Big Data Research 27 (2022) 100291

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Force-Directed Timelines: Visualizing & Exploring Temporal Patterns

António Cruz ∗ , Joel P. Arrais, Penousal Machado
University of Coimbra, CISUC, Department of Informatics Engineering, Coimbra 3030-290, Portugal

a r t i c l e i n f o a b s t r a c t

Article history: Visualization has shown to be a valuable tool in the analysis of large and complex temporal datasets,
Received 14 February 2021 aided by the emergence of new models such as Time Curves, which distorts timelines to position
Received in revised form 9 August 2021 time points based on their similarity with each other, reflecting changes in the data over time. In
Accepted 28 October 2021
this paper, we further explore time-series functionally and aesthetically by presenting an interactive
Available online 10 November 2021
and parameter-based implementation of the Time Curves model, complemented with the addition of
Keywords: supporting visualizations and data analysis methods. In our implementation we introduce Time Paths,
Data visualization a force-directed layout that can dynamically transform the original model to not only smoothen the
Time-series analysis transitions between time points, but also reduce visual noise in favor of portraying overall patterns. The
Interactive systems proposed addition of visual elements to the model includes temporal glyphs and a supporting timeline
graph which help discover and better understand temporal patterns across complex datasets. Through
interactive exploration, we demonstrate how these methods can be used to analyze and identify the main
agents at the source of significant instances in three biological datasets. These methods are presented
within CroP, a data visualization tool with coordinated multiple views aimed at the analysis of biological
datasets.
© 2021 Elsevier Inc. All rights reserved.

1. Introduction which is not only capable of representing the overall temporal

Multiple disciplines must contend with the study of subjects
which contain temporal variables, requiring the analysis of com-
plex datasets that describe diverse processes changing over time
simultaneously [1,2]. For instance, biological datasets often contain
large quantities of multivariate data, including temporal and spa-
tial attributes, that must be complemented with data from external
databases. Visualization can be a powerful tool in data analysis,
providing users with the means to navigate, brush and filter in-
formation through simple representations, as well as new ways to
visualize data, highlighting patterns and significant moments [3,4].
Through this, it may be possible to obtain a deeper understand-
ing of observed behaviors in datasets, identify their sources and
potentially predict future events.
In this paper, we present new visual and interactive approaches
for the exploration and analysis of time-series datasets based on
the Time Curves layout [5], where timelines are bent using multi-
dimensional scaling to position time points relatively to their sim-
ilarity. Our main contributions are twofold. Firstly, we present an
interactive, parameter-based implementation of the Time Curves,
* Corresponding author.
E-mail addresses: antonioc@dei.uc.pt (A. Cruz), jpa@dei.uc.pt (J.P. Arrais),
machado@dei.uc.pt (P. Machado).
patterns in diverse datasets, but also smoothing the resulting visu-
alizations to highlight predominant patterns. The latter is achieved
through Time Paths, a force-directed layout that redraws Time
Curve visualizations to control their sensitivity to variations in the
data. By increasing the level of smoothing, we can be used to not
only reduce visual clutter but also promote the representation of
predominant behaviors. Additionally, we can more easily control
the visual proprieties of edges using Time Paths, which allows for
smoother transitions between time points that more clearly repre-
sent the flow of time. Secondly, we complement this layout with
the addition of supporting visualization elements aimed at facili-
tating the identification of specific moments and behaviors in the
timeline, particularly when dealing with complex time curve vi-
sualizations. Specifically, we propose the addition of glyphs that
represent the dataset at each time point, as to show the evolu-
tion of the dataset without need of multiple views, and a timeline
graph visualization, which highlights moments marked by signif-
icant data variations or periods of stability. Furthermore, as time
curves mainly portray general behaviors, we also present a lens-
based approach that can be used to brush through time points and
identify the source of these behaviors so that they can be isolated
and studied further. These functionalities were implemented into
CroP, an existing data visualization tool that is capable of repre-
senting network and time-series datasets through multiple coordi-
nated views [6]. Despite being able to process relational datasets,

https://doi.org/10.1016/j.bdr.2021.100291
2214-5796/© 2021 Elsevier Inc. All rights reserved.
A. Cruz, J.P. Arrais and P. Machado
the focus of this paper is on the developed methods for the repre-
sentation and analysis of time-series data.
The paper is structured as follows: Section 2 features an
overview of related work in representing time-series data; Sec-
tion 3 provides an overview of CroP as the framework for our
main contributions; Section 4 presents the updated time curve
model and its new functionalities; Our experimental results are
showcased in Section 5, while the validation of our methods is
presented in Section 6; Finally, Section 7 provides a closing sum-
mary and future work.
2. Related work
2.1. Time representation
Timelines have been used to describe sequences of events
across many disciplines for centuries, having had multiple types
of representations to help portray and analyze time-series within
various contexts [7]. M. Brehmer et al. surveyed existing timeline
visualizations in the context of storytelling, using these as a means
to portray information coherently and in such a way that it en-
gages the viewer [8]. Linear representations were found to be the
most common as they advantage of portraying sequences of events
with an easily perceived order, with scatter plots, line charts and
histograms being common examples of simple supporting visual-
izations used to portray time-series data in various tools [9,10].
Alternatively, radial layouts also share this advantage, displaying
ordered events on a circular outline. However, this shape is bet-
ter suited for portraying cyclical or periodic events, as the timeline
loops and its beginning and end share similar positions [8]. Spi-
ral layouts portray a similar concept except with multiple loops,
either expanding from or converging into the center. While spirals
can portray cycles, they are space-filling layouts, making them use-
ful for displaying large amount of time points with a defined order
within large areas [11,12].
Timelines can easily encode a small number of variables
through shape, size and color, but may not be feasible when accu-
rately representing complex systems changing over time, such as
large networks where each time point represents a different state
for each data point. While animation can be employed as a nat-
ural way to convey changes over time, where each state of the
entire system can be represented in successive frames, it is lim-
ited by human perception capabilities, as people are more likely
to only focus on significant changes [13]. Alternatively, complex
glyphs or small multiples can be used to show a representation of
the state of the data for each time point [14,15]. For instance, Cir-
cleView [16] utilizes segmented pie charts to represent multiple
attributes over time in a simple visual artefact that not only uses
similarity and ordering algorithms to help viewers identify signif-
icant elements and even patterns, but also user interaction such
as selections, filtering and drilling-down to allow the exploration
of more complex datasets. However, in any of these methods scal-
ability must be considered, as showing thousands of time points
simultaneously will significantly increase the complexity of visu-
alizations and the excess of information may result in overlaps or
even overwhelm the viewers.
2.2. Time curves
To manage visual complexity, visualizations may seek to reduce
the size of the information space, condensing visualizations or
even aggregating groups into singular visual elements. This often
entails a loss of information in favor of reducing visual noise and
highlighting general patterns. Bach et al. presented Time Curves, a
visualization model which utilizes multidimensional scaling to po-
sition time points in low-dimensional space in such a way that
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Big Data Research 27 (2022) 100291
their relative distance reflects the similarity between their at-
tributes [5]. This is achieved by calculating the similarity between
time points using data-specific metrics and then applying a force-
directed layout on the timeline to attract time points based on
their similarity, resulting in a bent timeline whose shape reflects
the behaviors of the data, such as significant events, cyclical pat-
terns, regressions and outliers.
Elzen et al. presented a similar concept which further showed
how this layout is able to represent the overall behaviors of com-
plex systems over time [17]. In their work, the properties of a
network at each point in time are abstracted into a point on a
two-dimensional plane to build a Time Curve, which will then por-
tray the structural changes in the network over time. Through the
Time Curve it is possible to identify the periods in which the net-
work remained with a specific structure, the moments when this
structure changed, the intensity of these changes, and when the
network returned to similar, previous structures.
2.3. Interactive visualization
Visualization tools can employ interactive functions that pro-
vide users with the ability to navigate and filter the data, giving
them control over the amount of information displayed on screen.
Regarding navigation, visualization tools can employ a details-on-
demand approach by allowing users control over the timeline
to switch between time points and visualize additional informa-
tion through supporting visualizations [18,19]. Switching between
levels of detail can also be achieved through semantic zooming,
where the amount of information displayed regarding each time
point increases as the user zooms in on a section of the time-
line [20].
Filtering or highlighting information can be achieved through
queries. These can be performed indirectly through user interface
elements, such as search bars to find specific values and sliders
that set threshold values to filter less relevant data, or directly
through brushing, where data is selected by interacting with its
graphical representations. For instance, TimeSearcher and MaTSE
allow users to select sections of time-series data visualizations in
order to find temporal patterns that are similar to the one within
the selected area [21,22]. Such methods are also advantageous in
dynamic visualizations, such as those employed by DEVIS [23], a
tool for visualizing and analyzing the evolution of relaxed func-
tional dependencies over time. This tool utilizes a line plot and
a dependency table that dynamically adapt to continuous discov-
ery processes, allowing users to interact with the results through
queries and filters, including the selection of an interval of time
through a brush to analyze the changes to the dependencies dur-
ing that period. An alternative method for exploratory queries is
lens-based approaches [24]. These can be used as both a seman-
tic zooming tool and as area brushes, as users can control which
elements and information falls within their radius to be expanded.
3. Framework
The methods presented in this paper were integrated into
CroP [6], a data visualization tool created in Java using the Pro-
cessing library [25]. CroP employs a multiple coordinated views
layout to visualize user-provided datasets at different levels of de-
tail through various visualization models contained within flexible
panels, including relational networks, tabular visualizations, linear
graphs, and an implementation of time curves (Fig. 1).
While CroP was designed for the analysis of biological datasets,
specifically protein-protein interaction networks and gene expres-
sion time-series datasets, it is also capable of processing generic
relational and temporal data. A list of every loaded node and edge
A. Cruz, J.P. Arrais and P. Machado
Fig. 1. Screenshot of CroP, representing a dataset clustered into five groups: a Data Table (1), a Network panel (2), and a Time Curve panel (3) that can be divided into three
areas: a time curve layout (a), an options menu for this layout (b), and a timeline slider with a graph (c). Time points are displayed with pie chart glyphs that represent node
clusters; when brushed with the mouse lens, a larger chart represents similarity between clusters (d). (For interpretation of the colors in the figure(s), the reader is referred
to the web version of this article.)
is displayed in the Data Table panel (Fig. 1.1), while in the Net-
work panel these are displayed through various layouts that reflect
their attributes (Fig. 1.2). When temporal data exists, users can ex-
plore change in values over time through the timeline slider at the
bottom of the panel. This data can also be clustered using a hierar-
chical algorithm to create groups of nodes that are based on either
their relationships or temporal patterns [26,27]. This algorithm has
the advantage of being more versatile, only needing to calculate
similarly once before allowing users to choose between the num-
ber of clusters while the visualization updates dynamically. How-
ever, as one algorithm may not be ideal for every problem, the
framework has been prepared to support the future addition of
more clustering algorithms. After being clustered, node groups on
the network panel are sorted with a spiral layout which orders
nodes by similarity within each cluster. While time-series can be
loaded and analyzed without relational data, networks will posi-
tion clusters based on the edges between their nodes, meaning
that closer clusters will contain higher numbers of related nodes.
Regarding node representation, values are mapped between
black, which represents minimum values, and saturated colors,
which represent maximum values. As the default colors hues, blue
is used to represent time-series values and orange represents time
progression. These hues can be switched with any color on the
rainbow spectrum, allowing users to pick a color scheme that they
feel comfortable with. Depending on the dataset and type of tem-
poral behaviors being studied, color can be mapped to the direct
values of each node, to their variation, or to their tendency. We de-
fine variation as the difference between the current value and that
of the previous time point, as to represent how values are varying
over time. Tendency is an alternative approach that does not take
into account values, only how the data shifts between the previous
and next time points. Here, the brightest color represents a peak
of values and black represents a valley, while a darker blue will
represent increasing values, and grey dark blue represents values
decreasing. This can be used in the analysis of patterns in tendency
shifts across complex datasets, such as gene expression time-series
where peaks of values represent over-expressed proteins.
In this paper, our focus is on the Time Curve panel, which pro-
motes the discovery of relationships between time points through
a visualization model based on the layout presented by Bach et
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Big Data Research 27 (2022) 100291
al. [5]. The following section describes our revisions to the model
and methods for visualizing and exploring time-series.
4. Exploring time curves
In this section, we describe the Time Curve panel (Fig. 1.3) and
our implementation of the time curve layout, as well as a force-
directed approach for smoothing this layout which we named Time
Paths. These layouts are supported by a timeline graph as to help
users understand sequences of events, as well as through a lens-
based approach that is used to analyze temporal behaviors and
identify their source.
4.1. Time curve panel
CroP’s Time Curve panel consists of a visualization layout, an
options menu and a timeline slider (Fig. 1.a,b,c). When temporal
data is loaded into CroP, each time point is displayed sequentially,
laid out either as a horizontal line or as a spiral, the latter being
used when the length of the former surpasses the width of the
window. After the initial layout is loaded, the timeline can be dis-
torted into a time curve through a force-directed layout comprised
of springs between every time node. The formula used to calculate
the force applied to each spring is based on Hooke’s law [28] and
each spring’s ideal stretching length is determined using a similar-
ity matrix. The similarity between any two time points t i and t j is
determined through the function f (i , j ), described below, where
N is the number of nodes in a dataset, and P is a node containing
the time series t. It is performed by calculating both the difference
of the values of the time points v (i , j ) and the difference of their
variation b(i , j ), averaged between every point in the dataset. By
using both of these operations in calculating similarity, time points
are positioned based not only on their current values, but also in
relation to whether these values are increasing or decreasing sim-
ilarly over time.

N
v (i , j ) = | P ti − P t j | (1)
P =0
A. Cruz, J.P. Arrais and P. Machado

N
b (i , j ) = |( P t i − P t i−1 ) − ( P t j − P t j−1 )| (2)
P =0

v (i , j ), if i=0
f (i , j ) = v (i , j )+b(i , j ) (3)
2
, else
Values are averaged across every node in the dataset when cal-
culating similarity, meaning that the distance between time points
will reflect the percentage of nodes that are behaving similarly be-
tween them. As such, closer time points reflect higher amounts
of nodes manifesting similar behaviors at those moments in time.
However, if only a smaller percentage of the dataset is manifesting
a behavior pattern, time points would be scattered without per-
ceivable correlation. For such cases, we added a slider that controls
how similarity is mapped to the distance between time points. For
instance, if time points are close to each other when the slider is
set to 60% maximum similarity, then at least 60% of all data in
the dataset should be behaving similarly at those time points (as
shown by the selected time points in Fig. 1.b). Furthermore, as to
more quickly identify an ideal parameter, the maximum similarity
between every time point in the current dataset is marked on its
slider (shown in Fig. 1.a).
By dragging the timeline slider (Fig. 1.c), every time node will
be highlighted in sequence, hiding every edge except those be-
tween the time points that the slider crossed to create an animated
transition between those selected. Additionally, the mouse can be
used to pan and zoom the time curve layout, and time points
can be selected by clicking them, which displays their names and
marks them on the timeline graph with a circle. The menu on the
top-left (Fig. 1.b) lists options to control the layout, such as tog-
gling the visibility of nodes and edges, changing parameters of the
layout, and switching the color scheme. The default color scheme
maps temporal progression from the initial time point to the last
using a gradient from black to orange.
4.2. Time paths
While the time curve layout is able to position time points
relatively to their similarity, visual complexity increases with the
number of time points, making edge representation particularly
important. The Processing library provides several options to man-
age the proprieties of the edges, including the creation of curved
edges across multiple points, but these methods offer little control
over visual attributes. To resolve this, we implemented a method
that creates segmented edges with adjustable proprieties, allow-
ing us to smoothen time curves by controlling their trajectory and
curvature.
Time Paths is a layout that smoothens an existing time curve vi-
sualization by redrawing it with a brush controlled by parameter-
based attraction forces. This brush consists of a moving point
which is first placed at the initial time point on the original time
curve, and it is then pulled towards the following time point us-
ing a spring, calculated using Hooke’s law and a fixed attraction
strength. The brush’s route is mapped by intermediate points that
are left behind as it moves, and after a set number of points, it is
pulled towards the next time point. However, the new spring does
not immediately replace the previous one, as we apply momen-
tum: a percentage value that defines how quickly the attraction
force to the previous time point is converted into the attraction
force to the next point. Once the brush reached the final time
point, every edge of the new curve is defined by the sets inter-
mediate points that were left in its path. This provides increased
control over the visual representation throughout the edge as we
can define gradual transitions of both color and size between any
time node, as well as easily animate visual elements along the
drawn trajectory. Using this, we added two animations that convey
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Big Data Research 27 (2022) 100291
the flow of time: a pulse created from increasing and decreasing
the weight of each segment in sequence, and arrow particles that
move across the time curve, increasing in speed when edges are
far apart to convey the intensity of variation between time points.
We defined two variables that can be controlled through slid-
ers to dynamically update the layout: the number of intermediate
points and momentum. The number of intermediate points be-
tween each time point controls the detail of each curve. Momen-
tum controls the speed of forces converging between time points,
where decreasing it will create sharp turns between points, and in-
creasing it will create wider loops. The calculation of a Time Path
only needs to be performed once for each set of parameters, as
all of the intermediate points are saved along with their proper-
ties. Additionally, overlapping intermediate points will be removed,
cleaning the visualization and improving drawing speed. However,
it should be addressed that time paths distort the position of the
time nodes from the original time curve, in which their position
best reflected their similarity. To diminish this, after the time path
has been calculated, we move time nodes along the new path to a
point that is closest to their original position on the time curve.
4.3. Supporting timeline
As the force-directed layout distorts the timeline, the order of
the time points becomes harder to perceive. While interaction and
animation can help users better perceive temporal order, these
methods may not be ideal to identify significant moments when
dealing with large amounts of time points. In order to more easily
understand the sequence of events in a time series, regardless of
the visual complexity of its time curve, we added a graph that rep-
resents the behaviors of the data over time to the timeline slider.
The height of each bar in the graph is mapped to the distance
that time point and the next in the time curve, from zero to the
largest current distance. As such, the size of the bar will repre-
sent the intensity of the changes in the data from one time point
to the next in the current time curve. To exemplify, Fig. 2 shows
a graph representing an instance where the distance between the
first three time points is large, while the following ones are close
together. This indicates that there were three large shifts in values,
followed by a period of stability where values presented mini-
mal changes. However, when represented as a bar chart, the initial
three significant shifts present similar heights (Fig. 2.a), which may
result in the viewer perceiving these time points as being similar.
To better distinguish significant shifts in the data, we altered the
bar representation so that shifts are represented as spikes, where
their sharpness matches the intensity of the shifts, and stability
is represented by smooth low portions. (Fig. 2.b). To better con-
vey the flow of these shifts over time, the shape of the graph is
then curved, smoothing the transitions between points (Fig. 2.c).
To achieve the spike shape, the height of the point between two
sequential time points is calculated based on their height. The for-
mula to calculate the middle point h located between time points
t1 and t2 is described below where T is an array of the average
values of every time point, max( T ) and min( T ) are the maximum
and minimum values in T, respectively, and av g (t1, t2) is the aver-
age value of t1 and t2. This formula describes how h is calculated
by mapping av g (t1, t2) from the set [min( T ), max( T )] into the set
[av g (t1, t2), min( T )], meaning that the height of both time points
increases (which would indicate two sequential large shifts of data)
the middle point’s height decreases.
av g (t1, t2) − min( T )
h = (1 − )×(av g (t1, t2)− min( T ))+ min(t )
max( T ) − min( T )
(4)
A. Cruz, J.P. Arrais and P. Machado Big Data Research 27 (2022) 100291

Fig. 2. Timeline graph showing high variation for the first three steps and then a period of minimal changes: as a basic bar chart (a), with middle points (b) and then
smoothed (c).

However, as this representation is more complex than the ini-

tial bar chart, we also established a minimum pixel width for each
bar so that the spikes will not be drawn whenever the width
of the graph is too small. As such, only the bar chart will be
shown whenever the graph is too small for the spikes to be read-
able, which also saves processing power whenever there are too
many time points. Additionally, there is a “similarity” color scheme
that also helps discern behaviors independently of the number of
time points. When selected, the color of time nodes is mapped
to the similarity values every time point that has been selected.
As such, when selecting a time point, every point that is similar
will be highlighted on the graph. As before, selected time points
are marked with a circle above their corresponding section of the
graph.

4.4. Analyzing temporal patterns

A limitation of the Time Curves layout is that it can only show

how the data generally behaves over time. When viewing a time
curve that is representing the general behavior of thousands of
nodes, it does not provide any information regarding the nodes
contributing to such behaviors. As such, we are interested how
the model can be used to portray the state of the data at each
time point to better understand its pattern, as well as providing
the means to dig-down and discern the potential sources of these
behaviors.
Our first challenge was to provide graphical representations of
the dataset at each time point, allowing these to be compared after
being positioned by Time Curves without having to rely on inter-
action or additional views. To assure that our approach is scalable
to any dataset, we chose to portray data clusters as these repre-
sent a flexible number of groups of data points that have similar
proprieties. Upon clustering the dataset, time nodes in the time
curve layout are replaced with pie chart glyphs. Each slice repre-
sents one of the clusters, where the width of its arc represents the
number of nodes in the cluster and the color corresponds to the
average properties of every node in the group at that time point.
The pie chart slices are sorted relatively to the positions of the
clusters on the network visualization, allowing them to be more
easily matched to their corresponding cluster (Fig. 3.2).
To further explore the relationships between nodes and their
temporal patterns, we introduced a lens-based approach that pro-
vides an on-demand visualization which highlights the similarities
and differences between any group of time points. Right-clicking
over the Time Curve panel will create a circular area around the
mouse, allowing users to brush over multiple time nodes simul-
taneously and creating a larger pie chart visualization (Fig. 1.d).
This pie chart represents an aggregate of all the glyphs, where the
color of each slice represents the average of each cluster across
the selected time points. Moreover, the radius of each slice is
now variable, matching the average similarity of their respective
Fig. 3. Network panel (left) with HIV-1 dataset nodes clustered into six groups and
Time Curve panel (right). 1 - Maximum similarity at 100%. 2 - Maximum similarity
at 60% and time points 12H and 18H are selected; clusters are represented with pie
slices (a, b & c).
cluster between the selected time points. This similarity is deter-
mined by calculating the standard deviation between their average
values, represent clusters with consistent behaviors through filled
slices (Fig. 3.2.a,c), while others will be shorter and less visible
(Fig. 3.2.b). Additionally, the scroll wheel can be used to increase
or decrease the size of the lens, and by using a keyboard shortcut,
nodes will remain selected even when no longer within the lens,
allowing users to brush through multiple distinct areas of a time
curve.
In order to identify the source of particular behaviors more
easily, selecting time points is also coordinated with the network
panel. When points are selected, the transparency and saturation
of each node in the network is mapped to their similarity across
the selected time points, highlighting nodes with consistent behav-
iors. Furthermore, two outlines are drawn around each cluster: the
first outline has a varying weight which increases based on the
percentage of similar nodes within the cluster, while the second
outline is fixed, marking the maximum size for the first outline. As
such, these outlines make it simpler to quickly identify how sim-
ilar each cluster is across every selected time point (Fig. 3.2). As
we highlight both significant individual nodes and significant clus-

5
A. Cruz, J.P. Arrais and P. Machado
Fig. 4. Time curve visualization of a sine wave dataset (a) and variations: an increase in amplitude (b), an increase of values (c), then combined with an increase of
frequency (d).
ters, users can more easily identify and isolate data groups that are
displaying behaviors that they might want to study further.
5. Experimental results
In this section, we present several visualizations created by our
models, first from simple datasets comprised of a single time-
series that can be easily matched with their results, and then from
biological datasets that contain thousands of nodes with individual
time-series, where we employ the developed methods to identify
patterns and their source.
5.1. Individual time-series
While the representation of a single time-series may not offer
much insight that is not already observable in a linear represen-
tation of the data, the following datasets allowed us to test the
representation abilities of our layouts, as the resulting visualiza-
tions can be compared with each time-series. To demonstrate our
implementation of the time curve layout, we conducted tests using
a sine wave dataset with 500 time points, which depicts a simple
consistent behavior: a cycle, where values increase and decrease
repeatedly between a minimum and a maximum. Following this,
the dataset was altered to depict other predictable behaviors, as
shown in Fig. 4. The visualization of the basic sine wave dataset
resulted in an oval that represents the shifts in variation over time,
where the number of loops matches the number of cycles in the
dataset (Fig. 4.a). When the minimum and maximum values were
altered, the shape’s height also changed to match the amplitude
of each cycle (Fig. 4.b). Adding a consistent value increase over
time resulted in a gradual position shift for the ovals represent-
ing each cycle (Fig. 4.c). Finally, increasing frequency resulted in
stronger value variations, which increased the width of the cy-
cle’s loops. To make this more noticeable, we combined it with
the previous value increase (Fig. 4.d). In these initial experiments,
our implementation of the time curves layout was able to position
time points based on their values and variations, creating visual-
izations that conveyed the overall behaviors of each time-series.
In order to test the Time Paths layout, we used two time-series
gathered from real events describing cyclical behaviors with differ-
ent trends and variations. These datasets were chosen to not only
test the impact of different parameters, but also demonstrate how
the layout smoothens curves to reduce visual clutter and highlight-
ing general trends. The first dataset is “Wolfer’s Sunspot Numbers”,
a yearly measurement of sunspots from 1770 to 1869 [29]. It con-
tains 100 time points and presents cycles with similar minimums
but varying peak values, resulting from periodic value increases
of different intensities. The second dataset depicts “Monthly Milk
Production” from January 1962 to December 1975 [30], contain-
ing 168 time points and characterized by a yearly production cycle
with minor jumps in variation and a consistent increasing trend
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Big Data Research 27 (2022) 100291
until the final five years, where the production increase stabilizes.
In both cases, the Time Curve depicted each cycle with circular
patterns whose sizes and positions matched the respective vari-
ations and trends observable in the dataset, which is consistent
with previous results. For instance, the “Monthly Milk Production”
dataset is represented with shifted loops, up until the final cycles
when production no longer increases yearly, resulting in overlaps.
The Time Path layout was then applied with four different sets of
parameters, increasing the level of smoothing with each one. The
results are depicted in Figs. 5 & 6.
The first of each set of results (3.a) shows the default param-
eters, which generally smoothed the initial time curve (2.) while
remaining sensitive to small variations. We can note a small loop
in the center that highlights a slight increase in values within a
decreasing trend. In the second result set (3.b), the number of
intermediate points is reduced while momentum is increased, re-
ducing the perturbations that indicate moments with small varia-
tion shifts, like the previous loop. In the third set (3.c) momentum
was further increased, removing almost all visual clutter in favor
of representing the overall cycles. In the last parameter set (3.d),
momentum was increased again to create exaggerated depictions
of the previous cycles, particularly large data variations such as
the two largest increases in the sunspots dataset (Fig. 5.3.d). The
time curves model was generally able to represent how time-series
vary over time, while time paths helped reduce visual noise and
highlight the main tendencies of the time-series, while offering al-
ternative representations of otherwise simple datasets.
5.2. Biological datasets
Biological datasets can be generally characterized as complex,
containing large quantities of data points with multiple variables.
Unlike in the previous datasets, tendencies and significant mo-
ments are not easily identified without data analysis methods.
First, we present a visualization of a gene expression time-series
RNA-Seq dataset over a network of 7,590 proteins in reaction to the
HIV-1 infection, measured every 2 hours over a period of 24 hours.
As this dataset was shown to present cyclical tendencies in early
versions of our layout [31], we sought to explore these behaviors
in its current iteration. The results are shown Figs. 1 & 3, where
the time curve was able to depict two cycles through three distinct
groups of time points, where at least half of the dataset presented
the same behaviors. Through the time curve lens, it was possible
to quickly identify which nodes had similar behaviors at the same
points in time. For instance, in Fig. 1 we show the lens being used
on the group of time points for 4, 10 and 16 hours, resulting in a
chart with one full slice colored in blue. Even without the network
view, we can infer that this represents a cluster that only contains
nodes that present peaks of expression across the selected time
points. Moreover, the remaining slices also indicate that the other
clusters also contain large quantities of nodes expressing other
A. Cruz, J.P. Arrais and P. Machado Big Data Research 27 (2022) 100291

Fig. 5. Visualizations of the “Wolfer’s Sunspot Numbers” dataset, depicted as a line chart (1), a Time Curve (2), and through Time Paths (3) with different parameters (a to d).

Fig. 6. Visualizations of the “Monthly Milk Production” dataset, depicted as a line chart (1), a Time Curve (2), and through Time Paths (3) with different parameters (a to d).

Fig. 7. Time curve of the Plasmodium Falciparum dataset (left), and close-ups of two sets of time points being brushed with the mouse lens (a, b).

consistent behaviors. In Fig. 3, we compare the dataset between
12 and 18 hours to identify that most of the dataset presents the
same patterns of expression between these time points, with the
exception of the bottom-most cluster (Fig. 3.b). Such clusters can
be easily selected and isolated so they can be studied further.
Secondly, we analyzed a gene expression time-series of the de-
velopmental cycle of Plasmodium Falciparum, the agent responsi-
ble for human malaria. The dataset contains 5,080 genes, whose
values were measured with an hour interval over 48 hours. The
time curve visualization of this dataset shows a general continuous
behavior throughout, small shifts in variation between subsequent
time nodes, without overlaps (Fig. 7). Additionally, the dataset has
near 90% maximum similarity, meaning that genes present very
similar behaviors. This matches the description of this data in a
previous study [32] which referred to the behavior of the genes
as a cascade of continuous expression that lacks sharp transitions.
Moreover, near the end, the dataset appears to return to a state
similar to where it began, characteristic of a cycle. By using the
lens, we can compare two time points near the beginning and end
of the timeline, TP2 and TP45, to observe that most of the dataset
does appear to present similar values and variations at those in-
stances (Fig. 7.a). Despite the lack of sharp transitions, we can
observe that the data does not present consistent variations. In the
supporting timeline graph, we can easily identify both moments of
stable variation and some significant shifts in the data. Using the
lens to analyze some of these larger shifts, we can identify which
groups of nodes present differences between time points instead
of similarities. When comparing TP12 and TP13, we can identify
that the two clusters on the left were responsible for the spike in
the time curve, and just by observing their glyph colors, we can
also conclude that these clusters had a significant increase in val-
ues (Fig. 7.b).
Finally, we visualized transcription profiles across a yeast cell
cycle, where 4,381 alpha factor synchronized cells were followed
across two cell cycles, sampled every 5 minutes throughout 2
hours [33]. The resulting time curve loops in the middle, which
may be related to the second cell cycle (Fig. 8). Despite maximum
similarity being set at 80%, the cycles appear to be significantly
different from each other, although this is also substantiated by
previous studies [33]. In particular, we can observe that the end
of the second cycle is marked by a very significant shift in values,
characterized mainly by a large decrease of values in one cluster
and a large increase in three others (Fig. 8.b), followed by a re-
turn to values in line with the previous tendency. There is also

7
A. Cruz, J.P. Arrais and P. Machado
Fig. 8. Time curve of the yeast cell cycle dataset (left), and network visualizations of the dataset at 45 minutes (a) and at 105 minutes (b), clustered by temporal values.
another large shift at 45 minutes that breaks away from the ex-
pected tendency. We identified the cause as being a specific cluster
of nodes that presents very little activity throughout the dataset
until that point in time, during which the values of every node
increase sharply (Fig. 8.a), then return to normalcy.
6. User testing
Throughout the experiments performed using our implemen-
tation of the time curve model, we were able to observe various
types of behaviors in the visualization that were created. However,
one predominant concern is the comprehensibility of the model by
different types of users, in particular those with minimal knowl-
edge of data visualizations. To this end, we invited users with
knowledge of biological datasets but low-levels of experience with
visualization to perform interface tests on CroP. As these tests were
aimed at CroP as a tool, we will only present an overview and a
brief discussion of the results in the context of the presented visu-
alization methods. To further test the efficacy of our visualization
models, we also performed surveys on individuals from different
fields, focused on the interpretation of various time curve visual-
izations. The full tests and results are provided as supplementary
materials.
6.1. Interface tests
The interface tests were conceived with the objective of detect-
ing general usability problems in CroP and to better understand
how users with minimal knowledge of data visualization would
perform in navigating the tool, exploring data, and using its func-
tions to identify patterns. The tests were performed by 9 college
students from a Biochemistry degree, where all of which had a
low level of experience with visualization tools. These participants
were asked to load and explore the gene expression dataset of the
HIV-1 infection (Fig. 1), utilizing the data table, network and time
curve panels to solve various tasks. In what concerns the visualiza-
tion methods presented in this paper, participants were asked to
use clustering to identify a group of nodes with a similar profile to
that of another node and then use the time curve panel to search
for a pattern of behavior. This was followed by a multiple-choice
question regarding the behaviors they identified, how clearly they
were represented, and whether the time glyphs helped in under-
standing the pattern.
None of the participants showed any significant issues in nav-
igating the tool, applying clustering and layouts or exploring the
data. However, 4 users were not able to identify the intended
group in the clustering task and 2 users had difficulties in inter-
preting the time curve layout, stating that they could not perceive
neither continuous nor cyclical behaviors. Based on the received
feedback, we can attribute these difficulties to having no prior
knowledge of clustering and a lack of context on the data for low
8
Big Data Research 27 (2022) 100291
level users. This would have required a higher focus on the time
curves, such as more tasks or examples to help users further ex-
plore the model and surpass the inherent learning curve. In spite
of this, 7 out of the 9 participants were able to correctly identify
the pattern of the time curve as representing multiple cycles, rat-
ing the clarity of this representation with an average score of 5.6
out of 7. Additionally, these participants generally considered the
temporal glyphs as helpful in the understanding the pattern with
a score of 5.1 out of 7, as the visual similarity of adjacent nodes
helped distinguish each group. In the final feedback portion, par-
ticipants were asked to give a score to several affirmations from
a 1 (Strongly Disagree) to 5 (Strongly Agree). The following is the
average score given to each affirmation: they generally agreed that
CroP was accessible with 3.9, that they required more time to use
CroP properly with 3.9, and that they could see themselves using
this tool in the future with 4.1, while they generally disagreed that
the tool was complex with 1.6.
6.2. Visualization model survey
The survey consisted of a form containing several sets of
multiple-choice questions, involving the identification of behaviors
and patterns across multiple visualizations, as well as inquiries
into participants’ preferences regarding the representation of the
datasets. This study was conducted in person with university stu-
dents from various fields of study: out of the 25 participants, 8 had
an Information Visualization background, 4 had a Computational
Creativity background, 6 had a Computer Science background, and
7 had a Biomedical Science background.
At the start of the survey, participants were shown a time curve
from the sine waves dataset (Fig. 4.a), in which all of them were
able to identify that the predominant behavior being represented
was cyclical. When asked to match three modified sine wave time
curves (Fig. 4.b,c,d) to their respective datasets, 48% of the partic-
ipants correctly matched the first dataset, 84% of them were able
to correctly match the second dataset and 64% correctly matched
the third. Following this, they were asked to identify moments,
periods and specific characteristics from the dataset visualizations
presented in Figs. 6 & 5 and over 90% of participants were able to
correctly identify both increasing trends and periods of stabiliza-
tion, as well as moments with significant changes. However, only
54% were capable of identifying a specific outlier in the time curve
visualization, although this was in spite of their limited experience
with the model. When asked to choose between six Time Path
variations of these visualizations with different levels of smooth-
ing, we could observe that participants generally preferred rounder
curves with less variation details, as long as the visualization was
still able convey the overall behaviors of the original dataset. For
instance, the Sunspot dataset visualizations with high smoothing
parameters (Fig. 5.d) were unpopular as they distorted the repre-
sentation of the larger cycles.
A. Cruz, J.P. Arrais and P. Machado
From the initial questions we were able to observe that the
model is not immediately intuitive, which was also supported by
the received feedback where 9 participants commented on the
existence of a learning curve, especially to those without a vi-
sualization background. However, the average score given to the
model’s ability to represent behaviors was 4.1 out of 5, accom-
panied by feedback that the model should be useful tool in data
analysis after the learning curve is surpassed, one noting the abil-
ity to identify outliers that weren’t noticeable in the line chart. The
absence of interaction in these tests did highlight some limitations
on the static models, such as overlapping lines causing visual noise,
although this can be diminished when using the tool by scrolling
through the timeline or using animations. Participants also gave
the presentation of the Time Path visualizations an average score
of 3.9 out of 5, commenting that they were generally more visu-
ally appealing than traditional visualization models, but that their
application is very context-sensitive.
7. Conclusions & future work
In this paper, we presented new methods to further discover
and interpret the behavior patterns represented by the Time
Curves layout, integrated into CroP, our visualization tool for re-
lational and temporal data.
Firstly, we presented our implementation of the Time Curves
layout and demonstrated its ability to represent different types of
behaviors in time-series datasets. We complemented this model
with Time Paths, a parameter-based layout that dynamically trans-
forms Time Curve visualizations to represent the original behaviors
with different levels of detail or abstraction. In the experiments
performed, the model was capable of not only representing dif-
ferent types of behaviors over time, but also smoothen layouts to
reduce visual clutter and highlight overall trends. Time Paths also
gives additional control over the representation of edges, which al-
lowed for the creation of animated visual elements that convey
direction and variation more easily.
Secondly, we provided both visual and interactive methods
aimed at analyzing temporal patterns across large volumes of data
points, allowing users to dig-down on time curve visualizations.
When data is clustered, time nodes are replaced with glyphs that
represent the dataset at each time step, allowing time points to be
compared without the need of additional views. Furthermore, we
implemented a lens-based area brush that highlights nodes with
similar behaviors between groups of time points. This lens is co-
ordinated with the network panel to better identify groups and
individual nodes with significant behaviors. Throughout the exper-
iments performed with biological datasets, these methods helped
quickly discover the groups of nodes responsible for various behav-
iors, which can then be isolated and compared with other variables
to be studied further. Finally, we validated our models and meth-
ods through interface tests and visualization models, performed
with individuals from varied fields of study. While these confirmed
that the time curve model possesses an inherent learning curve,
even users with low knowledge of visualization were able to use
the tools to discover patterns and interpret them.
As future work, we plan to further explore the presented mod-
els, not only to further improve their representation of data, but
also to more easily portray significant information within complex
datasets. In particular, the time curve model still presents limita-
tions in its readability when representing large time-series, mainly
due to edge overlap. Supported by the timeline graph and interac-
tive methods which help pinpoint important moments, our models
are still capable of being used in the analysis of complex datasets
regardless of edge representation, but the integration of techniques
such as edge-bundling and aggregation may reduce overlap and
contribute to highlighting patterns. New layouts can also be inte-
9
Big Data Research 27 (2022) 100291
grated into CroP’s framework, either to provide alternative meth-
ods to map the position of time points to their similarity, such as
new clustering methods, or to add a new dimension to the visu-
alization, such as a 3D plot which would allow the exploration of
the data through different angles.
Funding
This work is funded by national funds through the FCT - Foun-
dation for Science and Technology, I.P. [SFRH/BD/124538/2016],
within the scope of the project CISUC - UID/CEC/00326/2020 and
by European Social Fund, through the Regional Operational Pro-
gram Centro 2020, and through D4 - Deep Drug Discovery and
Deployment [CENTRO-01-0145-FEDER029266].
Declaration of competing interest
The authors declare that they have no known competing finan-
cial interests or personal relationships that could have appeared to
influence the work reported in this paper.
Appendix A. Supplementary material
Supplementary material related to this article can be found on-
line at https://doi.org/10.1016/j.bdr.2021.100291.
References
[1] S. Nusrat, T.A. Harbig, N. Gehlenborg, Tasks, techniques, and tools for genomic
data visualization, Comput. Graph. Forum (2019), https://doi.org/10.1111/cgf.
13727.
[2] N. Kerracher, J. Kennedy, K. Chalmers, The design space of temporal graph vi-
sualisation, in: N. Elmqvist, M. Hlawitschka, J. Kennedy (Eds.), EuroVis - Short
Papers, The Eurographics Association, 2014.
[3] W. Aigner, S. Miksch, H. Schumann, C. Tominski, Visualization of Time-Oriented
Data, 1st edition, Springer Publishing Company, Incorporated, 2011.
[4] S.I. O’Donoghue, B.F. Baldi, S.J. Clark, A.E. Darling, J.M. Hogan, S. Kaur, L. Maier-
Hein, D.J. McCarthy, W.J. Moore, E. Stenau, J.R. Swedlow, J. Vuong, J.B. Procter,
Visualization of biomedical data, Annu. Rev. Biomed. Data Sci. 1 (1) (2018)
275–304, https://doi.org/10.1146/annurev-biodatasci-080917-013424.
[5] B. Bach, C. Shi, N. Heulot, T. Madhyastha, T. Grabowski, P. Dragicevic, Time
curves: folding time to visualize patterns of temporal evolution in data, IEEE
Trans. Vis. Comput. Graph. 22 (2016) 559–568, https://doi.org/10.1109/TVCG.
2015.2467851.
[6] A. Cruz, P. Machado, J.P. Arrais, CroP—Coordinated Panel visualization for bi-
ological networks analysis, Bioinformatics 36 (4) (2020) 1298–1299, https://
doi.org/10.1093/bioinformatics/btz688.
[7] D. Rosenberg, A. Grafton, Cartographies of Time: A History of the Timeline,
Princeton Architectural Press, 2013.
[8] M. Brehmer, B. Lee, B. Bach, N.H. Riche, T. Munzner, Timelines revisited: a
design space and considerations for expressive storytelling, IEEE Trans. Vis.
Comput. Graph. 23 (9) (2017) 2151–2164, https://doi.org/10.1109/TVCG.2016.
2614803.
[9] A. Theocharidis, S. Dongen, A. Enright, T. Freeman, Network visualisation and
analysis of gene expression data using biolayout express3d, Nat. Protoc. 4
(2009) 1535–1550, https://doi.org/10.1038/nprot.2009.177.
[10] A. Lex, M. Streit, H.-J. Schulz, C. Partl, D. Schmalstieg, P. Park, N. Gehlen-
borg, Stratomex: visual analysis of large-scale heterogeneous genomics data
for cancer subtype characterization, Comput. Graph. Forum 31 (3pt3) (2012)
1175–1184, https://doi.org/10.1111/j.1467-8659.2012.03110.x.
[11] J.V. Carlis, J.A. Konstan, Interactive visualization of serial periodic data, in:
Proceedings of the 11th Annual ACM Symposium on User Interface Software
and Technology, UIST ’98, ACM, New York, NY, USA, 1998, pp. 29–38, http://
doi.acm.org/10.1145/288392.288399.
[12] T. Bergstrom, K. Karahalios, Conversation clock: visualizing audio patterns in
co-located groups, in: 2007 40th Annual Hawaii International Conference on
System Sciences (HICSS’07), 2007, p. 78.
[13] T. von Landesberger, A. Kuijper, T. Schreck, J. Kohlhammer, J. van Wijk, J.-D.
Fekete, D. Fellner, Visual analysis of large graphs: state-of-the-art and future
research challenges, Comput. Graph. Forum 30 (6) (2011) 1719–1749, https://
doi.org/10.1111/j.1467-8659.2011.01898.x, https://onlinelibrary.wiley.com/doi/
pdf/10.1111/j.1467-8659.2011.01898.x, https://onlinelibrary.wiley.com/doi/abs/
10.1111/j.1467-8659.2011.01898.x.
A. Cruz, J.P. Arrais and P. Machado
[14] J. Zhao, S. Drucker, D. Fisher, D. Brinkman, Timeslice: interactive faceted
browsing of timeline data, in: AVI’12: Proceedings of the Interna-
tional Working Conference on Advanced Visual Interfaces, Capri Island,
Italy, 2012, https://www.microsoft.com/en-us/research/publication/timeslice-
interactive-faceted-browsing-timeline-data/.
[15] A. Lex, H.-J. Schulz, M. Streit, C. Partl, D. Schmalstieg, Visbricks: multiform visu-
alization of large, inhomogeneous data, IEEE Trans. Vis. Comput. Graph. (InfoVis
’11) 17 (12) (2011) 2291–2300, https://doi.org/10.1109/TVCG.2011.250.
[16] D.A. Keim, J. Schneidewind, M. Sips, Circleview: a new approach for visualiz-
ing time-related multidimensional data sets, in: Proceedings of the Working
Conference on Advanced Visual Interfaces, 2004, pp. 179–182.
[17] S. van den Elzen, D. Holten, J. Blaas, J.J. van Wijk, Reducing snapshots to
points: a visual analytics approach to dynamic network exploration, IEEE Trans.
Vis. Comput. Graph. 22 (1) (2016) 1–10, https://doi.org/10.1109/TVCG.2015.
2468078.
[18] C. Niederer, H. Stitz, R. Hourieh, F. Grassinger, W. Aigner, M. Streit, Taco: vi-
sualizing changes in tables over time, IEEE Trans. Vis. Comput. Graph. 24 (1)
(2018) 677–686, https://doi.org/10.1109/TVCG.2017.2745298.
[19] B. Bach, E. Pietriga, J. Fekete, Graphdiaries: animated transitions and temporal
navigation for dynamic networks, IEEE Trans. Vis. Comput. Graph. 20 (5) (2014)
740–754, https://doi.org/10.1109/TVCG.2013.254.
[20] D.A.G. Aguilar, R. Therón, F.J. García-Peñalvo, Semantic spiral timelines used as
support for e-learning, J. Univers. Comput. Sci. 15 (7) (2009) 1526–1545.
[21] H. Hochheiser, E.H. Baehrecke, S.M. Mount, B. Shneiderman, Dynamic query-
ing for pattern identification in microarray and genomic data, in: 2003 In-
ternational Conference on Multimedia and Expo. ICME ’03. Proceedings (Cat.
No.03TH8698), vol. 3, 2003, III–453.
[22] P. Craig, A. Cannon, R. Kukla, J. Kennedy, Matse: the microarray time-series
explorer, in: 2012 IEEE Symposium on Biological Data Visualization (BioVis),
2012, pp. 41–48.
[23] B. Breve, L. Caruccio, S. Cirillo, V. Deufemia, G. Polese, Visualizing dependencies
during incremental discovery processes, in: EDBT/ICDT Workshops, 2020.
10
Big Data Research 27 (2022) 100291
[24] C. Tominski, S. Gladisch, U. Kister, R. Dachselt, H. Schumann, Inter-
active lenses for visualization: an extended survey, Comput. Graph.
Forum 36 (6) (2017) 173–200, https://doi.org/10.1111/cgf.12871, https://
onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.12871, https://onlinelibrary.wiley.
com/doi/abs/10.1111/cgf.12871.
[25] C. Reas, B. Fry, Processing: programming for the media arts, AI & Society 20 (4)
(2006) 526–538, https://doi.org/10.1007/s00146-006-0050-9.
[26] A. Fahad, N. Alshatri, Z. Tari, A. Alamri, I. Khalil, A.Y. Zomaya, S. Foufou, A.
Bouras, A survey of clustering algorithms for big data: taxonomy and empirical
analysis, IEEE Trans. Emerg. Top. Comput. 2 (3) (2014) 267–279.
[27] D. Müllner, Modern hierarchical, agglomerative clustering algorithms, arXiv:
1109.2378, 2011.
[28] J. Rychlewski, On Hooke’s law, J. Appl. Math. Mech. 48 (3) (1984) 303–314,
https://doi.org/10.1016/0021-8928(84)90137-0, http://www.sciencedirect.com/
science/article/pii/0021892884901370.
[29] P.J. Brockwell, R.A. Davis, Time Series: Theory and Methods, Springer-Verlag,
Berlin, Heidelberg, 1986.
[30] J. Minichino, Recurrent neural networks course project: time series prediction
and text generation, https://github.com/techfort/aind2-rnn, 2017. (Accessed 2
December 2019).
[31] A. Cruz, J.P. Arrais, P. Machado, Interactive network visualization of gene ex-
pression time-series data, in: 2018 22nd International Conference Information
Visualisation (IV), 2018, pp. 574–580.
[32] Z. Bozdech, M. Llinás, B.L. Pulliam, E.D. Wong, J. Zhu, J.L. DeRisi, The transcrip-
tome of the intraerythrocytic developmental cycle of plasmodium falciparum,
PLoS Biol. 1 (1) (2003) e5, https://doi.org/10.1371/journal.pbio.0000005.
[33] T. Pramila, W. Wu, S. Miles, W.S. Noble, L.L. Breeden, The forkhead transcrip-
tion factor hcm1 regulates chromosome segregation genes and fills the s-phase
gap in the transcriptional circuitry of the cell cycle, Genes Dev. 20 (16) (2006)
2266–2278, https://doi.org/10.1101/gad.1450606.