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A Visual Analytics Approach for Exploration of

High-Dimensional Time Series Based on


Neighbor-Joining Tree
Michael Shell Homer Simpson James Kirk
School of Electrical and Twentieth Century Fox and Montgomery Scott
Computer Engineering Springfield, USA Starfleet Academy
Georgia Institute of Technology Email: homer@thesimpsons.com San Francisco, California 96678–2391
Atlanta, Georgia 30332–0250 Telephone: (800) 555–1212
Email: http://www.michaelshell.org/contact.html Fax: (888) 555–1212

Abstract—High-dimensional time series analysis through visual method. First, a property-based tree construction scheme is
techniques poses many challenges. Several visualization solutions used to organize image collection into a tree structure ac-
have been proposed for exploratory tasks on time series col- cording to user-defined properties. Then, this tree structure
lections. As the data sets grow large, the visual alternatives do
not allow for a good association between similar time series. is projected into a visualization plane, the desired correlations
In this paper we introduce a visual representation based on among images can be well reflected in the layout. Furthermore,
Neighbor-Joining Tree for high-dimensional time series data sets. a two-step visualization optimization scheme is applied to op-
The approach consists internally by six time series dimension timize image layouts such that image overlap and layout shape
reduction techniques widely used in this field and two similarity can be properly controlled. Finally, a tree-transfer scheme
measures with the aim to explore high dimensional Time series
data. is used which enables the adaptive updating of visualization
layouts.
I. I NTRODUCTION In this paper, we propose a visualization technique based
High-dimensional time series data is increasingly found in on Neighbor-Joining similarity tree for exploration of high
economics, biology, meteorology, and many other scientific dimensional time series. This approach consists internally
fields [1]. The ubiquity of such kind of data deserves the at- by six dimensionality reduction techniques widely used in
tention of scientific community due to temporal dimensionality time series analysis and two similarity measure. It also is
and complex dynamics [2]. Besides, we do not have enough equipped by interaction capabilities (such as zoom and details
tools to do exploratory analysis. on demand). We highlight the capabilities of similarity tree
One of the interesting tools to do exploratory analysis is to showing hierarchical relationship of high dimensional time
Temporal-PEx [3] which supports the user to have a general series. This technique provides visually the degree of similarity
view of time series collections, as well as to find groups between the time series in a hierarchical fashion.
with similar behavior. This tool is equipped by two projection The remainder of this paper is organized as follows. Section
techniques (IDMAP [4] and LSP [5]) and three dissimilarity II reviews related work regarding time series visualization
measures (Euclidean distance, DTW [6], and CDM [7]). and Neighbor-Joining similarity tree visualization. Section III
The problem with this tool is that only provides support to describes our proposal. Section IV discusses the experimental
projection techniques. results. Finally, we conclude this work in Section V.
Currently, trees as visualization technique are widely used
II. R ELATED W ORK
by providing hierarchical information of data collections. The
tree is capable of representing the degree of relationships A. Time Series Visualization
that allows the user to quickly assimilate the information Traditional time series visualization approaches such as line
contained in the datasets. The well-known tree-based vi- graph are lacking explorations that facilitate the analysis of
sualization method is Neighbor-Joining (NJ) similarity tree a large set of data. For this, recent studies that aim to join
technique which was initially used in the exploration of text temporal data with visual analysis have shown prominence to
document collection by mapping them on 2D space [8]. This approach this problem.
technique was also applied satisfactory to image organization Alencar [3] proposes a visual tool called temporal-PEx.
and classification [9] [10]. This tool allows the exploratory analysis of time series
Han [11] proposes a tree-based technique for visualizing collections by projecting in two-dimensional space through
image collections into arbitrary layout shapes. This work is a two techniques: IDMAP (Interactive Document Map) and
hybrid of the projection-based method and the image collage LSP (Least-Square Projection) and three similarity measures:
DTW (Dynamic Time-Warping), Euclidean distance and CDM In the text collection data, the first work that proposes the
(Compression-based Dissimilarity Measure). The usefulness use of NJ for visual analysis is Cuadros [8] by projecting
of this tool [12] was proved on a real dataset of time series them in 2D space (similar to a projection technique). In this
describing the behavior of hydroelectric power plants with the work, a tree is constructed that allows the visualization of
visual analysis. similarity by content. Likewise, applying the knowledge of
The above approaches are based on the similarity of entire the previous work, Polato [20] used the NJ method for a
time series but visual analysis does not only address these systematic revision of the literature to assess Apache Hadoop
issues. The visual exploration of time series is also useful in Research. The great amount of research in this area made
other branches of time series analysis such as [13] where it a challenge to give an overview of the entire literature. A
is applied successfully to find frequent patterns (also known recent work [21] used of phylogenetic trees (NJ) combined
as motifs) in large time series . The justification for using with summarization techniques (Themeriver and Wordclouds)
visual analysis lies in the fact that in a large set of time series to analyze text collections that change over time.
hundreds of motifs can be found. Another area of knowledge in which NJ has been applied
Visual analysis was also applied in the selection of suitable successfully is in the field of visual analysis of images. In [22],
models in the preprocessing stage of a time series by using a visual analysis tool called PEx-Image was introduced. This
interactive visual interfaces [14]. The aim of this work was tool is equipped by several projection techniques (including
to make time series preprocessing visible and accessible to neighbor joining method) with the aim to do visual exploration
domain experts by making to compose a pipeline of individual of sets of images. A related work proposes a visual classifi-
operations drawn from an extensible toolkit. The composition cation methodology (VCM) that makes use of visualization
is guided by a series of line-charts showing intermediate techniques for a better understanding of the nature of the data
results and statistics. A user learns about the characteristic used in the classification [23].
properties of the data, and how these properties are changed Projections of data using NJ were also applied in music
by every step of the pipeline. By exposing the preprocessing as in the work of [18] where it makes use of a visual
and its effects in a visual way, the confidence of the experts interface to explore collections of music, making use of Iconic
to the results have been increased greatly. Representation and then projecting them in a two-dimensional
More recent works offer a visualization where time series plane.
data obtained from sensor networks are analyzed to detect Finally, De Oliveira [24] proposed hybrid visualization
anomalies [15]. To achieve this task, dimensionality reduction that integrates multidimensional projections and parallel co-
is applied due to the large size of the data. After that, system ordinates in a single view for a better exploration and a
as a 2D projection method based on MotionExplorer [16] is better understanding of the data being treated. In a single
applied to visualize them. In [2], an approach to translate time view, the user can analyse the instances relationship and
series into the network graph for visualization and pattern attributes behaviour without using coordination mechanisms.
mining is introduced. This graph can able to encode both This approach overcome the challenge of keeping track of
temporal ordering and statistical dynamics of the original data elements highlighted among multiple views. In this paper,
time series through the Markov Transition Field. Within this Multidimensional Projection and a point placement based on
study a preprocessing is carried out by using reduction of tree were used to compute the graphical representations based
dimensionality for later visualization. on similarity, but any kind of visualization technique could be
Finally, Shurkhovetskyy [1] describes the challenges of used to display the similarities among data instances.
large time series visualization and substantiates the need for
abstraction by discussing the requirements that need to be
considered to find a suitable abstraction method for time III. P ROPOSAL
series visualization. A framework for the classification of time
series abstraction algorithms that specifies and justifies the The overview of our approach is shown in Figure 1. Our
essential criteria for informed method selection is proposed approach mainly includes four components. First, feature
and a classification of a large number of existing abstraction extraction algorithm are applied. Then, similarity measure can
methods, which can be practically used for method selection be selected. Finally, NJ algorithm and radial layout is convined
is provided. to organize time series data into a tree structure. All the process
is interactive and iterative.
B. Neighbour Joining Tree Method
The neighbor-joining method [17] was originally proposed
for reconstructing phylogenetic trees of species by using their A. Dimensionality Reduction
Deoxyribonucleic acid (DNA) as a feature vector. It has been
applied successfully to other areas of knowledge such as visual There are several techniques for dimensionality reduction
analysis of text documents [8], organization of images [9] [10], of time series.
visualization of music collections [18] and demonstrates its 1) Discrete Cosine Transformation (DCT): DCT only uses
usefulness in understanding visualization designs [19]. cosine functions to transform original time series into fre-
Fig. 1: A schematic overview of our proposed approach

quency domain. DCT for a time series x = {x1 , . . . , xn } of 3) Discrete Wavelet Transform (DWT): DWT represents
length n is defined as [25]: time series in terms of wavelets, which are basic functions
used to represent any other function. DWT processes data at
n   different scales or resolutions. The simplest form of wavelets
X π 1 is Haar Wavelet [27]. The complexity of DWT using the Haar
xf = K(f ) xi cos (i − )(f − 1) , f = 1, . . . , n
i=1
n 2 transformation is O(n). The main drawback of this technique
(1) is that the length of the time series n must be power of 2.
where f is a index of feature vector x and K(f ) is defined 4) Piecewise Aggregate Approximation (PAA): Let the time
as follows: series as x = {x1 , . . . , xn } of length n. The time series is
 divided into d windows of equal length k. The average of the
 √1 , when f = 1 data falling within each window is calculated [28].
n
K(f ) = q 2
 , n when 2 ≤ f ≤ n k∗i
1 X
xi = xj for 1 ≤ i ≤ d (4)
The feature vector is defined by the first d coefficients: k
j=k∗(i−1)+1

x = {x1 , . . . , xd } with d ≤ n where k = nd is the length of each window and d is the


 

desired dimension of feature vector x.


It is possible to calculate all DCT coefficients using Its representation is defined by:
O(n log n) operations in a similar way to the Fast Fourier
Transform (FFT). x = {x1 , ..., xd }
2) Singular Value Decomposition (SVD): SVD requires that
all the time series are of equal length represented by a matrix with d ≤ n.
X of dimension M × N [26]. 5) Chebyshev Polynomials (CP): Let us define time series
S = h(t1 , v1 ), ..., (tN , vN )i with −1 ≤ t1 ≤ ... ≤ tN ≤ 1 and
the intervals [29].
XM ×N = UM ×M × AM ×N × VN ×N (2)
 t1 +t2

where N is the length of all time series, M is the number 
 −1, 2 , if i = 1
h t +t t +t 
of time series, U is an orthogonal matrix by columns of order Ii =
i−1 i
, i i+1
, if 2 ≤ i ≤ N − 1 (5)
h 2 2
M × M , A is a diagonal matrix of order M × N and V is a 
 tN −1 +tN , 1 ,

if i = N
matrix N × N orthogonal by rows. 2

The reduction of the dimensionality is obtained by speci-


fying the value of d (desired dimension of the characteristic
Chebyshev polynomial  of degree N is defined as PN (t) and
their roots as tj = cos (j−0.5)∗π , 1 ≤ j ≤ N.
vector). N
The step function is defined by:

X M ×d = UM ×M × AM ×d = [λ1 u1 , . . . , λd ud ] (3) g(t) = vi , if t ∈ Ii for 1 ≤ i ≤ N (6)

where d ≤ N , {λi }di=1 are eigenvalues (diagonal elements where vi is the value of time series at time ti or the value
of matrix A) and {ui }di=1 are column vectors of the matrix U . at interval Ii .
The lower boundary lemma is satisfied with the inclusion 2) Dynamic Time Warping (DTW): DTW is useful when
of the chebyshev weight function and the length of each the two time series are not aligned to the X-axis. One of
subinterval: the drawbacks of DTW is its computational cost, however,
g(t) it presents good results when there is little data [31].
f (t) = p , if t ∈ Ii for 1 ≤ i ≤ N (7) The algorithm finds the distance between time series of
w(t)|Ii |
different length without any problem. Suppose time series
1
where g(t) is defined by Equation 6, w(t) = √1−t 2
and |Ii | X = x1 , x2 , ..., xm with length m and another time series
is the length of the subinterval Ii . Y = y1 , y2 , ..., yk with length k. The warping path W =
The feature vector is formed by the first chebyshev coeffi- w1 , w2 , ..., wN where max(k, m) ≤ N < k + m − 1 is
cients, n. found using dynamic programming to compute the cumulative
N N
distance Cd (i, j):
1 X 1 X
c0 = f (tj )P0 (tj ) = f (tj ) (8)
N j=1 N j=1

N
Cd (i, j) = dist(i, j)+
2 X min{Cd (i − 1, j − 1), Cd (i − 1, j), Cd (i, j − 1)} (14)
ci = f (tj )Pi (tj ), para 1 ≤ i ≤ n − 1 (9)
N j=1
Where the k × m matrix distance is defined such that the
6) Autoencoder (AUTOE): An autoencoder neural network
(i, j) element contains the distance of Xi and Yj [31].
is an unsupervised learning algorithm that applies backprop-
agation by setting the target values to be equal to the inputs. Path warping is subject to several constraints such as
The basic form of an autoencoder consists of the input layer boundary conditions, continuity, monotonicity, which are made
of visible units x, the layer of hidden units h and the to optimize the performance of its calculation.
layer of reconstructed units x b. These layers are connected
through the weight matrices W (1) and W (2) . The hidden layer C. Neighbor-Joining Tree
and the reconstruction layer have bias vectors b(1) and b(2) ,
respectively. The NJ algorithm receives as input a matrix of dissimilarity.
Since hidden units are less than input unit, the network Then, it joins two closest objects in each iteration and at the
is forced to learn a “compressed” representation of the input same time separates from the other objects, according to the
very similar to Principal Component Analysis (PCA) [30]. The function of separation S []. The result is a similarity tree
feedforward activations are calculated as: where each pair of nodes are joined by a hypothetical ancestor
node. The function to calculate the similarity between two
X
1 objects i and j is defined as:
hj = σ( Wji xi + b1j ) (10)
i
Pn P
k6=i,j (Dik + Djk ) Dij Dkl
X
x
bi = σ( Wij2 hj + b2i ) (11) S(i, j) = + +
k,l6=i,j
(15)
j 2(n − 2) 2 n−2
where σ(.) is the activation function. Once the pair of objects to group are selected, the length of
The cost function is defined as: the new edges must be calculated to the hypothetical ancestor
N
node by this equation:
1 X X (n) (n)
J(θ) = bi )2
(xi − x (12)
2N n i P P
1 k6=i,j Dik k6=i,j Djk
where N is the number training samples. DiX = (Dij + − ) (16)
2 n−2 n−2
B. Similarity Measure
1) Euclidean Distance: The Euclidean distance between P P
1 k6=i,j Djk k6=i,j Dik
two time series: X = x1 , x2 , ...xn and Y = y1 , y2 , ...yn is DjX = (Dij + − ) (17)
calculated as: 2 n−2 n−2

p When the objects i and j are joined and an object (ij) is


ED = (x1 − y1 )2 + (x2 − y2 )2 + ... + (xn − yn )2 (13) created as a consequence of removing the objects i and j, the
distance between (ij) to any different k node is calculated by
The use of Euclidean distance in time series has some limita- the equation:
tions: a) it is necessary that the two time series have the same
length and scale, b) the time series should not have any gaps, Dik + Djk
in addition, c) it is also sensitive to the presence of noise [31]. D(ij)k = (18)
2
D. Radial Layout
Radial Layout has been used in the visualization of the
NJ algorithm. Paiva [23] used to support classification tasks
through visual analysis of the data and Li [19] used to group
visualization designs generating a categorization. It was also
used with other types of trees such as minimum spanning
tree(MST) [32] to visulize financial markets.
The main idea of radial layout is to assign each subtree to a
wedge of angular width proportional to a number of leaves in
that subtree. The wedge of an inner vertex is divided among
its children, and tree edges are drawn along wedge angle
bisectors, so that they can have any length without violating
disjointness [33]. (a) DTW Distance (b) Euclidean Distance

IV. E XPERIMENTAL RESULTS Fig. 3: The results of our approach of plane dataset without
any reduction method
In this section we explore some of the results of our
approach in two datasets. The rest of the results, applying all
reduction methods and similarity measure can be found online
1
. The complete code is available in github 2 .
A. Dataset
In the experiments we used Plane dataset [34]. This is a
data set of plane outlines 2. This dataset has 7 classes a total
of 210 examples and a dimensionality of 144.

(a) DTW Distance (b) Euclidean Distance


Fig. 4: Applying autoencoder as dimensionality reduction. We
reduce to 72 dimensions
Fig. 2: Description of Plane dataset [35]

B. Detecting Similar Planes organization. In addition our approach allows to make zoom-
in interactions and we can also see time series in detail by
In the Figure 3, the Plane dataset without applying any hovering each node of the tree. This makes the analysis more
dimensionality reduction methods is showed. Visualization intuitive as shown in the Figure 5.
using DTW (Figure 3a) groups similar time series better than
using Euclidean distance (Figure 3b). In the Figure 4, the
reduction method based on autoencoders was used. We reduce
the dimensionality from 144 to 72. It seem that the DTW
distance 4a performs better than the Euclidean distance 4b.
We can also find interstering conclusions about the data in
analysis while we use the interation mechanism.
C. Interactive Exploration
The interaction offered by our approach allows us to inter- Fig. 5: Zoom-in to detail and visualize time series in the node
play between dimensionality reduction methods and similarity
measure techniques. Each of these choices will produce differ-
ent visualizations of the dataset while maintaining hierarchical V. C ONCLUSION
1 Results: https://rawgit.com/rjru/EvolutionOfThemes/master/cytoscape/ As one of the future work, we are interested in designing a
main visual/test2.html unified user interface to build a set of interaction mechanism to
2 Code: https://github.com/rjru/EvolutionOfThemes/tree/master/time series
and https://github.com/rjru/EvolutionOfThemes/tree/master/cytoscape/main enable the active exploring of the time series through similarity
visual trees by the users.
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