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Journal of Graph Algorithms and Applications

http://jgaa.info/ vol. 14, no. 1, pp. 53–74 (2010)

Efficient, Proximity-Preserving Node Overlap


Removal
Emden R. Gansner Yifan Hu

AT&T Labs,
Shannon Laboratory,
180 Park Ave.,
Florham Park, NJ 07932.

Abstract
When drawing graphs whose nodes contain text or graphics, the non-
trivial node sizes must be taken into account, either as part of the initial
layout or as a post-processing step. The core problem in avoiding or
removing overlaps is to retain the structural information inherent in a
layout while minimizing the additional area required. This paper presents
a new node overlap removal algorithm that does well at retaining a graph’s
shape while using little additional area and time. As part of the analysis,
we consider and evaluate two measures of dissimilarity for two layouts of
the same graph.

Submitted: Reviewed: Revised: Accepted:


November 2008 March 2009 May 2009 November 2009
Final: Published:
November 2009 January 2010
Article type: Communicated by:
Regular paper I. G. Tollis and M. Patrignani

E-mail addresses: erg@research.att.com (Emden R. Gansner) yifanhu@research.att.com (Yifan


Hu)
54 Gansner and Hu Efficient Node Overlap Removal

1 Introduction
Most existing symmetric graph layout algorithms treat nodes as points. In
practice, nodes usually contain labels or graphics that need to be displayed.
Naively incorporating this can lead to nodes that overlap, causing information
of one node to occlude that of others. If we assume that the original layout
conveys significant aggregate information such as clusters, the goal of any layout
that avoids overlaps should be to retain the “shape” of the layout based on point
nodes.
The simplest and, in some sense, the best solution is to scale up the drawing
while preserving the node size until the nodes no longer overlap [30]. This has
the advantage of preserving the shape of the layout exactly, but can lead to
inconveniently large drawings. In general, overlap removal is typically a trade-
off between preserving the shape and limiting the area, with scaling at one
extreme.
Many techniques to avoid overlapping nodes have been devised. One ap-
proach is to make the node size part of the model of the layout algorithm. It
is assumed that whatever structure that would have been exposed using point
nodes will still be evident in these more general layouts. For hierarchical lay-
outs, the node size can be naturally incorporated into the algorithm [11, 35].
For symmetric layouts, various authors [3, 19, 28, 37] have extended the spring-
electrical model [7, 12] to take into account node sizes, usually as increased re-
pulsive forces. Node overlap removal can also be built into the stress model [26]
by specifying the ideal edge length to avoid overlap along the graph edges. Such
heuristics, however, cannot guarantee all overlaps will be removed, so they typ-
ically rely on overly large repulsive forces, or the type of post-processing step
considered below. This problem was addressed by Dwyer et al. [5], who showed
how to encode overlap avoidance, as well as many other layout features, as lin-
ear constraints in a stress function, and then optimize the stress function using
stress majorization [13].
An alternative approach is to remove node overlaps as a post-processing
step after the graph is laid out. Here the trade-off between layout size and
preserving the graph’s shape is more explicit. In addition to many of the al-
gorithms mentioned above that can be adapted for this use, a number of other
algorithms have been proposed. For example, the Voronoi cluster busting algo-
rithm [15, 29] works by iteratively forming a Voronoi diagram from the current
layout and moving each node to the center of its Voronoi cell until no overlaps
remain. The idea is that restricting each node to its corresponding Voronoi
cell should preserve the relative positions of the nodes. In practice, because of
the number of iterations often required and the use of a rectangular bounding
box,1 the nodes in the final drawing can be homogeneously distributed within
a rectangle, the graph bearing little resemblance to the original layout.
Another group of post-processing algorithms is based on setting up pairwise
node constraints to remove overlaps and then performing some procedure to
1 The latter might be improved by using something like α-shapes [8] to provide a more

accurate boundary.
JGAA, 14(1) 53–74 (2010) 55

generate a feasible solution. The force scan algorithm [31] and its later vari-
ants [20, 24] proceed along these lines. More recently, Marriott et al. [30, 31]
have presented quadratic programming algorithms which remove node overlaps
while, if desired, minimizing node displacement. All of these techniques rely
on solving separate horizontal and vertical problems. They behave differently
if the layout is rotated by a degree that is not a multiple of π/2. We have also
found that, in practice, this asymmetry often results in a layout with a distorted
aspect ratio (e.g., Figure 4, bottom right).
One desideratum proposed [31] for overlap removal is the preservation of
orthogonal ordering, i.e., the relative ordering of the x and y coordinates of
two nodes should be the same in the original layout and the one with overlaps
removed. Thus, if a node is above and to the left of another node in the original
layout, it is above and to the left in the derived one. The idea is that, in
this manner, a user’s “mental map” of the graph is better preserved. Many of
the algorithms described above either inherently preserve orthogonal ordering,
or have simple variations that do. While preserving orthogonal ordering can
be important, it alone cannot ensure that the relative proximity relations [23]
between nodes are preserved. At other times, it is too restrictive, causing two
highly-related nodes to be moved far apart due to some largely unrelated third
node. For these reasons, our approach is to concentrate on proximity relations
and not deal with orthogonal ordering.
In this paper, we focus on the problem of removing overlaps rather than
avoiding them. To this end, we discuss (Section 3) metrics for the similarity
between two layouts which we believe better quantify the desired outcome of
overlap removal than minimized displacement or such simpler measures as as-
pect ratio or edge ratio (the ratio of the longest and the shortest edge lengths).
We then present (Section 4) a node overlap removal algorithm based on a prox-
imity graph of the nodes in the original layout. Using this graph as a guide,
it iteratively moves the nodes, particularly those that overlap, while keeping
the relative positions between them as close to those in the original layout as
possible. The algorithm is similar to the stress model [26] used for graph layout,
except that the stress function involves only a sparse selection of all possible
node pairs. Because of this sparse stress function, the algorithm is efficient and
is able to handle very large graphs. In Section 5, we evaluate our algorithm
and others using the proposed similarity measures. Finally, Section 6 presents
a summary and topics for further study.

2 Background
We use G = (V, E) to denote an undirected graph, with V the set of nodes
(vertices) and E edges. We use |V | and |E| for the number of vertices and
edges, respectively. We let xi represent the current coordinates of vertex i
in Euclidean space. For this paper we are interested in 2D layout, therefore
xi ∈ R2 .
The aim of graph drawing is to find xi for all i ∈ V so that the resulting
56 Gansner and Hu Efficient Node Overlap Removal

drawing gives a good visual representation of the information in the graph. Two
popular methods, the spring-electrical model [7, 12], and the stress model [26],
both convert the problem of finding an optimal layout to that of finding a
minimal energy configuration of a physical system. We shall describe the stress
model in more detail since we will use a similar model for the purpose of node
overlap removal in Section 4.
The stress model assumes that there are springs connecting all nodes of
the graph, with the ideal spring length equal to the graph theoretical distance
between nodes. The energy of this spring system is
!
wij ("xi − xj " − dij ) 2 , (1)
i!=j

where dij is the graph theoretical distance between vertices i and j, and wij is a
weight factor, typically 1/dij 2 . The layout that minimizes the above stress en-
ergy is an optimal layout of the graph. There are several ways to find a solution
of the minimization problem. An iterative approach can be employed. Starting
from a random layout, the total spring force on each vertex is calculated, and
the vertex is moved along the direction of the force for a certain step length.
This process is repeated, with the step length decreasing every iteration, until
the layout stabilizes. Alternatively, a stress majorization technique can be em-
ployed, where the cost function (1) is bounded by a series of quadratic functions
from above, and the process of finding an optimum becomes that of solving a
series of linear systems [13].
In the stress model, the graph theoretical distance between all pairs of ver-
tices has to be calculated, leading to quadratic complexity in the number of
vertices. There have been attempts (e.g., [2, 13]) to simplify the stress function
by considering only a sparse portion of the graph. Our experience, however,
with real-life graphs is that these techniques may fail to yield good layouts.
Therefore, algorithms based on a spring-electrical model employing a multi-
level approach and an efficient approximation scheme for long range repulsive
forces [18, 22, 36] are still the most efficient choices to lay out large graphs
without consideration of the node size.

3 Measuring Layout Similarity


The outcome of an overlap removal algorithm should be measured in two aspects.
The first aspect is the overall bounding box area: we want to minimize the area
taken by the drawing after overlap removal. The second aspect is the change
in relative positions. Here we want the new drawing to be as “close” to the
original as possible. It is this aspect that is hard to quantify.
When total node movement is optimized [6, 24], comparison is reduced to
measuring the amount of displacement of the vertices in the new layout from
those of the original graph. This measurement does not take into account pos-
sible shifts, scalings or rotations, nor the importance of maintaining the relative
position among vertices.
JGAA, 14(1) 53–74 (2010) 57

As far as we are aware, there is no definitive way to measure similarity of


two layouts of the same graph. We adopt two approaches. The first approach
is based on measuring changes in lengths of edges. The second approach, which
is a modification of the metric of Dwyer et al. [6], is based on measuring the
displacement of vertices, after discounting shift, scaling and rotation.
Before defining these two measures of similarity, we first introduce the con-
cept of a proximity graph. A proximity graph is a graph derived from a set of
points in space: points that are “neighbors” to each other in the space form
an edge in the proximity graph. There are many ways to create a proximity
graph [25]. In this paper, we shall work with the Delaunay triangulation (DT),
which is an approximation to the proximity graph, and has the advantage being
rigid. Two points are neighbors in DT if and only if there exists a sphere passing
through these two points, and no other points lie in the interior of this sphere.
One way to measure the similarity of two layouts is to measure the distance
between all pairs of vertices in the original and the new layout. If the two
layouts are similar, then these distances should match, subject to scaling. This
is known as Frobenius metric in the sensor localization problem [9]. Calculating
all pairwise distances is expensive for large graphs, both in CPU time and in
the amount of memory. As we want a metric feasible for very large graphs, we
instead form a DT of the original graph, then measure the distance between
vertices along the edges of the triangulation for the original and new layouts.2
If x0 and x denote the original and the new layout, and EP is the set of edges
in the triangulation, we calculate the ratio of the edge length

"xi − xj "
rij = , {i, j} ∈ EP ,
"x0i − x0j "
then define a measure of the dissimilarity as the normalized standard deviation
"!
{i,j}∈EP(rij −r̄)2
|EP |
σdist (x0 , x) = ,

where

1 !
r̄ = rij
|EP |
{i,j}∈EP

is the mean ratio.


The reason we measure the edge length ratio along edges of the proximity
graph, rather than along edges of the original graph, is that if the original
graph is not rigid, then even if two layouts of the same graph have the same
edge lengths, they could be completely different. For example, think of the
graph of a square, and a new layout of the same graph in the shape of a non-
square rhombus. These two layouts may have exactly the same edge lengths,
2 Another possibility would be to sample O(|V |) out of the |V |(|V | − 1)/2 possible vertex

pairs. Some care is needed in making sure that the resulting graph is rigid.
58 Gansner and Hu Efficient Node Overlap Removal

4 3

4 3

1 2 1 2

Figure 1: The edge lengths of these two layouts of a non-rigid graph are exactly
the same, but the layouts are clearly different.

but are clearly different (see Figure 1). The rigidity of the triangulation avoids
this problem.
Notice that σdist (x0 , x) is not symmetric with regard to which layout comes
first. Furthermore, in theory, this non-symmetric version could class a layout
and a foldover of it (e.g., a square grid with one half folded over the other) as
the same. We can symmetrize it by defining the dissimilarity between layout x
and x0 as (σdist (x0 , x) + σdist (x, x0 ))/2. This also resolves the “foldover prob-
lem”. The symmetric version may be more appropriate if we are comparing two
unrelated layouts. Since, however, we are comparing a layout derived from an
existing layout, we feel that the asymmetric version is adequate.
An alternative measure of similarity is to calculate the displacement of ver-
tices of the new layout from the original layout [6]. Clearly a new layout derived
from a shift, scaling and rotation should be considered identical. Therefore we
modify the straight displacement calculation by discounting the aforementioned
transformations. This is achieved by finding the optimal scaling, shift and ro-
tation that minimize the displacement. The optimal displacement is then a
measure of dissimilarity.
We denote by scalars r and θ the scaling and rotation,
# $
cos(θ) sin(θ)
T = (2)
− sin(θ) cos(θ)

the rotation matrix, p ∈ R2 the translation, and define the displacement dissim-
ilarity as
!
σdisp (x0 , x) = minp∈R2 ,θ,r∈R "rT xi + p − x0i "2 , (3)
i∈V

This is a known problem in the Procrustes analysis [1, 16] and the solution (the
Procrustes statistic) is
T T 1
σdisp (x0 , x) = tr(X 0 X 0 ) − (tr((X T X 0 X 0 X) 2 )2 tr(X T X), (4)
where tr(A) is the trace of a matrix A, X is a matrix with columns xi − x̄, X 0
is a matrix with columns x0i − x̄0 , and x̄ and x̄0 are the centers of gravity of the
new and original layout.
JGAA, 14(1) 53–74 (2010) 59

j
j

i i

Figure 2: Nodes i and j overlap (left). The overlap factor, according to (5), is
min((2 + 2)/3, (1 + 2)/2) = 1.33. Expanding the edge i − j by 33% removes the
overlap (right).

In the above we do not consider shearing, since we believe a layout derived


from shearing of the original should not be considered identical to the latter.
The quality of an overlap removal algorithm is a combination of how similar
the new layout is to the original, and how small an area it occupies. The
simplest overlap removal algorithm is that of scaling the layout until all overlaps
are removed. This has a dissimilarity of 0, but usually occupies a very large
area. The alternative extreme is to pack the nodes as close to each other as
possible while ignoring the original layout. This will have the smallest area, but
a large dissimilarity. A good solution should be a compromise between these
two extremes. We now describe one candidate.

4 A Proximity Stress Model for Node Overlap


Removal
Our goal is to remove overlaps while preserving the shape of the initial layout by
maintaining the proximity relations [23] among the nodes. To do this, we first
set up a rigid “scaffolding” structure so that while vertices can move around,
their relative positions are maintained. This scaffolding is constructed using an
approximate proximity graph, in the form of a Delaunay triangulation (DT).
Once we form a DT, we check every edge in it and see if there are any node
overlaps along that edge. Let wi and hi denote the half width and height of
the node i, and x0i (1) and x0i (2) the current X and Y coordinates of this node.
If i and j form an edge in the DT, we calculate the overlap factor of these two
nodes
% % & &
wi + wj hi + hj
tij = max min , ,1 . (5)
|x0i (1) − x0j (1)| |x0i (2) − x0j (2)|

For nodes that do not overlap, tij = 1. For nodes that do overlap, such overlaps
can be removed if we expand the edge by this factor, see Figure 2. Therefore
we want to generate a layout such that an edge in the proximity graph has the
60 Gansner and Hu Efficient Node Overlap Removal

ideal edge length close to tij "x0i − x0j ". In other words, we want to minimize the
following stress function
!
wij ("xi − xj " − dij ) 2 . (6)
(i,j)∈EP

Here dij = sij "x0i − x0j " is the ideal distance for the edge {i, j}, sij is a scaling
factor related to the overlap factor tij (see (7)), wij = 1/"dij"2 is a weighting
factor, and EP is the set of edges of the proximity graph. We call (6) the
proximity stress model in obvious analogy.
Because DT is a planar graph, which has no more than 3|V | − 6 edges, the
above stress function has no more than 3|V | − 6 terms. Furthermore, because
DT is rigid, it provides a good scaffolding that constrains the relative position
of the vertices and helps to preserve the global structure of the original layout.
It is important that we do not attempt to remove overlaps in one iteration
by using the above model with sij = tij . Imagine the situation of a regular mesh
graph, with one node i of particularly large size that overlaps badly with its
nearby nodes, but the other nodes do not overlap with each other. Suppose
nodes i and j form an edge in the proximity graph, and they overlap. If we
try to make the length of the edge equal tij "x0i − x0j ", we will find that tij is a
number much larger than 1, and the optimum solution to the stress model is to
keep all the other vertices at or close to their current positions, but move the
large node i outside of the mesh, at a position that does not cause overlap. This
is not desirable because it destroys the original layout. Therefore we damp the
overlap factor by setting

sij = min(tij , smax ) (7)


and try to remove overlap a little at a time. Here smax > 1 is a number limiting
the amount of overlap we are allowed to remove in one iteration. We found that
smax = 1.5 works well.
After minimizing (6), we arrive at a layout that may still have node overlaps.
We then regenerate the proximity graph using DT and calculate the overlap
factor along the edges of this graph, and redo the minimization. This forms an
iterative process that ends when there are no more overlaps along the edges of
the proximity graph.
For many graphs, the above algorithm yields a drawing that is free of node
overlaps. For some graphs, however, especially those with nodes having extreme
aspect ratios, node overlaps may still occur. Such overlaps happen for pairs of
nodes that are not near each other, and thus do not constitute edges of the
proximity graph. Figure 3(a) shows the drawing of a graph after minimizing
(6) iteratively, so that no more node overlap is found along the edges of the
Delaunay triangulation. Clearly, node 2 and node 4 still overlap. If we plot
the Delaunay triangulation (Figure 3(b)), it is seen that nodes 2 and 4 are not
neighbors in the proximity graph, which explains the overlap.
To overcome this situation, once the above iterative process has converged
so that no more overlaps are detected over the DT edges, we apply a scan-
JGAA, 14(1) 53–74 (2010) 61

8 7 6 8 7 6

9 5 9 5

11 11

10 4 with an extremely looong label 10 4 with an extremely looong label


2 with a 2 with a
1 tall 3 1 tall 3
label label

Figure 3: (a): A graph layout where nodes 2 and 4 overlap. (b): the proximity
graph (Delaunay triangulation) of the current layout. No two nodes linked by
an edge of the proximity graph overlap.

line algorithm [6] to find all overlaps, and augment the proximity graph with
additional edges, where each edge consists of a pair of nodes that overlap. We
then re-solve (6). This process is repeated until the scan-line algorithm finds
no more overlaps. We call our algorithm PRISM (PRoxImity Stress Model).
Algorithm 1 gives a detailed description of this algorithm.

Algorithm 1 Proximity stress model based overlap removal algorithm (PRISM)


Input: coordinates for each vertex, x0i , and bounding box width and height
{wi , hi }, i = 1, 2, . . . , |V |.
repeat
Form a proximity graph GP of x0 by Delaunay triangulation.
Find the overlap factors (5) along all edges in GP .
Solve the proximity stress model (6) for x. Set x0 = x.
until (no more overlaps along edges of GP )
repeat
Form a proximity graph GP of x0 by Delaunay triangulation.
Find all node overlaps using a scan-line algorithm. Augment GP with edges
from node pairs that overlap.
Find the overlap factor (5) along all edges of GP .
Solve the proximity stress model (6) for x. Set x0 = x.
until (no more overlaps)

We now discuss some of the main computational steps in the above algo-
rithm. Delaunay triangulation can be computed in O(|V | log |V |) time [10, 17,
27]. We used the mesh generator Triangle [33, 34] for this purpose.
The scan-line algorithm can be implemented to find all the overlaps in
O(l|V |(log |V | + l)) time [6], where l is the number of overlaps. Because we
only apply the scan-line algorithm after no more node overlaps are found along
edges of the proximity graph, l is usually a very small number, hence this step
can be considered as taking time O(|V | log |V |).
The proximity stress model (6), like the spring model (1), can be solved
62 Gansner and Hu Efficient Node Overlap Removal

using the stress majorization technique [13] which is known to be a robust


process for finding the minimum of (1). The technique works by bounding
(6) with a series of quadratic functions from above, and the process of finding
an optimum becomes that of finding the optimum of the series of quadratic
functions, which involves solving linear systems with a weighted Laplacian of the
proximity graph. We solve each linear system using a preconditioned conjugate
gradient algorithm. Because we use DT as our proximity graph and it has no
more than 3|V | − 6 edges, each iteration of the conjugate gradient algorithm
takes a time of O(|V |).
Overall, therefore, Algorithm 1 takes O(t(mk|V | + |V | log |V |)) time, where
t is the total number of iterations in the two main loops in Algorithm 1, m is
the average number of stress majorization iterations, and k the average number
of iterations for the conjugate gradient algorithm.
In practice, we found that the majority of CPU time is spent in repeatedly
solving the linear systems (which takes a total time of O(tmk|V |)). We ter-
minate the conjugate gradient algorithm if the relative 2-norm residual for the
linear system involved in the stress majorization process is less than 0.01. A
tighter tolerance is not necessary because the solution of each linear system con-
stitutes an intermediate step of the stress majorization. Furthermore, solution
of the proximity stress model (6) is an intermediate step itself in Algorithm 1,
so we do not need to solve (6) accurately either. Hence we set a limit of mmax
iterations. By experimentation, we found that a smaller value mmax gives a
faster algorithm, and that, in terms of quality, a smaller mmax is often just as
good as, if not better than, a larger value of mmax . Therefore, we set mmax = 1.

5 Numerical Results
To evaluate the PRISM algorithm and other overlap removal algorithms, we ap-
ply them as a post-processing step to a selection of graphs from the Graphviz [14]
test suite. This suite, part of the Graphviz source distribution, contains many
graphs from users. As such, these are good examples of the kind of graphs
actually being drawn.
Our baseline algorithm is Scalable Force Directed Placement (SFDP) [22], a
multilevel, spring-electrical algorithm. Using the layout of SFDP, we then apply
one of the overlap removal algorithms to get a new layout that has no node
overlaps, and compare the new layout with the original in terms of dissimilarity
and area.
In Table 1, we list the 14 test graphs, the number of vertices and edges, as
well as CPU time3 for PRISM and three other overlap removal algorithms. The
graphs are selected randomly with the criteria that a graph chosen should be
connected, and is of relatively large size. We compared PRISM with an imple-
mentation of the solve VPSC algorithm [6] provided by its authors. We also
evaluated the companion algorithm satisfy VPSC. This offered, at best, a 2%
3 All timings were derived on a 4 processor, 3.2 GHz Intel Xeon CPU, with 8.16 GB of

memory, running Linux.


JGAA, 14(1) 53–74 (2010) 63

Table 1: Comparing the CPU time (in seconds) of several overlap removal al-
gorithms. Initially the layout is scaled to an average edge length of 1 inch.

Graph |V | |E| PRISM VPSC VORO ODNLS


b100 1463 5806 1.44 14.85 350.7 258.9
b102 302 611 0.14 0.10 4.36 5.7
b124 79 281 0.03 0.01 0.02 0.5
b143 135 366 0.04 0.01 0.47 1.3
badvoro 1235 1616 0.54 71.15 351.51 73.6
mode 213 269 0.09 0.09 2.15 2.1
ngk10 4 50 100 0.01 0.00 0.02 0.14
NaN 76 121 0.01 0.01 0.11 0.27
dpd 36 108 0.01 0.01 0.02 0.1
root 1054 1083 0.89 7.81 398.49 46.9
rowe 43 68 0.00 0.00 0.04 0.1
size 47 55 0.01 0.00 0.06 0.09
unix 41 49 0.01 0.00 0.04 0.07
xx 302 611 0.13 0.10 8.19 5.67

reduction in time, while producing almost identical results concerning displace-


ment, dissimilarity and area. For this reason, in the sequel, we only consider
the solve VPSC algorithm, hereafter denoted as VPSC.4 We also evaluated the
Voronoi cluster busting algorithm [15, 29], denoted by VORO, as well as the
ODNLS algorithm of Li et al. [28], which relies on varied edge lengths in a spring
embedder. We note, in passing, that we also tested scaling using the algorithm
of Marriott et al. [30]. As expected, it outperformed all other algorithms in
terms of speed and dissimilarity, but at an unacceptably high cost in area. For
example, on the b143 graph, the time and dissimilarity were essentially 0 but
the area was 82.2. Overall, scaling produced areas at least 4.5 times larger than
PRISM and, more typically, at least an order of magnitude larger. We therefore
remove scaling from further consideration.
The initial layout by SFDP is scaled so that the average edge length is 1 inch.
From the table, it is seen that PRISM is usually faster, particularly for large
graphs on which it scales much better. The others are slow for large graphs,
with VORO the slowest.
Table 2 compares the dissimilarities and drawing area of the four overlap
removal algorithms. The smaller the dissimilarities and area, the better.
The ODNLS algorithm performs best in terms of smaller dissimilarity, fol-
lowed by PRISM, VPSC and VORO. In terms of area, PRISM and VPSC are
pretty close, and both are better than ODNLS and VORO, which can give ex-
4 Both versions of the VPSC algorithm can be extended to support the preservation of

orthogonal ordering. We did not have an opportunity to check these versions.


64 Gansner and Hu Efficient Node Overlap Removal

tremely large drawings. Indeed, in terms of area, scaling outperformed ODNLS


and VORO in 20%-30% of the examples.
Comparing PRISM with VPSC, Table 2 shows that PRISM gives smaller
dissimilarities most of the time. The two dissimilarity measures, σdist and σdisp ,
are generally correlated, except for ngk10 4 and root. Based on σdist , VPSC
is better for these two graphs, while based on σdisp , PRISM is better. The
first row in Figure 4 shows the original layout of ngk10 4, as well as the result
after applying PRISM and VPSC. Through visual inspection, we can see that
PRISM preserved the proximity relations of the original layout well. VPSC
“packed” the labels more tightly, but it tends to line up vertices horizontally
and vertically, and also produces a layout with aspect ratio quite different from
the original graph. It seems that σdist is not as sensitive in detecting differences
in aspect ratio. This is evident in drawings of the root graph (Figure 4, second
row): VPSC clearly produced a drawing that is overly stretched in the vertical
direction, but its σdist is actually smaller! Consequently, we conclude that σdisp
may be a better dissimilarity measure.
The fact that VPSC can produce very tall and thin, or very short and wide,
layouts is not surprising, and has been observed often in practice. VPSC works
in the vertical and horizontal directions alternatively, each time trying to remove
overlaps while minimizing displacement. As a result, when starting from a layout
with severe node overlaps, it may move vertices significantly along one direction
to resolve the overlaps, creating drawings with extreme aspect ratios. In fact,
for 9 out of 14 test graphs, VPSC produces layouts with extreme aspect ratios.
PRISM does not suffer from this problem.
When starting from a layout that is scaled sufficiently so that relative fewer
nodes overlap, VPSC’s performance can be improved. Table 3 compares the
four overlap removal algorithms, starting from layouts that are scaled to give
an average edge length that equals 4 times the average node size. Here the size
of a node is calculated as the average of its width and height.
From the table, we can see that in terms of dissimilarity, PRISM and VPSC
are now similar, closer to the better performing ODNLS. In terms of drawing
area, PRISM is better than VPSC, with VORO and ODNLS much larger. When
visually inspected, VPSC again suffers from extreme aspect ratio issue on at
least 5 out of the 14 graphs (b100, b143, badvoro, mode, root). Figure 5
shows the layout of badvoro (first row), on which VPSC performed badly based
on the two similarity measures. In the same figure, we also show b124 (second
row), on which PRISM is rated worse than VPSC based on the same measures.
On badvoro it is clear that VPSC performed badly, as the similarity measures
suggest. On the other hand, if we look at b124, VPSC perhaps performed better
than PRISM, but not as clearly as the similarity measures suggest. Overall,
visual inspection of the drawings of these 14 graphs, as well as drawings for
graphs in the complete Graphviz test suite (a total of 204 graphs in March
2008), shows that PRISM performs very well, and is overall better and faster
than VPSC and VORO. The ODNLS algorithm preserves similarity somewhat
better than PRISM, but at much higher costs in term of speed and area.
Considering a larger collection of graphs, Table 4 compares PRISM with
JGAA, 14(1) 53–74 (2010) 65

Table 2: Comparing the dissimilarities and area of overlap removal algorithms.


Results shown are σdist , σdisp and area. Area is measured with a unit of 106
square points. Initially the layout is scaled to an average length of 1 inch.

Graph PRISM VPSC


σdist σdisp area σdist σdisp area
b100 0.74 0.38 14.05 0.76 0.72 18.91
b102 0.44 0.25 2.45 0.58 0.8 2.71
b124 0.65 0.37 1.04 0.78 0.73 0.91
b143 0.59 0.35 1.5 0.78 0.83 2.16
badvoro 0.34 0.15 12.58 0.61 0.75 13.85
mode 0.59 0.37 0.79 1.02 0.77 1.29
ngk10 4 0.41 0.16 0.33 0.39 0.3 0.25
NaN 0.4 0.2 0.72 0.54 0.65 0.71
dpd 0.34 0.18 0.25 0.51 0.4 0.18
root 0.71 0.3 16.99 0.6 0.75 17.68
rowe 0.33 0.14 0.22 0.44 0.31 0.19
size 0.37 0.2 0.47 0.77 0.74 0.4
unix 0.39 0.23 0.39 0.51 0.67 0.36
xx 0.42 0.25 3.96 0.57 0.82 3.9
Graph VORO ODNLS
σdist σdisp area σdist σdisp area
b100 - - - 0.33 0.20 1.02E3
b102 0.8 0.3 31.79 0.30 0.16 53.13
b124 0.86 0.39 13.42 0.33 0.19 14.79
b143 0.99 0.45 22.91 0.49 0.34 23.79
badvoro 2.29 0.65 3.01E3 0.31 0.26 318.66
mode 0.97 0.54 10.84 0.38 0.27 49.45
ngk10 4 0.48 0.26 0.52 0.22 0.13 2.30
NaN 0.56 0.28 5.04 0.26 0.15 5.10
dpd 0.48 0.32 0.45 0.37 0.29 1.30
root 4.09 0.94 6.93E9 0.29 0.22 950.01
rowe 0.49 0.26 0.95 0.27 0.12 2.10
size 0.62 0.35 1.27 0.32 0.20 4.14
unix 0.6 0.35 0.85 0.26 0.13 2.35
xx 0.97 0.34 58.83 0.29 0.14 74.00
66 Gansner and Hu Efficient Node Overlap Removal

26

37
44

42 41
1 40

22
26 26 30 2
28
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47 38
31 29
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44 42 3741 9
22 41 8
30 40 3 30 40 13 24 39
11 32
20
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2 31 32 47 2 31 8
28
3 25 16
10 33
6
47 8 28 32 49 18 35
13 38 933 13 9 20
15 48
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24 39 11 46 39 11
16
33 6 14 7

49 18 35 25 43 48 24
46 12 43
45
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25
27
7 1250 19 15 45 48 34
18
50 43
14 7 15 19
34 27 45
36

36 17 4 34 27
12
19

21 5
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5 17 4
23 23 5
36 21
21 23

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668d636002 609E 8be0efdd94a6383e87fbfded4f 731E 85fc23f1c88b4

b656f0ed2202b8e46eb

797E 801E b9
da0d7bbcf30 57c77c341f94afddef07e6

c0174bbe7ae8

44cbb41a9cfc15497eacd294 8b98c3ddbe0b336
d4f7b7fba7afcf7a72397353ec

855d26296eda4eb7
21dff35936370ae5f
3703059dbc5a8
38b3b0d9
f9d09 1172dca23 08500a6044
fff03efcd
597E9ccd974150a18260b207b6584caa
31055116421c96b37f72a262bb
85a34bc9616ff
8a46e6 53069e384a2 969a58db14386cb9d2f51ec f722890f70a32dce3baff371a 65fd8495 efb52b499303115c33fd eedc819a68add6
bac77c3f414a

6a8f5bafb1
d9f4abac731a9e

acacfc83af504

53069e384a2 69f4ecb77d

cd1e9af3dec2
2759e82e30d6d 65fd8495 8cbae42a3900
6a8f5bafb1 084d4bfa5853e

c32d2697e8 7c0ab977f5a3c4ab6d625f5033 32b98f11f3d01d6 32fe7eee5283 c21eb96fe100a1efaa128181b7


8b98c3ddbe0b336

e84330eef281284a

8e307415fb435445ced7
53069e384a2
d 67219ef689f0146b544
8c932e1e502dca ccceeef40edda78
8c932e1e502dca

ff5c9b242337c

a387210a27b

d886e4b76537a99bc71b8a9331c94 3dafe1619016463f521f
f603819d560c5603259aa05dca

4f04c39708f f5d636e14a6cd716362158d
af0268dddd ee3b6be71d59b

9e650e89bb ff5c9b242337c
901b2105a902ee7791 6a8f5bafb1 4e12f7ff0918

21dff35936370ae5f
ff b38049e0086633c26be93ada8b20f234fdcd0e1fc50261ce8
52a6c2063bccd83110c32
c72df69b40156a3254
fbba7215e7c13173a60206 817 06209
02c2ba83680ab57f236a33d702

16a795a1d63f30df 275a0407e33e9b8aa9cdd051 f1b0d754353a6

632E

8bdb6a91c6dee925b557c705b3
c360aaeb167487c9578a8f
8df
855d26296eda4eb7 0a49c95f107c0aa57c9b5748 b7b899dc8bc6a32b28cb098fa16
4c52fdd8e396692

1de26f6b12b0d292f94184
a153512d982 af0268dddd

21dff35936370ae5f c338481d79773 6c93f24516f01d 102f1 2601085bde1b2450d64509f36

8f7c875500073 5e80f85274

275afb2b215b966d9fac51b96b9
d12bd75c24b110ef90cdd35d3

4995c71223c9f6067324d387a2 ee3b6be71d59b a2c4b1d72e2da483a86ae0c62e5


881d373

af0268dddd
6a8f5bafb1 6d52dd1b198bb

23f94655294d3ff537f2915fa
9c1305d59c37e9be9f13d7d049c 58e3dcc618 4e12f7ff0918 bdec8c86db51b9 8f95518f48528
c96782ef56711c5d6a3f69

f62b136b2171
eedc819a68add6

a77622f2ff77ffeeb2
4869e993f2bb10f
eee44624da 5e80f85274 658d208447d8ec5d6de8
89ced1a7906d58d687d5a04

4727c415d06bcbef
88a4f0337c2189c3fc7b31

fc73 8462bb2eec1a62d19a15865e57c92

bf65cfddeb00ff847feae0c
4399cf78123dedd0dfe9776104 0668
04390dec6f1779353c07f5

71cf45dd4e91bcca945137b40e c4507c22d19 e1d01ef89f f841118350a27b7ea29a9c9d


ccceeef40edda78

3eecb304bab2136a76deda
c21eb96fe100a1efaa128181b7

e33792703 16a795a1d63f30df

8e307415fb435445ced7 e1e8c 34d7bb6af4fcd8d630de72500c8 4c52fdd8e396692 7204950f6233bf9c9e1f00d4a870


bdec8c86db51b9

6a8f5bafb1
8fb60d769e4c387 8f95518f48528

af9c489df53 b074e 81 6d52dd1b198bb 49704867bee95 2ef209509e2a


8d52f183ec

908f9ad506eae9ab6ada185e3

ffd1b1af3b6864078f3
7e74e1587f3a4d208
d
665b76844ff78fc2cf66ca2

53069e384a2 38b3b0d9 c0174bbe7ae8 2043b477ac0393676a4309514d0 ac284d73563 a2c4b1d72e2da483a86ae0c62e5

bac77c3f414a 842bc5775657c1e0d67
cef12b6

a153512d982 af0268dddd 85a34bc9616ff be7d637c50c

a738ba39

82d201

8f9cdc26798117dd3e9ee4a8770
881d373 8d52f183ec 6a8f5bafb1 67219ef689f0146b544
8066f87a88f4e

26fa7360ab81be9d4434a

801E

a2eab7c9fa641e5f
af0268dddd 6a8f5bafb1
4399cf78123dedd0dfe9776104

88ebe2e8782c af0268dddd 57c77c341f94afddef07e6 39d025b265f9790490781cb201 be9c5958196ed


8a46e6 1562abef0d8241

653ae44d45dcadeb481b53027d

0a963fef9
49704867bee95

f9d09 37f57e81ebed95 ab48d1f65812bc0f8ab6941c3b5 7204950f6233bf9c9e1f00d4a870


2ef209509e2a

1727041c622518c9dd24f7c211

8b06a67a
3703059dbc5a8
38fa61352f5086d2cb51 28f7bfc40c88e6a

d12bd75c24b110ef90cdd35d3 46e412a3 bd7aca295ca 28f7bfc40c88e6a


bb92d1da1f38d52f8ff 06eff1db45cdf
be9c5958196ed

9937ccba1469 582E
a738ba39 6a8f5bafb1
9e650e89bb 2043b477ac0393676a4309514d0

0efbd 582E 20f234fdcd0e1fc50261ce8


53069e384a2

f62b136b2171
8462bb2eec1a62d19a15865e57c92

1d4ea80c7194689d69f9592186
616d8a7b
630E
653ae44d45dcadeb481b53027d
4727c415d06bcbef

731E 665b76844ff78fc2cf66ca2 89ced1a7906d58d687d5a04 cef12b6


797E
1727041c622518c9dd24f7c211

91ecbe29a71f00ed5a3 342E
354E
8f9cdc26798117dd3e9ee4a8770
21dff35936370ae5f 801E b9 d66f542ef1ce4d02c59bec65e

21dff35936370ae5f 65694ca6d575 c96782ef56711c5d6a3f69 47b2da3d 38b3b0d9 597E


85a34bc9616ff

c360aaeb167487c9578a8f
855d26296eda4eb7

cd1e9af3dec2
9ccd974150a18260b207b6584caa

1b13908a9f0763c0ae54af9062080
8c7cd9b93b1cbe48e1
382E
620E
684E
696E
300E
370E
444Ee287d497450664a4c0f4efc338
630E d66f542ef1ce4d02c59bec65e
3703059dbc5a8 08500a6044

f9d09cd1e9af3dec2
1172dca23

1d529eb4
fff03efcd

503737b64d432c60d6ac557e0e6
a78eb40ae56aaa9 a8e9422E
234E
be7d637c50c
31055116421c96b37f72a262bb

616d8a7b
8e307415fb435445ced7

a8e9
67219ef689f0146b544

275a0407e33e9b8aa9cdd051 8fb60d769e4c387
d 3dafe1619016463f521f

8bdb6a91c6dee925b557c705b3 da0d7bbcf30
53069e384a2
20f234fdcd0e1fc50261ce8

e3fd0c7b3
d886e4b76537a99bc71b8a9331c94

ff

3cfae
07 82d201
30d6138b63eb
21dff35936370ae5f

2601085bde1b2450d64509f36 38fa61352f5086d2cb51 04390dec6f1779353c07f5


52a6c2063bccd83110c32

8df 342E 26fa7360ab81be9d4434a e287d497450664a4c0f4efc338 8cbcf5cb5 9ccd974150a18260b207b6584caa

341E6472c2861e0e0dd681 bd7aca295ca
46e412a3
e33792703
c72df69b40156a3254

8c7cd9b93b1cbe48e1
86633c26be93ada8b

8066f87a88f4e b9 99da1f8a5

dcc5d5e9d6c4e
a8e9 95e93c4a13
24dfe1a997a
3a8173d6c
86e9b0428
65a1 1d529eb4
07 31055116421c96b37f72a262bb
c360aaeb167487c9578a8f

8bdb6a91c6dee925b557c705b3

2d7b7fb6c9ad6821752651f7
ff

3f9ddf1ffbc0d38b
b62cd1d0a0
381E
369E
a8e9
0759a8b435ccd
5a7a610a8a
8f143077e
f0f45e707
33e1de 99da1f8a5
e3fd0c7b3
47b2da3d
382E 8df

901b2105a902ee7791
275afb2b215b966d9fac51b96b9

88a4f0337c2189c3fc7b31 0fabab47

a0befe6dd1ca7b165786835
619E
683E
a8e9 c0f34a600
0da9135
0fabab47
1b82200
534E
a77622f2ff77ffeeb2 8df
8df

3cfae 354E 696E 300E 370E 444E 23f94655294d3ff537f2915fa

676bbe7d1c1fb71742df534ce8 233E
01 2d7b7fb6c9ad6821752651f7
bf141dbce
30d6138b63eb
e64f22a31
0f167280
fe821bce
c96cb3
8cbcf5cb5
597E 06eff1db45cdf c0f34a600
a77622f2ff77ffeeb2

81dabfaba8
4869e993f2bb10f

08500a6044 fff03efcd 1562abef0d8241

37d80ae421dba4a70730338860 ffccaa9e3 81dabfaba8


684E
bf65cfddeb00ff847feae0c

341E
3eecb304bab2136a76deda

ac284d73563 620E
b38049e00

162d8039483d8
3b1563a23eb9 c5d5be3942
ffd1b1af3b6864078f3

7e74e1587f3a4d208

797E

e82f47b8d4949ba4af69b38cbc19
9f24ba80192c339a64c0
f8128d574c356631b8a9 0acc5bb8ca4
fbdc3ca37406f66635c8b226e
f713a8b311ffa05ce3683ad10
eb8eb8 81dabfaba8
bb92d1da1f38d52f8ff
8f9cdc26798117dd3e9ee4a8770

4869e993f2bb10f bf65cfddeb00ff847feae0c 3eecb304bab2136a76deda 422E 234E 52a6c2063bccd83110c32 0da9135 fe821bce 1b82200 c5d5be3942 fbdc3ca37406f66635c8b226e f713a8b311ffa05ce3683ad10
a2eab7c9fa641e5f

6448451ac2ceade90715378b
5eea496cc301b2a9721
b06bbfa920aa95dd
ac487676a04e4 45827dbdd8
eb8
eb8 d370c12dbc
534E
0a963fef9 582E

381E
8b06a67a

9937ccba1469

86633c26be93ada8b

6aae8d25951 5e9156098c064
46f754ea06f070dbc023e571a876
0acc5bb8ca4
45827dbdd8
910b00285f11bb90d0a15641
81dabfaba8
80874aa8
630E

a8e9 3dafe1619016463f521f
1d4ea80c7194689d69f9592186

616d8a7b

bf01c8a262 c1c30f30d40c4f1f84924622f
fa2afbd869
533E
dcc5d5e9d6c4e b62cd1d0a0 91ecbe29a71f00ed5a3

342E

11bb8ed3ae227d3acefc
08dade990b2282
3b2f08d52e4bca3f9ca7bbbd6
81dabfaba8
0f940646
81dabfaba8
f0bd1521
81dabfaba8
354E

a8e9 07 369E a8e9 bf141dbce 0f167280 e64f22a31 444E

1d163eac141def176461c
6c632ad9c42228bb337
f78e145a127014eb43345a0c
382E

1172dca23 619E 910b00285f11bb90d0a15641 8c7cd9b93b1cbe48e1

370E

84e4f1c582427a98d7b
ea890ccca2f7c2107351
dca32af03698c988b22
18115fa32ff1cb99
696E

1d4ea80c7194689d69f9592186 d370c12dbc
300E

3f9ddf1ffbc0d38b 683E c96cb3 1b13908a9f0763c0ae54af9062080

cd0d985a366cad7e 173fd00917644f0f1f3e3
0c72a426929600000f5
3cdc90c57243373efaba65a
fb039d7a2a9fe73b5f468eba9
a27037332d9fa5c43bcfe94c0
c72df69b40156a3254 a78eb40ae56aaa9 620E

e287d497450664a4c0f4efc338

24431c3eb075102f07cc2c1be
75ba8d840070942eb4e737849
e3bdbca0e2256fffa8a59018
81dabfaba8
684E 82d201

01 233E 234E

07f8a9e55a16beddb3c9153b0
4a38abc630c82b0c48dfbf5271
86276bb1e23f2c7ffcbe82a0
422E

d886e4b76537a99bc71b8a9331c94 a0befe6dd1ca7b165786835
503737b64d432c60d6ac557e0e6

95e93c4a13 c1c30f30d40c4f1f84924622f
a8e9

9c9e2e0f2da8758e436c
07

24dfe1a997a 533E 80874aa8 3cfae

81dabfaba8
6472c2861e0e0dd681

37d80ae421dba4a70730338860 3b1563a23eb9 65a1 6472c2861e0e0dd681 fa2afbd869 dcc5d5e9d6c4e


341E

a8e9
65a1

95e93c4a13
bd7aca295ca

46e412a3

e82f47b8d4949ba4af69b38cbc19
a8e9 86e9b0428

381E 24dfe1a997a

3a8173d6c 1d529eb4

8f143077e e3fd0c7b3

23f94655294d3ff537f2915fa 275afb2b215b966d9fac51b96b9 3a8173d6c


5a7a610a8a 47b2da3d

81dabfaba8
33e1de 99da1f8a5

b06bbfa920aa95dd 8f143077e 5a7a610a8a 86e9b0428 81dabfaba8 f0bd1521 3b2f08d52e4bca3f9ca7bbbd6 3f9ddf1ffbc0d38b

b62cd1d0a0

369E
f0f45e707

59a8b435ccd

162d8039483d8 9f24ba80192c339a64c0 f8128d574c356631b8a9


07 0fabab47

a8e9 c0f34a600

33e1de 0f940646
619E 1b82200

ac487676a04e4
683E 0da9135

f0f45e707 f78e145a127014eb43345a0c a0befe6dd1ca7b165786835 534E

fe821bce

a2eab7c9fa641e5f
676bbe7d1c1fb71742df534ce8

30d6138b63eb
233E

5eea496cc301b2a9721 fb039d7a2a9fe73b5f468eba9
8cbcf5cb5

59a8b435ccd 2d7b7fb6c9ad6821752651f7
bf141dbce

e64f22a31

b38049e00 5e9156098c064
01

37d80ae421dba4a70730338860
c96cb3

0f167280

0acc5bb8ca4
162d8039483d8 ffccaa9e3 81dabfaba8

a78eb40ae56aaa9 bf01c8a262 ffccaa9e3 a27037332d9fa5c43bcfe94c0


c5d5be3942
3b1563a23eb9

6448451ac2ceade90715378b eb8
45827dbdd8

cd0d985a366cad7e
f713a8b311ffa05ce3683ad10

eb8 45827dbdd8 24431c3eb075102f07cc2c1be e3bdbca0e2256fffa8a59018


9f24ba80192c339a64c0

eb8

eb8

fbdc3ca37406f66635c8b226e

3cdc90c57243373efaba65a
0acc5bb8ca4

81dabfaba8

676bbe7d1c1fb71742df534ce8 ffd1b1af3b6864078f3 eb8


f8128d574c356631b8a9

91ecbe29a71f00ed5a3 eb8
e82f47b8d4949ba4af69b38cbc19

6aae8d25951 eb8 b06bbfa920aa95dd

9c9e2e0f2da8758e436c 45827dbdd8 45827dbdd8


eb8

ac487676a04e4

0a963fef9 4a38abc630c82b0c48dfbf5271 75ba8d840070942eb4e737849


6448451ac2ceade90715378b

eb8 d370c12dbc

eb8

7e74e1587f3a4d208
5eea496cc301b2a9721

0acc5bb8ca4 46f754ea06f070dbc023e571a876 6aae8d25951 45827dbdd8

910b00285f11bb90d0a15641

11bb8ed3ae227d3acefc
81dabfaba8

45827dbdd8 80874aa8

8b06a67a 1d163eac141def176461c 08dade990b2282


5e9156098c064

07f8a9e55a16beddb3c9153b0 86276bb1e23f2c7ffcbe82a0
46f754ea06f070dbc023e571a876

1b13908a9f0763c0ae54af9062080
0acc5bb8ca4

bf01c8a262 fa2afbd869

533E

81dabfaba8

c1c30f30d40c4f1f84924622f

81dabfaba8

9937ccba1469
81dabfaba8

84e4f1c582427a98d7b 6c632ad9c42228bb337 08dade990b2282

11bb8ed3ae227d3acefc

ea890ccca2f7c2107351 dca32af03698c988b22
cd0d985a366cad7e

3b2f08d52e4bca3f9ca7bbbd6
0f940646

f0bd1521

6c632ad9c42228bb337

503737b64d432c60d6ac557e0e6
1d163eac141def176461c

f78e145a127014eb43345a0c

dca32af03698c988b22

18115fa32ff1cb99
84e4f1c582427a98d7b

ea890ccca2f7c2107351

18115fa32ff1cb99

0c72a426929600000f5
fb039d7a2a9fe73b5f468eba9

a27037332d9fa5c43bcfe94c0

0c72a426929600000f5

3cdc90c57243373efaba65a

173fd00917644f0f1f3e3

173fd00917644f0f1f3e3 24431c3eb075102f07cc2c1be

e3bdbca0e2256fffa8a59018

75ba8d840070942eb4e737849

07f8a9e55a16beddb3c9153b0

9c9e2e0f2da8758e436c 4a38abc630c82b0c48dfbf5271

86276bb1e23f2c7ffcbe82a0

root root+PRISM root+VPSC

Figure 4: Divergence of dissimilarity measures: for both graphs, σdist estimates


that VPSC gives layout closer to the original, while σdisp predicts the opposite.

hstntx72
hstntx75
hstntx73
hstntx70
hstntx71
hstntx74 hstntx67
hstntx16 hstntx69
hstntx23
hstntx68
hstntx17 brhmal71
hstntx22 brhmal67brhmal68
brhmal66
brhmal70
ftwotx64 hstntx82 brhmal69
ftwotx61 brhmal72
ftwotx62 ftwotx60 brhmal74brhmal73 jcvlfl68
ftwotx63
ftwotx65 brhmal75 tampfl81 jcvlfl66
brhmal77
hstntx80
hstntx65 brhmal76 brhmal60 jcvlfl67
miamfl80
hstntx64 brhmal81
hstntx60 hstntx61 brhmal64brhmal63
brhmal62
hstntx62 hstntx63
dllstx24 brhmal65
ftwotx80
austtx61 dllstx72
snantx80
dllstx70 brhmal61
austtx64 dllstx71 jcvlfl81 wpbhfl80
austtx60 dllstx25 brhmal82 ojusfl80
austtx65 nworla81 atlnga33jcvlfl61
austtx63 dllstx67 atlnga32
austtx62 dllstx22 dllstx28 atlnga76jcvlfl63
atlnga31 jcvlfl62
dnvrco79
dnvrco66 dllstx68 hstntx81 atlnga25 jcvlfl60
dnvrco77
dnvrco70
dnvrco67 dllstx29
dllstx69 dllstx21
dllstx80 brhmal80 tampfl80 atlnga75jcvlfl64
atlnga30 jcvlfl65
dnvrco69 dllstx31 atlnga77
anhmca73 dnvrco78 austtx80 chrlnc64
anhmca72 anhmca69 dnvrco65 lsvlky81
anhmca78 anhmca70 dnvrco68 dllstx76 clmasc61
orlnfl81 atlnga80 jcvlfl80
chrlnc69 chrlnc71
anhmca75 anhmca65
anhmca67 dllstx74 atlnga56atlnga64 atlnga71
atlnga70 chrlnc60
anhmca76 anhmca68 okcyok80 dllstx77 atlnga79 clmasc60chrlnc70
anhmca77 anhmca66
anhmca71 dllstx78 dllstx81 dllstx73atlnga59
atlnga65
atlnga69
nsvltn80
atlnga78
atlnga16
chrlnc65
clmasc62chrlnc61
anhmca79 anhmca63 dnvrco81 dllstx55 dllstx75 atlnga58 atlnga34 chrlnc62
mmphtn80
anhmca74
anhmca82
anhmca60
anhmca62 anhmca61 sndgca80 dllstx59
dllstx56 dllstx62 atlnga57 atlnga63atlnga35 atlnga74chrlnc63
clmasc80 hmsqnj61
hmsqnj60
anhmca64
anhmca81 stlsmo81 atlnga09
chrlnc66
tcsnaz80 dllstx57 dllstx61 dllstx58 cncnoh63 atlnga62 atlnga36rlghnc80
chrlnc80 hmsqnj62
kscymo21
kscymo18 dllstx79
dllstx83 atlnga83
cncnoh64 chrlnc68atlnga72 gnbonc60
dllstx65 cncnoh61 atlnga67 atlnga73
anhmca80 kscymo67 dllstx66 dllstx60
dllstx63 atlnga68 chrlnc67atlnga37gnbonc61
kscymo63 atlnga66 atlnga61atlnga81 gnbonc62
grdnca62 kscymo23tulsok80 kscymo64
kscymo71 dllstx82 cncnoh62 cncnoh60 atlnga60
chrlnc81 hmsqnj80
grdnca60 shokca80 kscymo68 kscymo65 kscymo61cncnoh81 atlnga82
kscymo73
kscymo69 kscymo62
grdnca61snfpca81
grdnca80 kscymo24 kscymo80 kscymo81 cncnoh69 gnbonc80
dnvrco60 phnxaz81 kscymo60
mmphtn81
dnvrco62lsanca80 kscymo22 kscymo82 cncnoh73
cncnoh72 phlapa82
dnvrco63 kscymo72kscymo17 chcgil63
chcgil58 bltmmd66
snjsca80 dnvrco61 kscymo83 lsvlky80
cncnoh68 washdc81 phlapa83 bltmmd64
cncnoh71
dnvrco64 dnvrco80 chcgil08 chcgil60 chcgil79 cncnoh82 cncnoh70 bltmmd68
bltmmd71
kscymo70
snfcca81 chcgil32 chcgil80 chcgil62 nwrknj82bltmmd65
chcgil72
chcgil34 chcgil82 chcgil37 bltmmd63 bltmmd70
slkcut80 lsanca82 chcgil59 chcgil81 nycmny82 bltmmd81 bltmmd69
scrmca80 snfcca82
chcgil33 chcgil64 chcgil30 phlapa80
phlapa81 bltmmd80 bltmmd62 bltmmd67
dnvrco82lsanca81 chcgil09 chcgil70 chcgil65 nybwny80
cmbrma61
snfpca80 chcgil71 chcgil61
chcgil35 chcgil29
cncnoh80 chcgil38
chcgil69 washdc82 noc30k80 bltmmd61 cmbrma60
chcgil36 nwrknj81 cmbrma81 cmbrma63 rcpknj80
dnvrco71 chcgil39
dnvrco72 cncnoh14 iplsin81 chcgil68
cncnoh13 nycmny81
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dnvrco75 chcgil83 cncnoh66chcgil67 hrbgpa80 washdt80 cmbrma65 cmbrma62
waynpa80
cncnoh16 hrbgpa62 cmbrma64
dnvrco76
dnvrco73 cncnoh65
cncnoh67
cncnoh15 pitbpa80 nycmny83
ptldor81 omahne80 desmia80chcgil76 dtrtmi80 cmdnnj80
dnvrco74 iplsin67 cdknnj80 slspmd80 cmbrma80cdknnj67 cmbrma69
chcgil77 chcgil73
chcgil74rlmdil80 iplsin66 washdc83 cdknnj81
iplsin68 hrbgpa61 cmdnnj62cdknnj71cdknnj66
cmbrma13
cmbrma68
chcgil75 dtrtmi81
chcgil78 hrbgpa60
sttlwa80 desmia64
desmia60desmia62 dtrtmi61 cdknnj61 cmbrma16whplny81
cdknnj68
dtrtmi62clevoh80
dtrtmi64 clmboh81 hrfrct81 artnva80 grcyny80 cdknnj70
cmdnnj61
cmdnnj60 cmbrma67
desmia61
desmia65desmia81 dtrtmi60 iplsin80 cdknnj64 whplny80 cdknnj69
dtrtmi63 cdknnj60 cdknnj62 grcyny61
desmia63 dtrtmi67 cdknnj63cdknnj65 cmbrma82 grcyny62 cmbrma83 cmbrma58
dtrtmi65
dtrtmi68
milwwi80
clmboh80 pitbpa81 hrfrct66artnva60grcyny63
hrfrct68 grcyny64 cmbrma76
cmbrma59
dtrtmi70 clmboh71 hrfrct67
clmboh69 artnva65grcyny65 cmbrma72 cmbrma77
artnva67
okbril80 dtrtmi69 iplsin65 clevoh60 hrfrct60
artnva66 cmbrma53
desmia67 dtrtmi66iplsin61 clevoh63 cdknnj82
clmboh67 cmbrma73 cmbrma79
chcgcg80 clmboh68 clmboh66hrfrct62artnva62artnva63 grcyny60 cmbrma57
desmia68
stplmn81 iplsin63clevoh62clevoh61
clevoh65 clmboh70 hrfrct61artnva64 artnva61 cmbrma74 cmbrma52
cmbrma71 cmbrma55
desmia66 iplsin60iplsin62 clevoh64 artnva68
cmbrma56
iplsin64 albyny80
milwwi81 clevoh81 clmboh62
clmboh61bflony80 cmbrma75 cmbrma78
cmbrma70 cmbrma54
mplsmn81 chcgcg63 chcgcg60 clmboh64clmboh63 cdknnj76
rlmdil81 hrfrct80
chcgcg61 clmboh65
clmboh60 cdknnj72
hrfrct82 cdknnj73
chcgcg64
chcgcg65 cdknnj75
cdknnj74 albyny63
mplsmn80 stplmn82 dytnoh80 akrnoh80 cdknnj77
chcgcg62 dtrtmi82 bflony60 albyny64 hrfrct03
clevoh66 bflony62 albyny65albyny60 hrfrct02
bflony61
syrcny80 albyny62 hrfrct65
clevoh68 albyny61
clevoh67 bflony65 bflony64 hrfrct70 hrfrct63
hrfrct64
bflony63 hrfrct72hrfrct71 hrfrct04
chcgcg81 hrfrct05
dtrtmi71dtrtmi75 dytnoh65
dytnoh60 hrfrct74 hrfrct73
hrfrct69
dtrtmi74 dtrtmi79
dtrtmi72 dytnoh62 dytnoh64 akrnoh62
dytnoh61 akrnoh61
dtrtmi76
dtrtmi73 dtrtmi77dytnoh63 akrnoh60
dtrtmi78
chcgcg71
chcgcg66chcgcg70
chcgcg68 chcgcg67
chcgcg69

badvoro badvoro+PRISM badvoro+VPSC

b124 b124+PRISM b124+VPSC

F gure 5 Compar ng PRISM and VPSC on two graphs Or g na ayouts are


sca ed to have an average edge ength that equa s 4 t mes the abe s ze
JGAA, 14(1) 53–74 (2010) 67

Table 3: Comparing the dissimilarities and area of overlap removal algorithms.


Results shown are σdist , σdisp and area. Area is measured with a unit of 106
square points. Initially the layout is scaled to an average edge length that equals
4 times the average label size.

Graph PRISM VPSC


σdist σdisp area σdist σdisp area
b100 0.74 0.36 14.59 0.95 0.62 25.33
b102 0.41 0.18 2.62 0.44 0.33 2.77
b124 0.52 0.12 3.39 0.28 0.06 3.04
b143 0.5 0.22 2.59 0.67 0.41 4.26
badvoro 0.35 0.15 11.85 0.65 0.58 11.71
mode 0.57 0.35 0.78 0.84 0.59 1.45
ngk10 4 0.25 0.05 0.54 0.16 0.03 0.53
NaN 0.25 0.06 1.15 0.15 0.04 1.15
dpd 0.14 0.03 0.54 0.1 0.03 0.53
root 0.73 0.28 16.02 0.73 0.7 25.93
rowe 0.16 0.04 0.38 0.11 0.03 0.38
size 0.35 0.11 0.54 0.28 0.08 0.57
unix 0.25 0.07 0.6 0.13 0.04 0.59
xx 0.39 0.18 4.23 0.45 0.34 4.54
Graph VORO ODNLS
σdist σdisp area σdist σdisp area
b100 - - - 0.49 0.24 1.09E3
b102 1.18 0.47 131.55 0.33 0.15 41.01
b124 0.69 0.36 19.09 0.43 0.26 14.64
b143 0.84 0.39 19.35 0.57 0.36 29.39
badvoro 3.8 0.9 4.45E5 0.34 0.10 166.53
mode 1.09 0.58 20.02 0.44 0.28 45.21
ngk10 4 0.46 0.2 0.79 0.23 0.12 2.21
NaN 0.49 0.22 2.28 0.33 0.18 4.86
dpd 0.43 0.23 0.6 0.38 0.29 1.45
root 4.14 0.94 3.68E8 0.39 0.14 1.52E3
rowe 0.41 0.2 0.68 0.25 0.11 2.01
size 0.62 0.34 2.07 0.28 0.16 3.35
unix 0.55 0.24 0.64 0.20 0.09 2.01
xx 1.13 0.44 185.7 0.30 0.11 45.18
68 Gansner and Hu Efficient Node Overlap Removal

Table 4: Comparing dissimilarity and area of overlap removal algorithms on the


Rome suite of test graphs. # stands for the number of graphs within the size
range specified.

sizes # PRISM VPSC VORO ODNLS


σdisp area σdisp area σdisp area σdisp area
10–19 1407 0.009 0.16 0.09 0.061 0.14 0.069 0.07 0.34
20–29 839 0.02 0.27 0.11 0.12 0.14 0.15 0.078 0.92
30–39 2036 0.03 0.36 0.13 0.19 0.13 0.26 0.078 1.85
40–49 1800 0.035 0.43 0.14 0.25 0.12 0.36 0.074 2.71
50–59 1045 0.042 0.51 0.15 0.32 0.11 0.53 0.074 4.53
60–69 1172 0.046 0.58 0.17 0.39 0.11 0.70 0.074 6.18
70–79 1008 0.051 0.64 0.17 0.46 0.11 0.94 0.073 8.44
80–89 788 0.05 0.71 0.17 0.52 0.10 1.20 0.07 9.99
90–99 1296 0.054 0.78 0.18 0.59 0.10 1.49 0.069 13.26
100–109 140 0.055 0.82 0.18 0.61 0.10 1.7 0.068 14.14

VPSC, VORO and ODNLS on the Rome test suite of graphs [4]. This suite has
a total of 11534 graphs5 of relatively small size. Due to space limitation, we only
give the similarity measure σdisp and the area, and we average the results over
graphs of similar sizes. Again, PRISM achieves the best compromise between
being close to the original drawing, and having a smaller drawing area.
We note that while there is no theoretical result guaranteeing that PRISM
algorithm converges to an overlap free layout in a finite number of iterations, in
practice, out of thousands of graphs tested, some as large as tens of thousands
of vertices, PRISM always converges within a few hundred total number of
iterations in the two main loops in Algorithm 1. In our implementation we set
a limit of 1000 iterations, even though this limit has never been observed to be
reached. Table 5 gives the number of iterations taken for the 14 test cases in
Tables 2-3. As can be seen, for these graphs, the maximum number of iterations
is 122.
As a demonstration of the scalability of PRISM, we consider its application
to a large graph. This is a tree from the Mathematics Genealogy Project [32].
Each node is a mathematician, and an edge from node i to node j means that j
is the first supervisor of i. The graph is disconnected and consists of thousands
of components. Here we consider the second largest component with 11766
vertices. This graph took 31 seconds to lay out using SFDP, and 15 seconds
post-processing using PRISM for overlap removal. PRISM converges in 81 itera-
tions. Important mathematicians (those with the most offspring) and important
edges (those that lead to the largest subtrees) are highlighted with larger nodes
5 Three graphs were dropped from the test because they were disconnected.
JGAA, 14(1) 53–74 (2010) 69

Table 5: Number of iterations taken in the two main loops in Algorithm 1. A:


initially the layout is scaled to an average edge length of 1 inch. B: initially the
layout is scaled to an average edge length that equals 4 times the average label
size.

Graph |V | |E| A B
b100 1463 5806 122 75
b102 302 611 66 44
b124 79 281 43 19
b143 135 366 46 26
badvoro 1235 1616 53 32
mode 213 269 43 26
ngk10 4 50 100 29 8
NaN 76 121 34 9
dpd 36 108 26 6
root 1054 1083 103 119
rowe 43 68 28 7
size 47 55 29 14
unix 41 49 32 8
xx 302 611 53 46

and thicker edges. Figure 6(top) gives the overall layout, which shows that
PRISM preserved the tree structure of the layout very well after node overlap
removal. Figure 6(bottom) gives a close up view of the details of a small area in
the center-left part of Figure 6(top) with many famous mathematicians of early
generations. Additional drawings of this and other components of the Mathe-
matics Genealogy Project graph, including that of the largest component, are
available [21].

6 Conclusions and Future Work


A number of algorithms have been proposed for removing node overlaps in
undirected graph drawings. For graphs that are relatively large with nontrivial
connectivities, these algorithms often fail to produce satisfactory results, either
because the resulting drawing is too large (e.g., scaling, VORO, ODNLS), or
the drawing becomes highly skewed (e.g., VPSC). In addition, many of them
do not scale well with the size of the graph in terms of computational costs.
The main contributions of this paper is a new algorithm for removing overlaps
that is both highly effective and efficient. The algorithm is shown to produce
layouts that preserve the proximity relations between vertices, and scales well
with the size of the graph. It has been applied to graphs of tens of thousands of
vertices, and is able to give aesthetic, overlap-free drawings with compact area
70 Gansner and Hu Efficient Node Overlap Removal

in seconds, which is not feasible with any algorithm known to us.


It is possible that algorithms such as VPSC, which rely on separate passes in
the X and Y directions, might be improved by randomizing which overlaps are
removed in which pass or by gradually removing overlaps using many alternating
X and Y passes. This would, however, further increase their computational cost,
which is already much higher than the algorithm proposed in this paper.
For future work, we would like to extend the overlap removal algorithm to
deal with edge-node overlaps. We would also like to explore the possibility of
using the proximity stress model for packing disconnected components.

Acknowledgments
We would like to thank Tim Dwyer and Wanchun Li for making their imple-
mentations of VPSC and ODNLS, respectively, available to us. We would like
to thank Yehuda Koren and Stephen North for helpful discussions, and Stephen
Kobourov for bringing our attention to the term “Frobenius metric”. Finally,
the reviewers’ comments were very helpful, especially in making the exposition
clearer and more accurate.
JGAA, 14(1) 53–74 (2010) 71

Karagrigoriou

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N w

F gure 6 The second argest component from the Mathemat cs Genea ogy
Project Top overa ayout w th node over ap removed Bottom c ose up
v ew of a sma area of the center- eft part of above
72 Gansner and Hu Efficient Node Overlap Removal

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