm DBSCAN. For each
point of a cluster its Eps-neighborhood for some given Eps > 0 has to contain at least a
minimum number of points, i.e., the “density” in the Eps-neighborhood of points has to
exceed some threshold. DBSCAN meets the above requirements in the following sense:
first, DBSCAN requires only one input parameter and supports the user in determining an
appropriate value for it. Second, it discovers clusters of arbitrary shape and can distinguish
noise, and third, using spatial access methods, DBSCAN is efficient even for large spatial
databases.
In this paper, we present the algorithm GDBSCAN generalizing DBSCAN in two impor-
tant ways. First, we can use any notion of a neighborhood of an object if the definition of the
neighborhood is based on a binary predicate which is symmetric and reflexive. For exam-
ple, when clustering polygons, the neighborhood may be defined by the intersect predicate.
Second, instead of simply counting the objects in the neighborhood of an object, we can use
other measures, e.g., considering the nonspatial attributes such as the average income of a
city, to define the “cardinality” of that neighborhood. Thus, the generalized GDBSCAN
algorithm can cluster point objects as well as spatially extended objects according to both,
their spatial and their nonspatial attributes. Furthermore, we present four applications using
2D points (astronomy), 3D points (biology), 5D points (earth science) and 2D polygons
(geography) demonstrating the applicability of GDBSCAN to real-world problems.
The rest of the paper is organized as follows. We discuss well-known clustering algo-
rithms in Section 2 evaluating them according to the above requirements. In Section 3,
we present our density-based notion of clusters and Section 4 introduces the algorithm
GDBSCAN which discovers such clusters in a spatial database. In Section 5, we present
an analytical as well as an experimental evaluation of the effectiveness and efficiency
of GDBSCAN. Furthermore, a comparison with the well-known clustering algorithms
CLARANS and BIRCH is performed. In Section 6, four applications of GDBSCAN are
discussed and Section 7 concludes with a summary and some directions for future research.

2. Related work on clustering algorithms

Two main types of clustering algorithms can be distinguished (Kaufman and Rousseeuw,
1990): partitioning and hierarchical algorithms. Partitioning algorithms construct a parti-
tion of a database D of n objects into a set of k clusters. The partitioning algorithms typically
start with an initial partition of D and then use an iterative control strategy to optimize an
objective function. Each cluster is represented by the gravity center of the cluster (k-means
algorithms) (MacQueen, 1967) or by one of the objects of the cluster located near its center
(k-medoid algorithms) (Vinod, 1969). Consequently, a partition is equivalent to a voronoi
diagram and each cluster is contained in one of the voronoi polygons. Thus, the shape of
all clusters found by a partitioning algorithm is convex (Kaufman and Rousseeuw, 1990),
which is very restrictive for many applications.
GDBSCAN: DENSITY-BASED CLUSTERING 171

Ng and Han (1994) explore partitioning algorithms for mining in spatial databases. An
algorithm called CLARANS (Clustering Large Applications based on RANdomized Search)
is introduced which is an improved k-medoid method restricting the huge search space us-
ing two additional user-supplied parameters. Compared to former k-medoid algorithms,
CLARANS is more effective and efficient. Our experimental evaluation indicates that the
runtime of a single call of CLARANS is close to quadratic (see Table 1, Section 5). Con-
sequently, it is possible to run CLARANS efficiently on databases of some thousands of
objects, but not for really large n. Methods to determine the “natural” number knat of clusters
in a database are also discussed in Ng and Han (1994). They propose to run CLARANS
once for each k from 2 to n. For each of the discovered clusterings the silhouette coefficient
(Kaufman and Rousseeuw, 1990) is calculated, and finally, the clustering with the maxi-
mum silhouette coefficient is chosen as the “natural” clustering. Obviously, this approach
is very expensive for large databases, because it implies O(n) calls of CLARANS.
Hierarchical algorithms create a hierarchical decomposition of a database D. The hi-
erarchical decomposition is represented by a dendrogram, a tree that iteratively splits D
into smaller subsets until each subset consists of only one object. In such a hierarchy, each
level of the tree represents a clustering of D. The dendrogram can either be created from
the leaves up to the root (agglomerative approach) or from the root down to the leaves
(divisive approach) by merging or dividing clusters at each step. In contrast to partitioning
algorithms, hierarchical algorithms do not need k as an input parameter. However, a ter-
mination condition has to be defined indicating when the merge or division process should
be terminated, e.g., the critical distance Dmin between all the clusters of D. Alternatively,
an appropriate level in the dendrogram has to be selected manually after the creation of the
whole dendrogram.
The single-link method is a commonly used agglomerative hierarchical clustering method.
Different algorithms for the single-link method have been suggested (e.g., Sibson, 1973;
Jain and Dubes, 1988; Hattori and Torii, 1993). Here we have only described the basic idea.
The single-link method starts with the disjoint clustering obtained by placing every object
in a unique cluster. In every step the two closest clusters in the current clustering are merged
until all points are in one cluster. The runtime of algorithms which construct the single-link
hierarchy depends on the technique for retrieving nearest neighbors. Without any spatial
index support (see Section 5.1 for a brief introduction into spatial access methods) for
nearest neighbor queries, the runtime complexity of single-link algorithms is O(n 2 ). This
runtime can be significantly improved when using multidimensional hash- or tree-based
index structures (see Murtagh, 1983).
Unfortunately, the runtime of most of the above algorithms is very high on large databases.
Therefore, some focusing techniques have been proposed to increase the efficiency of
clustering algorithms: (Ester et al., 1995) presents an R∗ -tree-based focusing technique
(1) creating a sample of the database that is drawn from each R∗ -tree data page and
(2) applying the clustering algorithm only to that sample.
In Zhang et al. (1997), compact descriptions of subclusters, i.e., Clustering Features (CF),
are incrementally computed containing the number of points, the linear sum and the square
sum of all points in the cluster. The CF-values are organized in a balanced tree. In the first
phase, BIRCH (Balanced Iterative Reducing and Clustering using Hierarchies) performs a
172 SANDER ET AL.

linear scan of all data points and builds a CF-tree, i.e., a balanced tree with branching factor
B and threshold T . A nonleaf node represents a cluster consisting of all the subclusters
represented by its entries. A leaf node has to contain at most L entries and the diameter
of each entry in a leaf node has to be less than T . A point is inserted by inserting the
corresponding CF-value into the closest leaf of the tree. If an entry in the leaf can absorb
the new point without violating the threshold condition, then the CF-values for this entry
are updated, otherwise a new entry in the leaf node is created. In an optional phase 2, the
CF-tree can be further reduced until a desired number of leaf nodes is reached. In phase 3,
an arbitrary clustering algorithm, e.g., CLARANS, is used to cluster the CF-values of the
leaf nodes of the CF-tree.
The efficiency of BIRCH is similar to the R∗ -tree-based focusing technique cited above.
Experiments with synthetic data sets show that the clustering quality using BIRCH in
combination with CLARANS is even higher than the quality obtained by using CLARANS
alone.

3. Density-connected sets

In Section 3.1, we present “density-connected sets” which are a significant generalization of

“density-based clusters” (see Ester et al., 1996), and indicate some important specializations
of density-connected sets in Section 3.2 illustrating the high expressiveness of this concept.
In the following, we assume a spatial database D to be a finite set of objects characterized
by spatial and nonspatial attributes. The spatial attributes may represent, e.g., points or
spatially extended objects such as polygons in some d-dimensional space S. The nonspatial
attributes of an object in D may represent additional properties of a spatial object, e.g., the
unemployment rate for a community represented by a polygon in a geographic information
system.

3.1. A generalized definition of density-based clusters

The key idea of a density-based cluster is that for each point of a cluster its Eps-neighborhood
for some given Eps > 0 has to contain at least a minimum number of points, i.e., the “density”
in the Eps-neighborhood of points has to exceed some threshold (Ester et al., 1996). This
idea is illustrated by the sample sets of points depicted in figure 1. In these examples, we
can easily and unambiguously detect clusters of points and noise points not belonging to
any of those clusters, mainly because we have a typical density of points inside the clusters
which is considerably higher than outside of the clusters. Furthermore, the density within
the areas of noise is lower than the density in any of the clusters.
This idea of “density-based clusters” can be generalized in two important ways. First, we
can use any notion of a neighborhood instead of an Eps-neighborhood if the definition of
the neighborhood is based on a binary predicate which is symmetric and reflexive. Second,
instead of simply counting the objects in a neighborhood of an object we can as well use
other measures to define the “cardinality” of that neighborhood.
GDBSCAN: DENSITY-BASED CLUSTERING 173

Figure 1. Sample databases.

Definition 1. (neighborhood of an object) Let NPred be a binary predicate on D which

is reflexive and symmetric, i.e., for all p, q ∈ D : NPred( p, p) and, if NPred( p, q) then
NPred(q, p). Then the NPred-neighborhood of an object o ∈ D is defined as NNPred (o) =
{o0 ∈ D | NPred(o, o0 )}.

The definition of a cluster in Ester et al. (1996) is restricted to the special case of a distance-
based neighborhood, i.e., NEps (o) = {o0 ∈ D | |o − o0 | ≤ Eps}. A distance-based neigh-
borhood is a natural notion of a neighborhood for point objects, but if clustering spatially
extended objects such as a set of polygons of largely differing sizes it may be more ap-
propriate to use neighborhood predicates like intersects or meets for finding clusters of
polygons.
Although in many applications the neighborhood predicate is defined by using only
spatial properties of the objects, the formalism is in no way restricted to purely spatial
neighborhoods. We can as well use nonspatial attributes and combine them with spatial
properties of objects to derive a neighborhood predicate (see Section 6.4).
Another way to take into account the nonspatial attributes of objects is as a kind of
“weight” when calculating the “cardinality” of the neighborhood of an object. To keep
things as simple as possible, let us not introduce a weight function operating on objects,
but a weighted cardinality function wCard for sets of objects. The “weight” of a single
object o can then be expressed by the weighted cardinality of the singleton containing o,
i.e., wCard({o}).

Definition 2. (MinWeight of a set of objects) Let wCard be a function from the powerset
of the Database D into the nonnegative Real Numbers, wCard : 2 D → <≥0 and MinCard
be a positive real number. Then, the predicate MinWeight for a set S of objects is defined
to be true iff wCard(S) ≥ MinCard.

The expression wCard(S) ≥ MinCard generalizes the condition |NEps (o)| ≥ MinPts in
the definition of density-based clusters where cardinality is just a special case of a wCard
function. There are numerous possibilities to define wCard(S) for subsets of the database
D. Simply summing up the values of some nonspatial attribute for the objects in S is another
example of a wCard function. For example, if we want to cluster objects represented by
polygons and if the size of the objects should be considered to influence the “density” in
174 SANDER ET AL.

the data space, then the area of the polygons could be used as a weight for these objects.
A further possibility is to sum up a value derived from several nonspatial attributes, e.g.,
by specifying ranges for some nonspatial attribute values of the objects (i.e., a selection
condition). We can realize the clustering of only a subset of the database D by attaching
a weight of 1 to objects that satisfy the selection condition and a weight of 0 to all other
objects. Note that by using nonspatial attributes as a weight for objects one can “induce”
different densities, even if the objects are equally distributed in the space of the spatial
attributes. Also note that by means of the wCard function the combination of a clustering
with a selection on the database is possible, i.e., performing a selection “on the fly” while
clustering the database. This may be more efficient than performing the selection first
under certain circumstances because GDBSCAN can use existing spatial index structures
(see Section 5.1).
We can now define density-connected sets,analogously to the definition of density-based
clusters in Ester et al. (1996), in a straightforward way (see also Ester et al., 1997).
A naive approach could require for each object in a density-connected set that the weighted
cardinality of the NPred-neighborhood of that object has at least a value MinCard. However,
this approach fails because there may be two kinds of objects in a density-connected set,
objects inside (core object) and objects “on the border” of the density-connected set (border
objects). In general, an NPred-neighborhood of a border object has a significantly lower
wCard than an NPred-neighborhood of a core object. Therefore, we would have to set
the value MinCard to a relatively low value in order to include all objects belonging to the
same density-connected set. This value, however, will not be characteristic for the respective
density-connected set—particularly in the presence of noise objects. Therefore, for every
object p in a density-connected set C there must be an object q in C so that p is inside of
the NPred-neighborhood of q and the weighted cardinality wCard of NPred(q) is at least
MinCard. We also require the objects of the set C to be somehow “connected” to each other.
This idea is elaborated in the following definitions and illustrated by 2D point objects, using
a distance-based neighborhood for the points, and cardinality as wCard function.

Definition 3. (directly density-reachable) An object p is directly density-reachable from

an object q with respect to NPred, MinWeight if
(1) p ∈ NNPred (q) and
(2) MinWeight(NNPred (q)) = true (core object condition).

Obviously, directly density-reachable is symmetric for pairs of core objects. In general,

however, it is not symmetric if one core object and one border object are involved. Figure 2
shows the asymmetric case.

Figure 2. Core objects and border objects.

GDBSCAN: DENSITY-BASED CLUSTERING 175

Figure 3. Density-reachability and density-connectivity.

Definition 4. (density-reachable) An object p is density-reachable from an object q with

respect to NPred and MinWeight if there is a chain of objects p1 , . . . , pn , p1 = q, pn = p
such that for all i = 1, . . . , n − 1 : pi+1 is directly density-reachable from pi with respect
to NPred and MinWeight.

Density-reachability is a canonical extension of direct density-reachability. This relation

is transitive, but it is not symmetric. Figure 3 depicts the relations of some sample objects
and, in particular, the asymmetric case. Although not symmetric in general, it is obvious
that density-reachability is symmetric for core objects because a chain from q to p can be
reversed if also p is a core object.
Two border objects of the same density-connected set C are possibly not density-reachable
from each other because the core objects condition might not hold for both of them. How-
ever, for a density-connected set C we require that there must be a core object in C from
which both border objects are density-reachable. Therefore, we introduce the notion of
density-connectivity which covers this relation of border objects.

Definition 5. (density-connected) An object p is density-connected to an object q with

respect to NPred, MinWeight if there is an object o such that both, p and q are density-
reachable from o with respect to NPred, MinWeight.

Density-connectivity is a symmetric relation. For density-reachable objects, the relation

of density-connectivity is also reflexive (cf. figure 3).

Now, a density-connected set is defined to be a set of density-connected objects which is

maximal with respect to density-reachability.

Definition 6. (density-connected set) A density-connected set C with respect to NPred,

MinWeight in D is a nonempty subset of D satisfying the following conditions:

(1) Maximality: For all p, q ∈ D: if p ∈ C and q is density-reachable from p with respect

to NPred, MinWeight, then q ∈ C.
(2) Connectivity: For all p, q ∈ C: p is density-connected to q with respect to NPred,
MinWeight.

Note that a density-connected set C with respect to NPred and MinWeight contains at
least one core object: since C contains at least one object p, p must be density-connected
to itself via some object o (which may be equal to p). Thus, at least o has to satisfy the core
object condition. Consequently, the NPred-Neighborhood of o has to satisfy MinWeight.
176 SANDER ET AL.

The following lemmas are important for validating the correctness of our clustering
algorithm. Intuitively, they state the following. Given NPred and MinWeight, we can discover
a density-connected set in a two-step approach. First, choose an arbitrary object from the
database satisfying the core object condition as a seed. Second, retrieve all objects that are
density-reachable from the seed obtaining the density-connected set containing the seed.

Lemma 1. Let p be an object in D and MinWeight(NNPred ( p)) = true. Then the set
O = {o ∈ D | o is density-reachable from p with respect to NPred, MinWeight} is a density-
connected set with respect to NPred, MinWeight.

Proof:

(1) O is nonempty: p is a core object by assumption. Therefore p is density-reachable

from p. Then p is in O.
(2) Maximality: Let q1 ∈ O and q2 be density-reachable from q1 with respect to NPred,
MinWeight. Since q1 is density-reachable from p and density-reachability is transitive
with respect to NPred, MinWeight, it follows that q2 is also density-reachable from p
with respect to NPred, MinWeight. Hence, q2 ∈ O.
(3) Connectivity: All objects in O are density-connected via object p. 2

Furthermore, a density-connected set C with respect to NPred, MinWeight is uniquely

determined by any of its core objects, i.e., each object in C is density-reachable from any of
the core objects of C and, therefore, a density-connected set C contains exactly the objects
which are density-reachable from an arbitrary core object of C.

Lemma 2. Let C be a density-connected set with respect to NPred, MinWeight and let p be
any object in C with MinWeight (NNPred ( p)) = true. Then C equals to the set O = {o ∈ D | o
is density-reachable from p with respect to NPred, MinWeight}.

Proof:

(1) O ⊆ C by definition of O.
(2) C ⊆ O: Let q ∈ C. Since also p ∈ C and C is a density-connected set, there is an
object o ∈ C such that p and q are density-connected via o, i.e., both p and q are
density-reachable from o. Because both p and o are core objects, it follows that also o
is density-reachable from p (symmetry for core objects). With transitivity of density-
reachability with respect to NPred, MinWeight it follows that q is density-reachable
from p. Then q ∈ O. 2

Let us now define a clustering CL of a database D with respect to NPred and MinWeight
as the set of all density-connected sets with respect to NPred and MinWeight in D, i.e., all
clusters from a clustering CL are density-connected sets with regard to the same “parame-
ters” NPred and MinWeight. Noise will then be defined relative to a given clustering CL of
D, simply as the set of objects in D not belonging to any of the clusters of CL.
GDBSCAN: DENSITY-BASED CLUSTERING 177

Figure 4. Overlap of two clustures for MinCard = 4.

Definition 7. (clustering) A clustering CL of D with respect to NPred, MinWeight is a set

of density-connected sets with respect to NPred, MinWeight in D, CL = {C1 , . . . , Ck }, such
that for all C the following holds: if C is a density-connected set with respect to NPred,
MinWeight in D, then C ∈ CL.

Definition 8. (noise) Let CL = {C1 , . . . , Ck } be a clustering of the database D with respect

to NPred, MinWeight. Then we define the noise in D as the set of objects in the database
D not belonging to any density-connected set Ci , i.e., noiseCL = D\(C1 ∪ · · · ∪ Ck ).

There are other possibilities to define a clustering based on Definition 6. But this simple
notion of a clustering has the nice property that two clusters can at most overlap in objects
which are border objects in both clusters. Figure 4 illustrates the overlap of two clusters
using cardinality and MinCard = 4.

Lemma 3. Let CL be a clustering of D with respect to NPred, MinWeight. If C1 , C2 ∈ CL

and C1 6= C2 , then for all p ∈ C1 ∩ C2 it holds that p is not a core object, i.e.,
wCard(NPred( p)) < MinCard.

Proof: Since NPred and MinWeight are the same for all clusters in CL it follows that if
p ∈ C1 ∩ C2 would be a core object for C1 , then p would also be a core object for C2 . But
then it follows from Lemma 2 that C1 = C2 , in contradiction to the assumption. Hence, p
is not a core object. 2

3.2. Important specializations

The first specialization of a density-connected set obviously is a density-based cluster as

defined in Ester et al. (1996):

• NPred: “distance ≤ Eps”, wCard: cardinality, MinWeight(N ): |N | ≥ MinPts. Special-

izing this instance further yields a description of a level in the single-link hierarchy
determined by a “critical distance” Dmin = Eps (Sibson, 1973):
• NPred: “distance ≤ NN-dist ”, wCard: cardinality, MinWeight(N ): |N | ≥ 2, every point
p in the set noiseCL must be considered as a single cluster.
178 SANDER ET AL.

Figure 5. Different specializations of density-connected sets.

Note that if cardinality is used and MinCard ≤ 3 there exists no overlap between the
clusters of a clustering CL. But then, the well-known “single-link effect ” can occur, i.e.,
if there is a chain of points between two clusters where the distance of each point in the
chain to the neighboring point in the chain is less than Eps then the two clusters will not
be separated. Higher values for MinCard will significantly weaken this effect and even
for regular distributions where the k-distance values may not differ from the 1-distance
values for almost all points, a clustering according to Definitions 7 and 8, in general, is not
equivalent to a level in the single-link hierarchy.
A further specialization of density-connected sets allows the clustering of spatially ex-
tended objects such as polygons:

• NPred: “intersects” or “meets”, wCard: sum of areas, MinWeight(N ): sum of areas

≥ MinArea

There are also specializations equivalent to simple forms of region growing (Niemann,
1990), i.e., only local criteria for expanding a region can be defined by the weighted cardinal-
ity function. For instance, the neighborhood may be simply given by the neighboring cells
in a grid and the weighted cardinality function may be some aggregation of the nonspatial
attribute values.

• NPred: “neighbor ”, MinWeight(N ): aggr(nonspatial values) ≥ threshold

While region growing algorithms are highly specialized to pixels, density-connected
sets can be defined for any data types.

Figure 5 illustrates some specializations of density-connected sets.

4. GDBSCAN: Generalized density-based spatial clustering

of applications with noise

In Section 4.1, we present the algorithm GDBSCAN (Generalized Density Based Spatial
Clustering of Applications with Noise) which is designed to discover the density-connected
sets and the noise in a spatial database. To apply the algorithm, we have to know the NPred-
neighborhood, MinCard and the wCard function. In Section 4.2, the issue of determining
these “parameters” is discussed and a simple and effective heuristic to determine Eps and
MinCard for Eps-neighborhoods combined with cardinality as wCard function is presented.
GDBSCAN: DENSITY-BASED CLUSTERING 179

Figure 6. Algorithm GDBSCAN.

4.1. The algorithm

To find a density-connected set, GDBSCAN starts with an arbitrary object p and retrieves
all objects density-reachable from p with respect to NPred and MinWeight. If p is a core
object, this procedure yields a density-connected set with respect to NPred and MinWeight
(see Lemmas 1 and 2). If p is not a core object, no objects are density-reachable from p,
and p is assigned to NOISE. This procedure is iteratively applied to each object p which
has not yet been classified. Thus, a clustering and the noise according to Definitions 7 and
8 are detected.
In figure 6, we present a basic version of GDBSCAN omitting details of data types and
generation of additional information about clusters.
SetOfObjects is either the whole database or a discovered cluster from a previous run.
NPred and MinCard are the global density parameters and wCard is a pointer to a function
wCard(Objects) that returns the weighted cardinality of the set Objects. ClusterIds are from
an ordered and countable datatype (e.g., implemented by Integers) where UNCLASSIFIED
< NOISE < “other Ids”, and each object is marked with a ClusterId Object.ClId. The func-
tion nextId(ClusterId) returns the successor of ClusterId in the ordering of the datatype (e.g.,
implemented as Id := Id + 1). The function SetOfObjects.get(i) returns the ith element of
SetOfObjects. In figure 7, function ExpandCluster constructing a density-connected set for
a core object Object is presented in more detail.
A call of SetOfObjects.neighborhood(Object, NPred) returns the NPred-neighborhood
of Object in SetOfPoints as a list of objects. Obviously the efficiency of the above algorithm
depends on the efficiency of the neighborhood query because such a query is performed
exactly once for each object in SetOfObjects which satisfies the selection condition. The
performance of GDBSCAN is discussed in detail in Section 5, where we see that neighbor-
hood predicates based on spatial proximity like distance predicates or intersection can be
evaluated very efficiently by using spatial index structures.
The ClusterId of some objects p are to be marked NOISE because wCard(NPred( p)) <
MinCard may be changed later if they are density-reachable from some other object of the
180 SANDER ET AL.

Figure 7. Function ExpandCluster.

database. This may happen only for border objects of a cluster. Those objects are then not
added to the seeds-list because we already know that an object with a ClusterId of NOISE
is not a core object, i.e., no other objects are density-reachable from them.
If two clusters C1 and C2 are very close to each other, it might happen that some object
p belongs to both C1 and C2 . Then p must be a border object in both clusters according to
Lemma 3. In this case, object p will only be assigned to the cluster discovered first. Except
from these rare situations, the result of GDBSCAN is independent of the order in which the
objects of the database are visited due to Lemmas 1 and 2.
There may be reasons to apply a postprocessing to the clustering obtained by GDBSCAN.
According to Definition 7, each set of objects having MinWeight is a density-connected
set. In some applications (see, e.g., Section 6.1), however, density-connected sets of
GDBSCAN: DENSITY-BASED CLUSTERING 181

this minimum size are too small to be accepted as clusters. Furthermore, GDBSCAN
produces clusters and noise. But for some applications a non-noise class label for each object
is required. For this purpose, we can reassign each noise object and each object of a rejected
cluster to the closest of the accepted clusters. This postprocessing requires just a simple
scan over the whole database without much computation, in particular, no region queries
are necessary. Therefore, such postprocessing does not increase the runtime complexity of
GDBSCAN.
To conclude this section, we introduce the algorithm DBSCAN (Ester et al., 1996) as an
important specialization of GDBSCAN.

Definition 9. (DBSCAN) DBSCAN is a specialization of the algorithm GDBSCAN using

the following parameters: NPred: “distance ≤ Eps”, wCard: cardinality, MinWeight(N ):
|N | ≥ MinCarol.

4.2. Determining the parameters for GDBSCAN

GDBSCAN requires a neighborhood predicate NPred, a weight function wCard and a

minimum weight MinCard. The concrete parameters we are going to use, depends on the
goal of the application. In some applications there may be a natural way to provide values
without any further parameter determination. In other cases, we may only know the type of
neighborhood that we want to use, e.g., a distance-based neighborhood for the clustering
of point objects. In these cases we have to use a heuristic to determine the appropriate
parameters.
In this section, we present a simple heuristic which is effective in many cases to determine
the parameters Eps and MinCard for DBSCAN (cf. Definition 9), which is the most impor-
tant specialization of GDBSCAN. DBSCAN uses a distance-based neighborhood “distance
less or equal than Eps” and cardinality as the wCard function. Thus, we have to determine
appropriate values for Eps and MinCard. The density parameters of the “thinnest”, i.e.,
least dense, cluster in the database are good candidates for these global values specifying
the lowest density, which is not considered to be noise.
For a given k ≥ 1 we define a function k-distance, mapping each object to the distance
from its kth nearest neighbor. When sorting the objects of the database in descending order
of their k-distance values, the plot of this function gives some hints concerning the density
distribution in the database. We call this plot the sorted k-distance plot (see, e.g., figure 8).
If we choose an arbitrary object p, set the parameter Eps to k-distance( p) and set the
parameter MinCard to k + 1, all objects with an equal or smaller k-distance value will be
core objects, because there are at least k + 1 objects in an Eps-neighborhood of an object
p if Eps is set to k-distance( p). If we can now find a threshold object with the maximum
k-distance value in the “thinnest” cluster of D, we would obtain the desired parameter
values. Therefore, we have to answer the following questions. (1) Which value of k is
appropriate? (2) How can we determine a threshold object p?
Let us discuss the value k first, assuming it is possible to set the appropriate value for Eps.
The smaller we choose the value for k, the lower are the computational costs to calculate the
k-distance values and the smaller is the corresponding value for Eps in general. But a small
change of k for an object p, in general, only results in a small change of k-distance( p).
182 SANDER ET AL.

Figure 8. Sorted 3-distance plot for sample database 3.

Furthermore, our experiments indicate that the k-distance plots for “reasonable” k (e.g.,
1 ≤ k ≤ 10 in 2D space) do not significantly differ in shape and that also the results of
DBSCAN for the corresponding parameter pairs (k, Eps) do not differ very much. Therefore,
the choice of k is not very crucial for the algorithm. We can even fix the value for k
(with respect to the dimension of the dataspace), eliminating the parameter MinCard for
DBSCAN. Considering only the computational cost, we would like to set k as small as
possible. On the other hand, if we set k = 1, the k-distance value for an object p will be
the distance to the nearest neighbor of p and the “single-link effect” can occur. To weaken
this effect, we must choose a value for k > 1.
We propose to set k to 2∗ dimension − 1. Our experiments indicate that this value works
well for databases D where each point occurs only once, i.e., if D is really a set of points.
Thus in the following, if not stated otherwise, k is set to this value, and the value for MinCard
is fixed according to the above strategy (MinCard = k + 1, e.g., MinCard = 4 in 2D space).
To determine the parameter Eps for DBSCAN, we have to know an object in the “thinnest”
cluster of the database with a high k-distance value for that cluster. Figure 8 shows a
sorted k-distance plot for sample database 3 which is very typical for databases where the
density of clusters and noise are significantly different. Our experiments indicate that the
threshold object is an object near the first “valley” of the sorted k-distance plot (see figure 8).
All objects with a higher k-distance value (to the left of the threshold) will then be noise,
all other objects (to the right of the threshold) will be assigned to some cluster.
In general, it is very difficult to detect the first “valley” automatically, but it is relatively
simple for a user to recognize this valley in a graphical representation. Additionally, if
the user can estimate the percentage x of noise, a proposal for the threshold object can be
derived, because we know that most of the noise objects have a higher k-distance value
than objects of clusters. The k-distance values of noise objects are located on the left of
the k-distance plot, so that we can simply select an object after x percent of the sorted
k-distance plot.
There is always a range of values for the parameter Eps that yield the same clustering
because not all objects of the “thinnest” cluster need to be core objects. They may also
belong to the cluster if they are only density-reachable. Furthermore, the Eps value may be
larger than needed if the clusters are well separated and the density of noise is clearly lower
than the density of the thinnest cluster. Thus, the robustness of the parameter determination,
GDBSCAN: DENSITY-BASED CLUSTERING 183

i.e., the width of the range of appropriate Eps values, depends on the application. How-
ever, in general, the width of this range is broad enough to allow the parameters to be
determined in a sorted k-distance plot for only a very small sample of the whole database
(1–10%).
To summarize, we propose the following interactive approach for determining the pa-
rameters for DBSCAN.

• The user gives a value for k (default is k = 2∗ dimension − 1).

• The system computes and displays the k-distance plot for a sample of the database.
• The user selects an object as the threshold object and the k-distance value of this object
is used as the Eps value; MinCard is set to k + 1 (if the user can estimate the percentage
of noise, the system can derive a proposal for the threshold object from it).

Obviously, the shape of the sorted k-distance plot and hence the effectiveness of the
proposed heuristic depends on the distribution of the k-nearest neighbor distances. For
example, the plot looks more “stairs-like” if the objects are distributed more regularly
within each cluster, or the first “valley” is less clear if the densities of the clusters differ not
much from the density of noise (which also means that the clusters are not well separated).
Then, knowing the approximate percentage of noise in the data may be very helpful.
Although for some applications it may be difficult to determine the correct parameters,
we want to point out that the parameters may be reused in different but similar applications,
e.g., if the different datasets are produced by a similar process. We see in Section 6 that there
are even applications where the appropriate parameter values for GDBSCAN can be derived
analytically (e.g., Section 6.2), or a natural notion of a neighborhood for the application
exists, which does not require any further parameters (e.g., intersects for polygons).

5. Performance evaluation

In this section, we evaluate the performance of GDBSCAN. In Section 5.1, we discuss

the performance of GDBSCAN with respect to the underlying spatial index structure. In
Section 5.2, an experimental evaluation of DBSCAN and a comparison with the well-known
clustering algorithms CLARANS and BIRCH is presented.

5.1. Analytical evaluation

The runtime of GDBSCAN obviously is O(n ∗ runtime of a neighborhood query): n

objects are visited and exactly one neighborhood query is performed for each of them.
The number of neighborhood queries cannot be reduced since a ClusterId for each object
is required. Thus, the overall runtime depends on the performance of the neighborhood
query. Fortunately, the most interesting neighborhood predicates are based on spatial
proximity—like distance predicates or intersection—which can be efficiently supported by
spatial index structures. Such index structures are assumed to be available in a SDBS for
efficient processing of several types of spatial queries (Brinkhoff et al., 1994).
In the following, we introduce a typical spatial index, the R∗ -tree (Beckmann et al.,
1990). The R ∗ -tree (see figure 9) generalizes the one-dimensional B-tree to d-dimensional
184 SANDER ET AL.

Table 1. Runtime complexity of GDBSCAN.

Runtime complexity of A single neighborhood query The GDBSCAN algorithm

Without index O(n) O(n 2 )

With spatial index O(log n) O(n ∗ log n)
With direct access O(1) O(n)

Figure 9. Structure of an R∗ -tree.

data spaces, specifically an R∗ -tree manages k-dimensional hyperrectangles instead of

one-dimensional keys. An R∗ -tree may organize extended objects such as polygons us-
ing minimum bounding rectangles (MBR) as approximations as well as point objects as a
special case of rectangles. The leaves store the MBRs of the data objects and a pointer to
the exact geometry of the polygons. Internal nodes store a sequence of pairs consisting of
a rectangle and a pointer to a child node. These rectangles are the MBRs of all data or
directory rectangles stored in the subtree having the referenced child node as its root. To
answer a region query, starting from the root, the set of rectangles intersecting the query
region is determined and then their referenced child nodes are searched until the data pages
are reached.
The height of an R∗ -tree is O(log n) for a database of n objects in the worst case and
a query with a “small” query region has to traverse only a limited number of paths in the
R∗ - tree. Since most NPred-neighborhoods are expected to be small compared to the size
of the whole database, the average runtime complexity of a single neighborhood query is
O(log n).
Table 1 lists the runtime complexity of GDBSCAN with respect to the underlying spatial
index structure. Without any index support, the runtime of GDBSCAN is O(n 2 ). This does
not scale well with the size of the database. But, if we use a spatial index, the runtime is
reduced to O(n log n). If we have a direct access to the NPred-neighborhood, e.g., if the
objects are organized in a grid, the runtime is further reduced to O(n).

5.2. Experimental evaluation

We have implemented GDBSCAN in C++ based on an implementation of the R∗ -tree

(Beckmann et al., 1990). All experiments were run on HP 735/100 workstations. In order
GDBSCAN: DENSITY-BASED CLUSTERING 185

Figure 10. Clusterings discovered by CLARANS.

to allow a comparison with CLARANS and BIRCH—both use a distance-based neighbor-

hood definition—we evaluated the specialized DBSCAN algorithm (cf. Definition 9). For
an evaluation of the effectivity of the more general GDBSCAN, see the applications in
Section 6.
To compare DBSCAN with CLARANS in terms of effectiveness (accuracy), we use
the three synthetic sample databases which are depicted in figure 1. Since DBSCAN and
CLARANS are clustering algorithms of different types, they have no common quantitative
measure of the classification accuracy. Therefore, we evaluate the accuracy of both algo-
rithms by visual inspection. In sample database 1, there are four ball-shaped clusters of
significantly differing sizes. Sample database 2 contains four clusters of nonconvex shape.
In sample database 3, there are four clusters of different shape and size with additional
noise. To show the results of both clustering algorithms, we visualize each cluster by a
different color. To give CLARANS some advantage, we set the parameter k (number of
clusters) to 4 for these sample databases. The clusterings discovered by CLARANS are
depicted in figure 10.
For DBSCAN, the parameter Eps was set, giving a noise percentage of 0% for sample
databases 1 and 2, and 10% for sample database 3, respectively. The clusterings discovered
by DBSCAN are depicted in figure 11.
DBSCAN discovers all clusters (according to Definition 7) and detects the noise points
(according to Definition 8) from all sample databases. CLARANS, however, splits clusters
if they are relatively large or if they are close to some other cluster. Furthermore, CLARANS
has no explicit notion of noise. Instead, all points are assigned to their closest medoid.
To test the efficiency of DBSCAN and CLARANS, we use the SEQUOIA 2000 bench-
mark data. The SEQUOIA 2000 benchmark database (Stonebraker et al., 1993) uses real
data sets that are typical for Earth Science tasks. There are four types of data in the
database: raster data, point data, polygon data and directed graph data. The point data
set contains 62,584 Californian names of landmarks, extracted from the US Geological
Survey’s Geographic Names Information System, together with their location. The point
data set occupies about 2.1 MB. Since the runtime of CLARANS on the whole data set is
very high, we have extracted a series of subsets of the SEQUIOA 2000 point data set con-
taining 2–20% representatives of the whole set. The runtime comparison of DBSCAN and
CLARANS on these databases is shown in Table 2. The results of our experiments show
186 SANDER ET AL.

Table 2. Comparison of runtime (s).

Number of points 1252 2503 3910 5213 6256 7820 8937 10426 12512 62584

DBSCAN 3 7 11 16 18 25 28 33 42 233
CLARANS 758 3,026 6,845 11,745 18,029 29,826 39,265 60,540 80,638 ???

Figure 11. Clusterings discovered by DBSCAN.

that the runtime of DBSCAN is almost linear to the number of points. The runtime of
CLARANS, however, is close to quadratic to the number of points. The results show that
DBSCAN outperforms CLARANS by a factor of between 250 and 1,900 which grows with
increasing size of the database.
Since we found it rather difficult to set the parameters of BIRCH appropriately for the
SEQUIOA 2000 point data, we used the test data sets 1, 2 and 3 introduced by Zhang et al.
(1997) to compare DBSCAN with BIRCH. The used implementation of BIRCH—using
CLARANS in phase 3—was provided by its authors. The runtime of DBSCAN was 1.8, 1.8
and 12.0 times the runtime of BIRCH. Note, however, that in general the same restrictions
with respect to clusters of arbitrary shape apply to BIRCH as they apply to CLARANS.
Furthermore, the clustering features—on which BIRCH is based—can be only defined in a
Euclidean vector space implying a limited applicability of BIRCH compared to DBSCAN
(and compared to CLARANS).

6. Applications

In this section, we present four typical applications of GDBSCAN. In the first application
we cluster a spectral space (5D points) created from satellite images in different spectral
channels which is a common task in remote sensing image analysis. The second application
comes from molecular biology. The points on a protein surface (3D points) are clustered
to extract regions with special properties. To find such regions is a subtask for the problem
of protein-protein docking. The third application uses astronomical image data (2D points)
showing the intensity on the sky at different radio wavelengths. The task of clustering is to
detect celestial sources from these images. The last application is the detection of spatial
trends in a geographic information system. GDBSCAN is used to cluster 2D polygons
creating so-called influence regions which are used as input for trend detection.
GDBSCAN: DENSITY-BASED CLUSTERING 187

Figure 12. Relation between 2D image and feature space.

6.1. Application 1: earth science (5D points)

In this application, we use a five-dimensional feature space obtained from several satellite
images of a region on the surface of the earth covering California. These images are taken
from the raster data of the SEQUOIA 2000 Storage Benchmark. After some preprocessing,
five images containing 1,024,000 intensity values (8 bit pixels) for five different spectral
channels for the same region were combined. Thus, each point on the surface, corresponding
to an earth surface area of 1,000 × 1,000 m, is represented by a five-dimensional vector.
Finding clusters in such feature spaces is a common task in remote sensing digital image
analysis (e.g., Richards, 1983) for the creation of thematic maps in geographic information
systems. The assumption is that feature vectors for points of the same type of underground on
the earth are forming groups in the high-dimensional feature space (see figure 12 illustrating
the case of 2D raster images).
Application 1 has two characteristics that were not present in the synthetic databases used
in Section 5.2. First, the coordinates of points can only be integer values between 0 and
255 in each dimension. Second, many of the raster points have exactly the same features,
i.e., are represented by the same five-dimensional feature vector. Only about 600,000 of
the 1,024,000 feature vectors are different from each other.
We used “distance(X, Y ) < 1.42” as NPred(X, Y ). The neighborhoods are very small
due to the first characteristic of the application, e.g., for about 15% of the points the distance
to the ninth nearest neighbor is 0. We used cardinality as wCard function and set MinCard
to 20 to take into account the second characteristic of the data.
There are several reasons to apply a postprocessing to improve the clustering result of
GDBSCAN. First, GDBSCAN only ensures that a cluster contains at least MinCard points
(using cardinality as wCard function), but a minimum size of 20 points is too small for
this application, especially because many points have the same coordinates. Therefore, we
accepted only the clusters containing more than 200 points. This value seems arbitrary but
a minimum size can be chosen reasonably after the size of all clusters is known. Second,
GDBSCAN produces clusters and noise. But for this application a non-noise class label for
188 SANDER ET AL.

Figure 13. Visualization of the clustering result for the SEQUIOA 2000 raster data.

each raster point is required. Therefore, we reassigned each noise point and each point of
a rejected cluster to the closest of the accepted clusters. We obtained 9 clusters with sizes
ranging from 598,863 to 2,016 points.
To visualize the result, each cluster was coded by a different color. Then each point
in the image of the surface of the earth was colored according to the identificator of the
cluster containing the corresponding five-dimensional vector. The resulting image is shown
in figure 13. A high degree of correspondence between the obtained image and a physical
map of California can easily be seen. A detailed discussion of this correspondence is beyond
the scope of this paper.

6.2. Application 2: molecular biology (3D points)

Proteins are biomolecules consisting of some hundreds to thousands of atoms. Their mode
of operation lies in the interaction with other biomolecules, e.g., proteins, DNA or smaller
partner molecules. These interactions are performed by the so-called docking, i.e., the
process of connecting the partner molecules.
Molecular biologists point out that the geometry of the molecular surfaces at the interac-
tion site plays an important role along with the physicochemical properties of the molecules.
A necessary condition for protein-protein docking is the complementarity of the interaction
site with respect to surface shape, electrostatic potential, hydrophobicity, etc. We use the
crystallographically determined atom coordinates of proteins and protein complexes from
the Brookhaven Protein Data Bank (Bernstein et al., 1977, Protein Data Bank, 1994) and
derive for each protein a surface with some 10,000 equally distributed 3D points. For each
point on the protein surface, several geometric and physicochemical features are computed.
GDBSCAN: DENSITY-BASED CLUSTERING 189

The solid angle (SA), for example, (Connolly, 1986) is a geometric feature describing the
degree of convexity or concavity of the surface in the neighborhood of the considered point.
A database system for protein-protein docking has to process queries for proteins with
complementary surfaces. This search is performed at the level of surface segments, defined
as a set of neighboring surface points with similar nonspatial attributes, e.g., with similar
SA values. The segments should have a good correlation with the known docking sites of
the proteins, i.e., a docking site on a protein surface should consist of a small number of
segments. Therefore, finding a segmentation of protein surfaces is an important subtask for
a protein docking DB. We applied GDBSCAN for this task.
We used a wCard function performing a simple selection on the SA values. The SA values
are normalized in the interval [0, 1], such that high SA values indicate points on a convex and
low SA values indicate points on a concave surface segment. To find the convex segments,
we defined wCard(S) as the number of points in S with SA value between 0.75 and 1.00.
As the selection criterion for points on a concave surface segment, we used SA values
between 0.00 and 0.65. The parameters NPred and MinCard were determined analytically.
Since the surface points are equally distributed with a density of 5 points per Å2 , we used
“distance(X, Y ) < 0.6” as NPred(X, Y ) and set MinCard = 5. Note that if we would use
these parameters together with cardinality, only a single cluster containing all points of the
protein surface would be found. In applications with equally distributed points GDBSCAN
can only find reasonable clusters if the wCard function is defined appropriately, i.e., the
wCard function must “simulate” regions of different density. We searched for clusters
covering at least 1% of the surface points of the protein. For example, for the protein
133DA consisting of 5,033 surface points, only clusters with a minimum size of 50 surface
points were accepted. In this case 8 convex and 4 concave clusters (segments) were found by
using the above parameter settings. Figure 14 depicts the clustering results of GDBSCAN
for this protein. Note that some of the clusters are hidden in the visualization. GDBSCAN
discovered the most significant convex and concave surface segments of the protein, which
can easily be verified by visual inspection.

Figure 14. Visualization of the clustering results for protein 133DA.

190 SANDER ET AL.

6.3. Application 3: astronomy (2D points)

Surveys of the sky form an integral part of astronomy. Celestial sources detected in a survey
are typically classified by the domain scientists; large surveys detect many objects and
enable statistical studies of the objects in a given classification. Surveys may also reveal
exotic or anomalous objects or previously unidentified classes of objects. A typical result
of a survey is a two-dimensional grid of the intensity on the sky. The measured intensity
is typically the sum of the emission from discrete sources, diffuse emission (e.g., from the
atmosphere, interplanetary medium or interstellar medium), and noise contributed by the
surveying instrument itself. Modern surveys are capable of producing thousands of images
of the sky, consuming 10 GB–1 TB of storage space, and may contain 105 to 106 or more
sources, e.g., (Reid et al., 1991; Becker et al., 1995).
Maximizing the yield from a survey requires an accurate yet efficient method of detecting
sources. The traditional method of separating the discrete sources from the noise and other
emissions is to require that the sources exceed a predefined threshold, e.g., 5σ , where σ is
an estimate of the rms intensity in the image, e.g. (Becker et al. 1995). Recently, alternate
methods, which utilize the expected statistics of the intensity (Zepka et al., 1994) or classifier
systems (Weir et al., 1995), have been deployed.
An extreme example of a noisy image is shown on the left side of figure 16. The image
shows the intensity, as measured by the Very Large Array, in a direction towards the Galactic
center at a radio wavelength of 4,865 MHz. The image is dominated by a celestial source
near the center, and the sidelobes which appear as radial spokes and are produced by the
optics of the instrument. A second image of the same area at a slightly different wavelength
was also given for this application. Because of its similarity to the first image, it is not
depicted. The intensity values in the images range from −0.003084 to 0.040023 and from
−0.003952 to 0.040509, respectively. We applied GDBSCAN using the same parameter
settings for both images:

• NPred(X, Y ) is “distance(X, Y ) < 1.42”, i.e., the neighborhood of a raster point is a 3 × 3

array of points.
• wCard calculates the sum of the weights of all 9 points of the neighborhood weighting
each point by its intensity value.
• MinCard = 0.045 (i.e., the average intensity required for points in clusters = 0.005).

The resulting clusterings for both images are given in figure 15. For example, the brightest
celestial source can easily be identified as the cluster in the center.
For the other clusters it is not so easy to verify that they are in fact celestial sources. The
only way to confirm a weak source is to detect it again in different images, e.g., if it can
be detected again by looking at it at slightly different frequencies. A source is required
to appear at the same position, may be with a shift of a pixel or two, at all frequencies.
Therefore, we extracted only the clusters which are present in both images, there are 20 of
them. The result of this procedure is depicted on the right side of figure 16.
GDBSCAN: DENSITY-BASED CLUSTERING 191

Figure 15. Clustering results for both images.

Figure 16. Visualization of the astronomy data and the potential sources found by DBSCAN.

6.4. Application 4: geography (2D polygons)

In the following, we present a simple method for detecting spatial trends based on
GDBSCAN. GDBSCAN is used to extract density-connected sets of neighboring objects
having a similar value of the nonspatial attribute(s). To define the similarity on an attribute,
we partition its domain into a number of disjoint classes and consider the values in the
same class as similar to each other. The sets with the highest or lowest attribute value(s)
are most interesting and are called influence regions, i.e., the maximal neighborhood of a
center having a similar value in the nonspatial attribute(s) as the center itself. Then, the
resulting influence region is compared to the circular region representing the theoretical
trend to obtain a possible deviation. Different methods may be used for this comparison.
A difference-based method calculates the difference of both, the observed influence region
192 SANDER ET AL.

Figure 17. Approximating ellipsoid of the influence region of Ingolstadt.

Figure 18. Difference between the observed and the theoretical influence region of Munich.

and the theoretical circular region, thus returning some region indicating the location of a
possible deviation. An approximation-based method calculates the optimal approximating
ellipsoid of the observed influence region. If the two main axes of the ellipsoid differ in
length significantly, then the longer one is returned indicating the direction of a deviation.
GDBSCAN can be used to extract the influence regions from an SDBS. We define NPred
(X, Y ) as “intersect(X, Y ) ∧ attr-class(X ) = attr-class (Y )” and use cardinality as wCard
function. Furthermore, we set MinCard to 2 in order to exclude sets of less than 2 objects.
To illustrate the results of this approach, we discuss some typical influence regions ob-
tained by GDBSCAN. The influence region of Ingolstadt is elongated indicating a deviation
in west-east direction caused by the river Danube traversing Ingolstadt in this direction. Fig-
ure 17 shows the approximating ellipsoid and the significantly longer main axis in west-east
direction.
The influence region of Munich has four significant deviations from the theoretical region
(NE, SW, S and SE). Figure 18 illustrates the difference between the observed influence re-
gion and the theoretical circular region. These areas coincide with the highways originating
from Munich.

7. Conclusions

In this paper, we presented the clustering algorithm GDBSCAN generalizing the density-
based algorithm DBSCAN (Ester et al., 1996) in two important ways. GDBSCAN can
GDBSCAN: DENSITY-BASED CLUSTERING 193

cluster point objects as well as spatially extended objects according to both, their spa-
tial and their nonspatial attributes. After a review of related work, the general concept of
density-connected sets and an algorithm to discover them were introduced. A performance
evaluation, analytical as well as experimental, showed the effectiveness and efficiency of
GDBSCAN on large spatial databases. Furthermore, we presented four applications using
2D points (astronomy), 3D points (biology), 5D points (earth science) and 2D polygons
(geography) demonstrating the applicability of GDBSCAN to real-world problems.
Future research will have to consider the following issues. First, heuristics to determine
the parameters for GDBSCAN where wCard is different from the cardinality function should
be developed. Second, GDBSCAN creates a one-level clustering. However, a hierarchical
clustering may be more useful, in particular, if the appropriate input parameters cannot be
estimated accurately. An extension of GDBSCAN to detect simultaneously a hierarchy of
clusterings will be investigated.

Acknowledgments

We thank T. Joseph W. Lazio for making the astronomy data available to us and for his
substantial help in understanding and modeling the astronomy application. We also thank
Thomas Schmidt and Thomas Seidl for providing the protein data. We are grateful to
Henning Brockfeld for introducing us into the application of mining in the area of economic
geography.

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Jörg Sander is a research and teaching assistant in the Institute for Computer Science at the University of Munich.
His research interests include knowledge discovery and data mining, in particular clustering. He holds a MS degree
in philosophy of science and received his MS degree in computer science in 1996 from the University of Munich.

Martin Ester is a research and teaching assistant in the Institute for Computer Science at the University of Munich.
His research interests include spatial database systems and data mining. He received his MS in 1984 from the
University of Dortmund and his Ph.D. in 1990 from ETH Zurich. From 1990 to 1993 he worked for Swissair,
Zurich, specializing in expert systems.

Hans-Peter Kriegel is a full professor for database systems in the Institute for Computer Science at the University
of Munich. His research interests are in spatial database systems, particularly in query processing, performance
issues, similarity search, high-dimensional indexing and in parallel systems. Data exploration using visualization
led him to the area of knowledge discovery and data mining. Kriegel received his MS and Ph.D. 1973 and 1976,
respectively, from the University of Karlsruhe, Germany.

Xiaowei Xu is a research and teaching assistant in the Institute for Computer Science at the University of Munich.
His research interests include data mining and high-dimensional indexing. He received his MS 1987 from Shen
Yang Institute for Computer Technology, Chinese Academy of Sciences.