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Algorithms for Large Graph Visualization

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Algorithms for Large Graph Visualization

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Open Systems Laboratory

Indiana University

Bloomington, IN 47405

{chemuell,benjmart,lums}@osl.iu.edu

ABSTRACT

In this study, we examine the use of graph ordering algorithms for

visual analysis of data sets using visual similarity matrices. Visual

similarity matrices display the relationships between data items in a

dot-matrix plot format, with the axes labeled with the data items and

points drawn if there is a relationship between two data items. The

biggest challenge for displaying data using this representation is

nding an ordering of the data items that reveals the internal struc-

ture of the data set. Poor orderings are indistinguishable from noise

whereas a good ordering can reveal complex and subtle features of

the data.

We consider three general classes of algorithms for generating

orderings: simple graph theoretic algorithms, symbolic sparse ma-

trix reordering algorithms, and spectral decomposition algorithms.

We apply each algorithm to synthetic and real world data sets and

evaluate each algorithm for interpretability (i.e., does the algorithm

lead to images with usable visual features?) and stability (i.e., does

the algorithm consistently produce similar results?). We also pro-

vide a detailed discussion of the results for each algorithm across

the different graph types and include a discussion of some strate-

gies for using ordering algorithms for data analysis based on these

results.

CR Categories: I.3.6 [Computer Graphics]: Mehtodology and

TechniquesInteraction techniques; G.4. [Mathematric Software]:

User interfaces

1 INTRODUCTION

Visual similarity matrices (Figure 1), or similarity matrices, have

emerged as effective tools for visually examining relational data

sets represented as graphs [13]. While various forms of similar-

ity matrices have been used for over a century for analyzing small

data sets, very little literature exists that explores techniques for

generating usable images and scaling the visualization to support

larger data sets. In this paper, we examine the use of graph ordering

algorithms as similarity matrix layout algorithms. We apply a di-

verse collection of algorithms to synthetic and real world data sets

to study the utility of the ordering algorithms for generating lay-

outs for similarity matrices and we explore the limits of what the

orderings can expose about the relational structure of the data.

A graph, in the mathematical sense, is a collection of vertices

with edges between them. To represent data as a graph, each data

item is treated as a vertex in the graph and an edge connects two

vertices if there is a relationship between the items corresponding

to the vertices. This relationship can be any measure that relates

two items but it is most often either the presence of some shared

attribute or one of the many similarity or dissimilarity metrics used

for data clustering. If the measure used to create the edges has a

range of values, the value for a particular relation may be stored

Figure 1: Two visual similarity matrix visualizations of the National

Cancer Institutes AIDS screen data using dierent data orderings.

The one on the left, ordered by an expert, reveals structure within

the data while the one on the right ordered by a randomizer, is

indecipherable.

Figure 2: Matrix and node-link diagrams of the same graph. The

axes of the matrix view are labeled with the vertices (data items)

and edges (relationships) are dots in the plot area.

with the edge as an edge weight. These values are also used to lter

graphs to reduce the size and remove noisy edges. Representing

data as graphs opens open the possibility of using the many graph

theoretic algorithms that have been developed for analyzing graphs.

Visual similarity matrices, also known as shaded similarity ma-

trices, distance matrices, or proximity matrices, label their axes

with each data item and display a point in the plot area at (i, j)

when there is a relationship between the items (x

i

, y

j

) (Figure 2).

When most items are related, the visualization is a dense collection

of points. However, when the number of relations is smaller (e.g.,

in a ltered data set), similarity matrices can reveal data clusters

and other structural patterns.

Visual similarity matrices scale to hundreds of thousands of ver-

tices and millions of edges at interactive speeds on workstation-

class hardware, providing an effective way to visually explore a

large amount of data with a modest amount of resources. Because

each vertex only needs one point on the axis, modern displays can

interactively display up to 1500 vertices with each vertex assigned

to one column of pixels. If pixel-level resolution for individual ver-

tices is not required, anti-aliasing techniques can be used to display

millions of vertices interactively. Large-format displays (e.g., dis-

play walls) and high-resolution displays (e.g., printers) also extend

the size of data that can be displayed. Thus, visual similarity matri-

ces are an attractive solution for large graph visualization.

However, visual similarity matrices suffer from one serious aw

that can have a negative impact on their utility. The ordering of the

141

Asia-Pacific Symposium on Visualisation 2007

5 - 7 February, Sydney, NSW, Australia

1-4244-0809-1/07/$20.00 2007 IEEE

vertices on the axes has a tremendous impact on the interpretabil-

ity of the resulting visualization. A poorly ordered vertex set is

indistinguishable from noise while a well ordered one can reveal

complex relationships and structures. The biggest challenge in pre-

senting data using a matrix-based visualization is nding a good

ordering of the vertices.

There are three main strategies for ordering the items in a data

set. A default ordering is the ordering in which items were gener-

ated or acquired. Default orderings are often hand orderings created

by an expert curator. In the absence of a good default ordering, a

common method for ordering data sets is to use an attribute order-

ing, an order based on some attribute of the data items. For instance,

in a social network where the data items are people, an attribute or-

dering may be built using ages. Finally, structural orderings are

based on some exploitable structure within the data, such as the

presence of relationships between people in a social network graph.

By treating the data as a graph, graph theoretic algorithms can be

used to generate orderings based on its graph structure.

1.1 Vertex Ordering Algorithms for Visualization

A set of n vertices can be ordered n! different ways. In graph theory,

the problem of ordering the vertices to optimize a cost function is

known as minimum linear arrangement, or MINLA, and is a known

NP-hard problem [11]. For visualization, the cost function can be

thought of as nding the best layout for the data. Since NP-hard

problems cannot be solved in a reasonable amount of time, many

heuristic algorithms have been developed for ordering vertices that

generate orderings by meeting domain-specic optimization crite-

ria. These solutions are not perfect and have limitations, but are

usually a large improvement over random orderings.

To make algorithms practical for visualization, they need to run

in a reasonable amount of time. For interactive applications, this

would ideally be linear or better based on the number of vertices in

the graph. Attribute orderings can potentially achieve this runtime

behavior, but structural orderings generally visit most of the edges

in the graph. Thus, for structural orderings, a run that is linear

in the number of edges is preferred. In the worst case, this may

be quadratic in the number of vertices (one relationship between

each pair or vertices), but for ltered graphs it can be much closer

to the number of vertices times a small constant. The algorithms

should also not require memory beyond a few extra properties per

edge. Some algorithms derived from linear algebra use multiple

copies of the dense matrix and are impractical for interactive use on

workstations.

An important heuristic in most ordering algorithms is the choice

of the starting vertex. For some of the algorithms considered here,

auxiliary algorithms exist for selecting a good starting vertex. In

addition to the starting vertices, the layout of the graph in memory

can affect the result. Most algorithms process lists of edges for each

vertex and do not impose any order requirements on the edges. If

the edges were stored in memory using a good default ordering,

they may be returned to the algorithm in a good order and have a

positive effect on the result. While this is a good feature to exploit

in practice, it is dangerous for evaluating ordering algorithms. To

control for the inuence of the initial ordering, it is important to

evaluate algorithms against a default initial ordering and a shufed

initial ordering [32].

For this paper, we considered three general classes of ordering

algorithms, graph theoretic, sparse matrix, and spectral ordering.

Graph Theoretic Algorithms The simplest way to generate

an ordering of vertices in a graph is to simply number the vertices as

a they are visited by a graph theoretic algorithm, such as a search or

a partitioning algorithm. We use breadth-rst search (BFS), depth-

rst search (DFS), the separator tree partitioning algorithm, and an

ordering based on the degree (number of edges) of the vertices in

the graph.

Sparse Matrix Symbolic sparse matrix ordering algorithms

attempt to produce orderings that minimize ll-in during subse-

quent numerical factorization [12]. Some such algorithms attempt

to minimize the envelope occupied by non-zero (non-null) values in

the the matrix. For many sparse matrices, it is possible to pack the

non-zero elements around the diagonal. By pulling in the non-zeros

this way, the space between the diagonal and the most distant ele-

ments can be reduced. Interestingly, the visual representations of

these matrices are often similar to good default orderings for sim-

ilarity matrices. Here, we employ Reverse Cuthill McKee (RCM),

Kings algorithm, and Sloan ordering.

Spectral The nal algorithm we consider in this paper is an

ordering based on the spectral decomposition of graphs. The al-

gorithm uses the spectral properties of the Laplacian of a graph to

generate a suitable ordering of the vertices. While more expensive

than other methods, spectral decomposition is stable with respect

to the initial ordering as long as certain numerical constraints and

uniqueness conditions are met.

2 RELATED WORK

General matrix visualizations and their underlying similarity matri-

ces are important tools in cluster analysis. All classic texts on data

clustering include a section on similarity matrices (e.g., [9, 35]) and

their associated visualizations.

Feature-based matrix visualizations are closely related to visual

simulation matrices and have a long history, having been originally

used in the late 1800s by archaeologists for dating artifacts. With

the feature-based approach, data items are displayed along one ma-

trix axis and item attributes along the other. Using a process called

seriation, artifacts can be visually clustered using feature vectors

to form groups with similar features, with the nal order implying

a timeline [23]. The seriation problem has been studied rigorously

as an optimization problem ( [23], [25]) and feature-based matrix

visualizations have been applied heavily in archaeology, psychol-

ogy, operations research and, more recently, for comparing gene

expression proles [8].

Visual similarity matrices themselves appear to have their roots

in operations research in the 1960s [18] as an alternative to feature-

based visualizations for studying scheduling problems. In the

1970s, the dotplot was introduced for comparing genomic se-

quences [14]. Two genomes are placed on the axes of the plot

and dots are placed where they contain the same nucleotide. The

genomes have a default ordering that allows dots in the matrix to

reveal structural similarities between them. Helfman used a varia-

tion on the dotplot for studying texts and source code and also intro-

duced a basic vocabulary for discussing features in the plot [16].

We have recently extended this work by providing interpretations

for features in visual similarity matrices where there is no natural

default ordering [27]. In 1985, Murtagh phrased the matrix reorder-

ing problem as a general method for data clustering and included

the notion of thresholding the similarity matrix to improve the re-

sults [28]. Matrix-based visualizations have also been used to visu-

alize sparse matrices used in numerical computations, as a tool for

debugging and developing new algorithms [2, 22] and as a general

tool for software visualization [37]

Numerous small studies have been performed that combine vi-

sual similarity matrices with clustering algorithms on real-world

data sets. Gale describes a procedure for using hierarchical clus-

tering and seriation algorithms along with visual similarity matri-

ces for data analysis [10]. In a similar vein, Wang uses nearest

neighbor clustering and an ordering based on the decision tree algo-

rithm to visualize a similarity matrix [38]. Strehl introduces OPPO-

SUM [36], a modied version of the graph partitioning algorithm

METIS [19], to generate orderings and the CLUSION visualization

toolkit for visualization. Abello takes a slightly different approach

142

with his graph sketches by ordering the data with BFS and display-

ing a sketch of the similarity matrix that shows summary informa-

tion on the local density of the plot [1]. In his dissertation [32],

Schumaker used BFS, DFS, and a custom optimization algorithm

to order similarity matrices. He also introduced the idea of using

both default and shufed initial orderings for evaluation.

Sparse matrix ordering algorithms are described in detail in [12]

and can be found in many applications and libraries (Matlab [24],

Pajek [7], BGL [33]). Gibbs performed an early comparison of

ordering algorithms using sparse-matrix bandwidth and prole re-

duction as the measurement [15]. Spectral methods [39] are a more

recent development and have found widespread use not only in ma-

trix ordering applications, but also in gene sequencing and text

mining applications. In [3], Berry describes the use of RCM and

two spectral methods for browsing term-document feature matri-

ces for hypertext collections. The images in his tutorial suggested

their utility for general use in visualization and helped lead to this

study. Kumfert [21] and Hu [17] propose hybrid methods using of

Sloans algorithm and spectral methods for wavefront reduction in

sparse matrices. Images in their papers also suggest that similar

approaches may be useful for visualizations purposes.

Recently, two user studies have validated the use of similarity

matrices for identifying relationships and structural features in data.

In his dissertation [32], Schumaker performs a user study compar-

ing node-link diagrams and structure-based matrix visualizations

using attribute orderings, DFS and BFS derived orderings, and a

new algorithm based on the dynamics of social networks. The work

in [13] also contributed a user study that evaluated matrix-based

visualizations for common graph-based tasks, such as identifying

related vertices. Both studies conclude that similarity matrices are

effective tools for visually analyzing graphs.

As a testament to their general utility, many data analysis tools

include matrix visualizations (e.g., SPY in Matlab [24] and TV in

IDL [31]). Pajek [7] also includes numerous algorithms for par-

titioning and ordering the data (including BFS and DFS) and has

recently begun to include sparse matrix algorithms, inspired by an

earlier, unpublished version of this paper.

In this work, we extend [3] and [32] by combining and extending

the set of algorithms studied, introducing the use of multiple syn-

thetic data sets, and dening a method for evaluating orderings. We

also characterize the results to provide suggestions for further re-

nements of existing algorithms and directions for newalgorithms.

3 METHODS

To evaluate the ordering algorithms for use in visual similarity ma-

trices, each algorithm was tested against a collection of synthetic

and real graphs. Two versions of each graph were used: one built

using the default ordering of the vertices and the other built using a

randomordering of the vertices (Figure 1). Using randomly ordered

vertices allowed us to determine the inuence of the default order-

ing on the nal image. For the synthetic graphs, multiple graphs

were generated, varying the size and generator specic parameters

to get a representative collection of graphs of each type.

All data, parameters, images, and code used in this study are

available as supplementary material online [26].

3.1 Data

To test the algorithms in with different graph types, we used ve

types of synthetic graphs and three graphs derived from real data.

The synthetic graph types are as follows:

Erdos-Renyi. So-called random graphs connect vertices

based on a Gaussian probably distribution. If the probability

is 1.0, the graph is a clique.

Small World. Vertices are connected to k neighbors in a lin-

ear fashion. A re-wiring operation randomly rewires some

edges to add noise to the graph.

Power-law. Edges are added to the graph following a power-

law distribution.

K-partite. K sets of vertices have no intra-set edges and are

randomly connected to vertices in disjoint sets based on a

probability parameter

K-linear-partite. Similar to K-partite graphs, but sets are

only connected to two adjacent sets, forming a chain of k-

partite graphs.

Graphs of each type were generated with 100, 500, and 1000 ver-

tices and a small parameter sweep was performed on the parameters

for each graph type. For instance, the small world graphs were gen-

erated with 5 and 10 neighbors and re-wiring probabilities of 1%

and 10%, leading to 12 variations on the small world graph (or 24

variations when considering the initial ordering). The number of

edges is dependent on the graph type and is a small constant multi-

plier for small world graphs and a percentage of all possible edges

for the other graph types.

The real graphs were derived from two life science data sets. The

rst two graphs were generated from proteins listed in the COG

database [30] and similarity scores acquired from the PLATCOM

database [6]. The proteins comparison scores were ltered for dis-

similarities greater than 2.0 to create the full COG graph. Two

sub-graphs were extracted from the full graph. The COGsimilar

graph consisted of a set of COG families that had a large num-

ber of similarities between proteins in different families and was

highly connected. The COGdissimilar graph consisted of proteins

from families that had few relations. The graph was highly con-

nected within families but had few connections between families.

The COGsimilar graph contained 1770 vertices and 290,583 edges

and the COGdissimilar had 2030 vertices and 158,724 edges.

The nal two real graphs were built from the National Cancer In-

stitutes collection of chemical compounds and their AIDS screen-

ing annotations [29]. MolInspirations toolkit [5] was used to gen-

erate a list of properties for each compound, which were combined

with the AIDS annotations to form the feature vector for each data

item. The properties generated were: molecular weight, logP, to-

tal polar surface area (TPSA), number of atoms, number of hydro-

gen acceptors (nON) and donors (nOHNH), number of rule-of-5

violations, and number of rotatable bonds.Two graphs were gen-

erated from the data set, one containing the compounds that had

AIDS screening results, NCAall, and the other containing the 436

compounds that were conrmed active against AIDS (CA in the

annotation data), NCIca. A similarity matrix was created for each

data set using Euclidean distance and a feature vector containing

all computed properties. The NCAall matrix was thresholded at

10.0, resulting in a graph with 42,750 vertices and 3,292,778 edges.

The NCIca graph was thresholded at 100.0 and had 436 nodes and

18,683 edges.

3.2 Algorithms

The next few paragraphs provide brief descriptions of the ordering

algorithms and their complexity. Complexity is dened using big-

O notation in terms of the number of vertices V, the number of

edges E in the graph, and m=max{degree(v)|v in V}. More details

are available from the main reference or the Boost Graph Library

documentation [33].

Breadth-rst search (BFS) and depth-rst search (DFS) [39] are

both foundational graph theoretic algorithms that visit each vertex

in the graph in a predictable manner. When BFS visits a new vertex,

it adds each vertex connected to the current vertex to a buffer and

visits the vertices in the order they were added. It visits all nodes

143

connected to the starting vertex rst, and then proceeds to nodes

discovered during those visits. DFS, on the other hand, visits the

rst vertex from each node in the order they are discovered before

moving on to the second vertex in each node. Both DFS and BFS

have O(V +E) time complexity.

Degree ordering is an attribute ordering that orders the vertices

in the graphs by their degree, i.e. the number of edges connected to

a vertex. For vertices with the same degree, the order is undened.

The running time for degree ordering is dominated by the cost of

acquiring the degrees or by the cost of the sort operation, depending

on what data structures are used. In our implementation, the adja-

cency graph data structure provided O(1) degree access, so the time

complexity was determined by the sort algorithm at O(VlogV).

Reverse Cuthill-McKee (RCM) [12] and Kings [20] algorithm

are variations on breadth-rst search that use a local priority queue

to select the next vertex to visit, based on the vertices that have been

discovered but not already visited in the search. In RCM, the vertex

with the highest degree is visited next. Instead of ordering the ver-

tices based on their total degree, King orders the vertices in its pri-

ority queue based on the number of edges each vertex has to already

visited vertices. The time complexity for RCM is O(mlog(m)|V|)

and the time complexity for King is O(m

2

log(m)|E|).

In Sloans algorithm [34], start and end vertices are chosen to

maximize distance between the two vertices and all other vertices

are initially prioritized by their degree and their distance from an

end vertex. Low degree, distant vertices have highest priority. Then

one by one the algorithm goes through the vertices, increasing the

priority of the children and grandchildren of the vertex. After or-

dering one vertex, the highest priority of the remaining vertices is

chosen. The time complexity for Sloan is O(log(m)|E|).

The separator tree ordering is based on the recursive partitioning

algorithm in [4]. It uses graph separators, sets of vertices that

can be removed to partition the graph in to subgraphs with a xed

number of vertices, to partition the graph into subgraphs. Like the

sparse matrix ordering algorithms, it was designed to reduce the

storage requirements for large graphs.

Spectral ordering uses an order based on a constrained energy-

minimal linear representation of the graph (in which the sum of all

edge lengths squared is minimized). This is accomplished by nd-

ing the eigengvector corresponding to the second-smallest eigen-

value (the Fiedler vector) of the graphs Laplacian matrix, and

sorting the vertices according to their corresponding entries in the

eigenvector [39]. If the vertices have unique values, spectral meth-

ods are stable with respect to the initial ordering. That is, spectral

methods will return the same ordering for default ordered and shuf-

ed graphs. Spectral methods are known to be able to expose some

features of regular graphs and bipartite graphs [39].

Spectral ordering has a time complexity of O(V

3

) for implemen-

tations that use dense matrices and can achieve O(V

2

) for sparse

versions. As long as certain numerical stability constraints are sat-

ised, the spectrum of a graph should be independent of its initial

ordering. While spectra are expensive to compute and not practical

for interactive use, we felt this property was important enough to

warrant inclusion in this study.

3.3 Implementation Details

Except for separator tree and spectral ordering, all algorithms were

from version 1.33 of the Boost Graph Library (BGL) [33] and ac-

cessed using BGL/Python. All graphs and algorithms used the

boost.graph.Graph class. The separator tree and spectral order-

ing algorithms were implemented in Python, using the BGL graph

classes, with the latter using Numeric Python. For BFS and DFS,

the starting vertices were the rst vertices stored in the graph data

structure. For RCM and King, the starting vertices were selected

using the algorithms provided by the BGL. The experiments were

Figure 3: Stability and Interpretability Measurements. Thumbnails

for a 100 vertex small world graph ordered using DFS, starting with

the default ordering (left) and a shued ordering (right). In both

images, structure is visible. Using our stability evaluation criteria,

this pairing is assigned structure (I). Both ne and coarse structure

is visible, giving it a coarse and ne (CF) rating for interpretability.

run on an Apple dual 1.8 GHz G5 Mac with an nVidia 6800 graph-

ics card and 1 GB of RAM. The BGL code was compiled using

g++ 3.3 (build 1671) and the Python version was Apple framework

build of Python 2.3. The versions of the Python libraries used are:

OpenGL 2.0.1.04, Numeric 23.8, PIL 1.1.4. These libraries are all

thin wrappers around optimized C and C++ libraries and have min-

imal calling overhead.

3.4 Evaluation

Each graph type and ordering combination was evaluated for stabil-

ity and interpretability (Figure 3). These measures were designed

to measure consistency of the visualizations for each ordering and

how useful the visual features were. The term structure is used

strictly to identify visual structure imparted by the ordering algo-

rithm, and implies no underlying structure in the data. Detailed

exploration of the interpretation of visual structures for individual

algorithms is beyond the scope of this work.

Stability measures how similar the images are for the default or-

dering and random starting orderings for each algorithm. Each pair-

ing was assigned one of the following ratings:

Stable. The ordered and shufed images have structure and

are similar in appearance.

Structure. The ordered and shufed images have structure

but are not similar.

Ordered. The ordered image has structure, while the shufed

image has no structure.

No structure. Neither image contained structure.

Stability was determined by comparing the thumbnails (Fig-

ure 3). Images were determined to have structure if the overall vi-

sual density of the image was not uniform. Structures were deemed

similar if, in the thumbnail view, the overall images looked similar.

Interpretability measures the amount and type of structure

present in the image and is assigned to all images, not just image

pairs. Five interpretability categories were used:

Coarse and ne structure. Structure is present at all levels

of detail.

Coarse structure only. Large structural features are present,

but no features are discernible within the structures.

Fine structure only. Small features, such as horizontal or

vertical lines are visible in the large image, but there is no

obvious coarse structure.

Minimal structure. A minimal amount of algorithm-specic

coarse structure is present, but the image otherwise has no

structure.

144

No structure. No structure is present in the image

Coarse structures are large features in the images that are com-

posed of most or all of the edges in the graph and are often thick

diagonals or blocky regions. Fine structures are composed of a few

local edges and multiple instances of the same structure needed to

be present for an image to get this rating. Some algorithms added

a small amount of structure to otherwise random images. The min-

imal structure category distinguishes these cases from those where

there truly is no visible structure. Interpretability assignments were

also modied with a diagonal qualier when the structure was only

present around the diagonal.

These ratings were coarse gained enough that they almost ev-

ery image and pairing was unambiguously assigned a stability and

interpretability category. In the few cases where there was not an

obvious assignment, the value closer to no structure was used.

3.5 Visualization

The visual similarity matrices were generated using a custom ma-

trix viewer developed by the Open Systems Lab. The viewer is

built in Python and uses the Python OpenGL bindings to render the

images. Each dot in the matrix was drawn as a GL POINT. The im-

ages were rendered using an nVidia 6800 graphics card at a resolu-

tion of 1000x1000 with point anti-aliasing (GL POINT SMOOTH)

enabled. 1000x1000 images represent a realistic size for interactive,

on-screen visualization. Each image was read directly off the card

and saved as a PNG using the Python Imaging Library (PIL). The

thumbnails were generated using the BICUBIC sampling algorithm

from PIL and saved as 100x100 PNG les. For the paper, the im-

ages were processed to change the background from black to white

using Photoshop 7.0 on OS X. The images were inverted then con-

verted to grayscale and back to RGB to remove color information.

4 RESULTS

The overall stability and interpretability results are listed in tables

1 and 2. All images used to generate these results are available on-

line [26]. In the next few sections, we discuss the results from dif-

ferent perspectives. First, we present the stability and interpretabil-

ity results. Then, we break down the results by ordering algorithm

and graph type. We conclude with observations about scalability

and the effects of the graph structures.

Table 1: Stability Results Stability measures the similarity in appear-

ance between the default ordered images and the shued images. S

= Stable, both have structure and are similar, I = Structure present,

but not similar, O = Ordered only has structure, N = No structure

Graph Ctrl BFS DFS King RCM Deg Spc ST Sloan

sw O S I S S O S S S

pl O S I S S S S S S

er N S S S S N N S S

kp2 O S S S S N S S S

kp5 O I S S S N N S S

kl2 O S S S S N S S S

kl5 O I I I I S S S S

COGsim O S I I I S S I S

COGdis O I I I I S S S S

NCAca O I I S S S S I S

4.1 Stability

All algorithms except degree were stable or contained structure for

both the default and shufed orderings for a majority of the graph

types. The control pairing (i.e., the default ordered image and the

shufed image) consistently generated good images for the default

ordering and noisy images for the shufed ordering.

Table 2: Interpretability Results Interpretability measures the quality

of the structure. C = Coarse grained structure, F = Fine grained

structure, M = Minimal structure, D = Diagonal structure, N = No

structure

Graph Ctrl BFS DFS King RCM Deg Spc ST Sloan

sw CF CF CF CF CF M C CF CF

pl N C C C C C C C C

er N M MD M M N N MD M

kp2 C C CD C C N C CD CF

kp5 C M MD M M N N CD C(FD)

kl2 C C MD C C N C CD CF

kl5 C CF C CF CF C C C C

COGsim C CF CF CF CF C C C C

COGdis C C C C C C C C C

NCAca C C C C C C C C C

Figure 4: Three dierent orderings (left to right: BFS, DFS, degree)

of a 100 vertex power law graph show enevelope, horizon, and galaxy

footprints, respectively.

On synthetic data, the orderings were almost always stable

against shufing. The only exceptions were DFS and degree. For

graphs with more ne grained structure, DFS generated different,

but usable images depending on the initial ordering. Degree typ-

ically generated images that were indistinguishable from noise.

However, when the degree distribution was meaningful to the graph

type (e.g., power law), the degree orderings exposed this.

On real data, all algorithms generated images with some struc-

ture. BFS, DFS, King, RCM, and separator tree generated different,

but usable structures for the default and shufed initial orderings

(the structure category using our ranking system). While degree

and spectral were stable, the type of structure present in the images

was difcult to use to explore the underlying data.

4.2 Interpretability

Coarse grained structure was present in almost all images and var-

ied with the type of graph, size of graph, and algorithm. If there

was course grained structure in the graph, (e.g. bi-partite graphs),

all algorithms except degree were able to generate consistent pat-

terns. The patterns did not always reveal the intrinsic structure of

the graph, but did provide clues as to the presence of such a struc-

ture.

The algorithms resolved coarse structures better as the size of

the graph increased. Smaller synthetic graphs contained too few

nodes and too many random connections to reveal their structure

except under the default ordering. However, as the size of the graph

increased, consistent patterns developed in the images.

Some algorithms had a characteristic footprint (Figure 4)that was

evident across all graph types. The graphs with the least amount of

coarse grained structure (e.g., ER and 5-partite graphs) led to im-

ages with patterns dominated by the algorithms footprint. As the

amount of internal structure increased in the graph, the footprint be-

came less noticeable and the graph structure became more evident.

The footprints fell into three main categories: envelopes, galaxies,

and horizons. Envelopes form a bubble centered on the diagonal

that contains all the edge dots and are characteristic of BFS-based

algorithms. Galaxies are dense regions of dots centered on the di-

agonal. These are generated by the spectral and degree orderings.

Horizon footprints are tight lines of dots that follow the main diag-

onal and sometimes branch at oblique angles off the main diagonal

and are indicative of DFS and separator tree. Both envelopes and

145

horizons highlight the path the algorithm took through the graph.

The edges that make up the feature are the edges that were directly

used by the algorithm.

The small world and real graphs both contain ne-grained struc-

ture and all algorithms generated more detailed patterns that could

be used to trace relations between vertices and groups of vertices

in these graphs. This was most apparent with BFS, King, RCM,

DFS, and Sloan, though separator tree also exposed some detail in

the small world graphs. These ne-grained patterns were not de-

pendent on the size of the graph and were present in the 100 vertex

small world graphs. While the characteristic footprint for each algo-

rithmwas visible in these cases, it only affected the overall structure

of the image at the boundaries of the more detailed sections. RCM

and King both introduced a secondary footprint to dense regions of

the images that added some order compared to BFS.

4.3 Algorithms

BFS BFS orderings are characterized by an envelope footprint.

The BFS envelope is generally solid and the interior of the envelope

can reveal some of the graph structure. In cases where there was

coarse structure and the graph was not too dense (e.g., bipartite, 5-

linear-partite, real data), the interior contained overall patterns of

connectedness but could not separate them further. For instance, in

the 5-linear-partite graph, BFS created a simple checkerboard pat-

tern with two dark and two light squares that appear to wrap around

the image. This reveals the partite nature of the graph but fails to

provide more insight into how many sets make up the graph. Dense

graphs, such as ER and 5-paritite, proved challenging and the in-

terior of the envelope contained no structure. Small world graphs,

on the other hand, had two consistent features: a solid envelop and

a diagonal composed of many tight clusters. Between the diago-

nal and the envelope, a few small clusters and outliers occupied an

otherwise empty expanse. In the real world graphs, BFS produced

tight clusters with little internal structure connected by envelopes.

DFS DFS orderings varied the most between default and shuf-

ed initial orderings, but always left a horizon footprint that exposes

the path it tool through the graph. If there is ne-grained internal

structure in the graph, DFS generated images with ne-grained fea-

tures. Small world graphs resembled Rorschach ink-blots that var-

ied in appearance depending on the initial ordering of the graphs.

A strong diagonal was always present and clusters either trailed off

at oblique angles or sat away from the diagonal in the plot area. On

real world graphs, the diagonal tied together components, similar

to those found in BFS images. However, unlike BFS, DFS gener-

ated some internal structure in the components, leaving a distorted

checkerboard with rectangular squares of various aspect ratios con-

nected by stocky, angular clusters.

For shufed power-law graphs, DFS consistently generated a

secondary footprint. In power law graphs, the diagonal eventually

trailed off, but before it did, a strong horizon-like front emerged or-

thogonally from it. The region preceding the horizon contained the

majority of the edges and the area outside this region was void save

for a few small clusters clinging to the diagonal. The horizon effect

was also evident in the 5-partite and 5-linear-partite graphs where

it was strong enough that not even the diagonal passed through. In

the latter case, the empty region past the horizon serves the same

purpose as the empty squares generated by BFS and hints at the

partite nature of the graph.

Degree Degree orderings were the poorest overall. Degree or-

dering is an attribute ordering on the vertices, and in most graphs

the degree distribution is fairly small. Thus, large numbers of ver-

tices have the same degree, and within those sets the initial order-

ing dominates. Power-law graphs were an exception and degree

ordering immediately revealed the power-law nature of the graph.

The nodes with the highest degree are generally interconnected and

Figure 5: Three dierent orderings (left to right: BFS, RCM, King)

of a 1000 vertex 5-linear-partite graph demonstrate how renements

of a core algorithm add additional structure. RCM and King are built

on BFS and maintain the same overall structure. But, RCM further

separates the dense areas into comb-like structures while King adds

combs and a faint hash pattern to the image.

formed a dense galaxy footprint around the origin. Real world

graphs also showed some structure under degree ordering. Often,

cluster within the data were cliques or near cliques. Because all ver-

tices in the cluster had the same degree and the sizes of the cluster

tended to be unique, clusters appeared using degree ordering.

Separator Tree Separator tree orderings were characterized

by fat diagonals and variations in the density of remaining dots

when structure was present in the graph. Separator tree was one

of the algorithms that nearly reproduced the default ordering for a

graph type. The diagonal produced by the algorithm recovered the

overall visual structure of the default small world graph ordering

for the shufed small world graphs. The effect improved as the

number of vertices increased. In power-law graphs, a dense cluster

sat on the diagonal that decreased in density further out from its

center, similar to the power-law structure at the origin in degree

orderings. On real world graphs, separator tree separated the graph

into clusters and generated localized patterns similar to those of the

synthetic graph in each cluster.

RCM and King RCM and King both rened the images pro-

duced by BFS (Figure 5). The envelope was still evident, but when

there was more structure to the graph, both algorithms generated

regular patterns in the regions within the envelope. The 5-linear-

partite graphs demonstrated this effect most vividly but it was also

visible in the real world graphs. RCM adds long, wedge shaped

striations to the clusters and King imparts a crosshatched structure,

with short wedges making up each hatch.

Sloan Sloan ordering revealed structure in all graphs that con-

tained structure and was the only algorithm without a characteristic

footprint. Rather, Sloan generated images reminiscent of the default

orderings and enough features were present to identify the overall

structural features in the graphs. Small-world graphs had strong

diagonals and k-partite and k-linear-partite graphs all had dened

block structures. Of the synthetic graphs, power-law graphs re-

solved the least. A single dense region formed, but it was not as

tightly packed as in other orderings. On the real data, Sloan packed

the edges along the diagonal in block structures that all contained

some internal structure. As with the Sloan orderings for synthetic

data, the Sloan orderings for real data were visually similar to the

expert default orderings.

Spectral Decomposition Spectral decomposition performed

well on structured graphs and in the case of 5-linear-partite graphs

with greater than 10%connectivity, completely recovered the visual

structure of the default ordering. For other graphs and less con-

nected 5-linear-partite graphs, it generally produced a galaxy foot-

print with the shape of the galaxy indicative of the graph structure.

Small world graphs with few nodes appeared as fat diagonals that

spread out into edge-on galaxy views as the number of nodes and

re-wiring probabilities increased. Power-law graphs were square

galaxies. The various k-partite graphs all contained distinct holes

that were indicative of the number of sets in the graph. As the size

146

of and connectivity of the graph increased, these holes resolved into

the gaps in the default ordering. It is known that eigenvalues, the

basis for spectral ordering, can reveal properties about regular and

bipartite graphs [39], so the results for small world and k-partite

graphs are not unexpected.

While spectral ordering generated good images for the synthetic

data, it did not work as well on real data. If the real data was densely

connected and had small world properties (e.g., NCAca), it gave

orderings similar to BFS. However, when the relationships between

vertices were more complex, the data resolved to a fewclusters with

little internal structure.

4.4 Graph Types

Among the graph types, small world and 5-linear-partite graphs al-

most always had useful structures visible. For small world graphs,

most orderings generated strong diagonals and showed the lack of

relations among most of the vertices. 5-linear-partite graphs, espe-

cially with a large number of nodes and high connectivity were eas-

ily ordered and resolved into images that contained important clues

to their structure. On the other hand, ERand 5-partite graphs almost

never contained useful structures. For ER graphs, this is expected.

5-partite graphs, with lots of connections between the sets, are very

close to ER graphs and thus display similar behavior. Power law

graphs almost always had some structure that showed a power-law

distribution in the connections but, except for the curious horizon

pattern generated by DFS, rarely had any other consistent structure.

Real world graphs (Figure 6) always contained some structure,

though in some cases it was only at the level of the densely con-

nected regions within the graph and little revealing structure. For

the large real world graphs, many of the nal images looked the

same, regardless of the ordering algorithm. This is because, at the

resolution used, only the connected components appear as small

clusters. In fact, the components are large and zooming in on them

reveals the structure more characteristic of each algorithm.

5 DISCUSSION AND CONCLUSIONS

Visual similarity matrices have a much higher information density

than most information visualization techniques. For graphs, tradi-

tional node-link graph diagrams can only display tens to a few hun-

dred nodes with a small number of edges before they become un-

readable. Scatter plots can display a large number of points, but re-

quire multiple visual dimensions (e.g., size, color) to display com-

plex relations. Similarity matrices, when ordered properly, can eas-

ily display thousands of vertices and millions of edges with detailed

structures between them. In this study, we examined a core set of

algorithms for ordering vertices to generate usable images. Most

algorithms were capable of coaxing some visual information out of

the graphs, but none consistently generated images good enough

that it could be blindly applied to any data set and reveal its struc-

ture. Despite this, there are some important conclusions, directions

for future research, and practical advice for using similarity matri-

ces that can be derived from this study.

First, and most importantly, if structure is present in the data,

the ordering algorithms will consistently provide clues to it. The

characteristic footprints of many of the algorithms provide a basic

framework for exploring the data. Once the algorithmic artifacts

are identied, they can be used to trace relationships (e.g. blots

in DFS, striations and crosshatches in King and RCM) or identify

broad trends in the data (e.g. galaxies in separator tree and spectral

orderings).

The connectedness and amount of randomness in the graph is di-

rectly related to the quality of the ordering. Dense graphs with lots

of random connections rarely resolved into usable images. Sparse

graphs, especially those with structure, tended to resolve to good

images. This suggests that care should be taken when ltering data

to produce the graph and multiple versions may be necessary to

nd the correct ltering level. While locally dense regions will still

suffer, the overall structure can be determined and local regions pro-

cessed independently.

The algorithms that looked at the local and global properties

tended to produce the most detail. Whereas breadth-rst search

showed coarse structure, the modications made by King and RCM

to take into account local features improved the patterns in the im-

ages. Sloan generated very good images by considering the starting

and ending vertex from the beginning. One caveat is that when al-

gorithms worked off a local priority queue, such as those used in

King and RCM, the resolving power was limited to the average size

of the queue, which was often quite small. New algorithms should

look to exploit and extend these techniques by identifying other

methods of including more global information in the algorithm be-

yond starting and ending nodes and better ways of managing the

priority queues.

When used for data analysis, these ordering algorithms are most

appropriate at the exploratory stage. As part of a pipeline for exam-

ining data, different algorithms can be applied with different initial

orderings. In the same way that many different attributes are used

as axes for scatter-plots in scatter-plot matrices, different vertex or-

derings can enable a user to quickly see the structure of the data

from many different perspectives. Combined and linked with other

interactive visualization tools, the user can use the maps provided

by the orderings to identify and explore regions of interest within

the data. Our results with augmenting similarity matrices with other

views of the data suggest that this is a powerful method for studying

large data sets [27].

Because the use of automatic ordering algorithms is relatively

new for similarity matrices, the types of patterns and their meanings

are not fully understood in analytical contexts. Typically, attribute

orderings are scanned and those that contain block structures are

accepted. As these algorithms show, structural orderings contain

other types of patterns that are repeatable and can reveal more infor-

mation about the data. As these techniques get applied to more real

data sets, a common vocabulary for describing the features could

emerge that gives analysts another tool for discussing data [27].

For this study, we looked at algorithms that relied only on the

structure of the data. However, more information is present in the

graphs, often in the form of edge weights or attributes on the ver-

tices. Most of these algorithms could be modied to use this addi-

tional information and possibly produce better orderings.

This study systematically examined a number of vertex ordering

algorithms against a collection of real and synthetic data and de-

scribed and evaluated the results. Visual similarity matrices have

the potential to be a powerful visual analytical tool, but still have

some hurdles to overcome. Our results suggest that algorithms de-

signed for graph and sparse matrix analysis are useful for visually

discerning coarse and ne grained features in data sets. Further re-

search will help rene these algorithms for regular use on real data

and to develop algorithms designed specically for visualization.

6 ACKNOWLEDGMENTS

This work was funded by a grant from the Lily Endowment. Doug

Gregor provided support for the Boost Graph Library and its Python

bindings. Jeremiah Willcock supplied the separator tree implemen-

tation and many useful insights through the course of this project.

This work was originally suggested by Sun Kim, who maintains the

PLATCOM database and provided important feedback early on in

the project. Katy B orners group provided feedback and end-user

perspectives that helped drive this study.

147

Figure 6: All orderings for the COGsimilar data set. The top row contains orderings using the default initial ordering from the COG database

and the bottom row used the shued initial ordering.

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148

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