Journal of Theoretical and Applied Information Technology

XXst Month 201x. Vol. x No.x

© 2005 - 2012 JATIT & LLS. All rights reserved.

ISSN: 1992-8645 www.jatit.org E-ISSN: 1817-3195

MODIFIED DYNAMIC TIME WARPING FOR

HIERARCHICAL CLUSTERING
1
MAHMOUD SAMMOUR, 2 ZULAIHA OTHMAN
Center for Artificial Intelligence Technology, Faculty of Information Science and Technology, Universiti
Kebangsaan Malaysia 43600 Bangi, Selangor Darul Ehsan, Malaysia.
E-mail: 1mahmoud.samour@gmail.com

ABSTRACT

Time series clustering is the process of grouping sequential correspondences in similar clusters. The key
characteristic behind clustering time series data lies on the similarity/distance function used to identify the
sequential matches. Dynamic Time Warping (DTW) is one of the common distance measures that have
demonstrated competitive results compared to other functions. DTW aims to find the shortest path in the
process of identifying sequential matches. DTW relies on a dynamic programming to obtain the shortest path
where the smaller distance is being computed. However, in the case of equivalent distances, DTW is selecting
the path randomly. Hence, the selection could be misguided in such randomization process which
significantly affect the matching quality. This is due to randomization may lead to longer path which drift
from obtaining the optimum path. This paper proposes a modified DTW that aims to enhance the dynamic
selection of the shortest path when handling equivalent distances. Experiments were conducted using twenty
UCR benchmark datasets. Results shown that the modified DTW reveal superior results in compared to the
standard. This can demonstrate the effectiveness of the proposed modification in which optimizing the
shortest path has enhanced the performance of clustering.
Keywords: Hierarchical Clustering, Dynamic Time Warping, Distance Measures

1. INTRODUCTION proposed to integrate with clustering techniques such

Time series has been emerged as a response to the
data evolution of chronological representation where
the data been made in time intervals (Fu, 2011).
There are many kinds of time series data such as
financial, weather forecasting, pattern recognition,
etc. (Wismüller et al., 2002). The common task of
time series data mining is the process of identifying
similar sequences. Such process is performed using
clustering techniques.
Clustering time series data aims to identify
sequential correspondences among two time
sequences (Rani and Sikka, 2012). Several domains
have been examined in the context of time series
such as financial, weather forecasting, pattern
recognition, etc. (Wismüller, et al., 2002). Clustering
can be performed using two main approaches;
partitioning (e.g. k-means clustering) and
hierarchical clustering (e.g. agglomerative
clustering) (Badr et al., 2015). In fact, each clustering
technique is integrated with a particular similarity
(distance) measure that has the ability to identify
similarity among the objects. In fact, integrating an
appropriate similarity measure with an appropriate
clustering technique is a challenging task (Kalpakis
et al., 2001). Several similarity functions have been
as Euclidean distance, Minkowski distance and
Dynamic Time Warping (DTW) measures. DTW has
been widely used for time series data due to its ability
to identify sequential correspondences.
Dynamic Time Warping (DTW) is one of the
common similarity functions that has demonstrated
competitive results compared to other measures.
DTW aims to find the shortest path in the process of
identifying sequential matches. DTW relies on a
dynamic programming to obtain the shortest path
where the smaller distance is being computed.
However, in the case of equivalent distances, DTW
is selecting the path randomly. Hence, the selection
could be misguided in such randomization process
which significantly affect the matching quality. This
is due to randomization may lead to longer path
which drift from obtaining the optimum path.
Several studies have addressed this problem by
proposing specific modifications for the DTW such
as computing a global averaging (Petitjean et al.,
2016; Petitjean et al., 2011) or computing the shifting
estimation (Yuan et al., 2011). However, these
modifications may not fit multiple time series with
different lengths. Therefore, this paper proposes a
modified DTW that aims to enhance the dynamic
selection of the shortest path when handling

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 Journal of Theoretical and Applied Information Technology
XXst Month 201x. Vol. x No.x
© 2005 - 2012 JATIT & LLS. All rights reserved.
ISSN: 1992-8645 www.jatit.org
equivalent distances. In order to demonstrate the
effectiveness of the proposed modification, multiple
time series datasets with different lengths, have been
used in the experiment. In addition, the proposed
modified DTW has been compared with three
similarity measures including standard DTW,
Euclidean and Mikowski distance measures.
2. RELATED WORK
In fact, many research efforts have proposed
enhancement and modification for the Dynamic
Time Warping (DTW) in order to improve its
functionality regarding specific domains. Such
enhancements have intended to reduce the time
consumed which leads to improve the efficiency, as
well as, acquiring better accuracy which leads to
improve the effectiveness. For instance, Efrat & Fan
(Efrat et al., 2007) have addressed the problem of
curve matching which is considered as a drawback
of DTW in which the curves are being sampled as
sequences to identify the similarity among two time-
series. The authors suggested that such sampling of
curve is directly affect the quality of the results. In
this manner, the authors have proposed a continuous
DTW for calculating similarity among curves using
exact and approximate matching algorithms. The
proposed continuous DTW has been evaluated using
signature verification dataset and compared with the
traditional DTW. The proposed continuous DTW
has outperformed the traditional (i.e. discrete) DTW.
In addition, Petitjean et al. (2011) have proposed
a global averaging mechanism for DTW regarding
clustering time series sequences. The authors have
concentrated on the drawback of using DTW with
pairwise sequence similarity in which a two
individual sequences are being compared with each
other. The main drawback behind the pairwise
matching lies on the sensitivity of sequence ordering.
The influence on sequence ordering has a significant
impact on the equality of results. Twenty UCR
benchmark datasets have been used to evaluate the
proposed averaging DTW. Results shown superior
performance for the proposed method compared to
the pairwise matching.
In the context of gene expression, Yuan et al.
(2011) have figured out that the traditional DTW
cannot be applied to genes that have significant
differences in different time series. Such differences
may indicate significant factor rather than a simple
time change. Therefore, time shift estimation
appears to be insufficient in terms of identifying
similarity among two genes expressions. Therefore,
a modified version of DTW has been proposed to
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E-ISSN: 1817-3195
overcome both time shifting estimation and
significant indicators detection.
Zhu et al. (2012) have addressed the problem of
time-consumption when using DTW for large-scale
time series clustering. The authors have proposed a
novel approximation for DTW in which the DTW
distances can be bound between LB-Keogh and
Euclidian distance functions. The key characteristic
behind the proposed method lies on the accurate
approximation gained by the two bounds LB and ED
together. This can be performed by analyzing the
best ‘mixing weight’ of the upper and lower bounds
by sampling a tiny fraction of the true DTW
distances. Many UCR benchmark datasets have been
used to evaluate the proposed approximation.
Results shown a significant reduction regarding
consumption when using the proposed
approximation of DTW.
Begum et al. (2015) proposed a pruning strategy
in order to accelerate the performance of DTW. Such
strategy aims to utilize both upper and lower bounds
to prune off a large fraction of the expensive distance
calculations. Using different domains of time series,
the authors have demonstrated the efficiency of the
proposed pruning strategy.
Petitjean et al. (2016) Have addressed the problem
arises when combining nearest neighbor
classification with DTW for time series data. Such
problem can be represented as the inaccurate
centroid resemble in terms of the actual instances. In
this vein, the authors have utilized the global
averaging mechanism introduced by Petitjean et al.
(2011) in order to generate efficient nearest centroid
classifiers.
Silva et al. (2016) have addressed the problem of
DTW in terms of discarding the prefixes and suffixes
of two time series. Such problem can be represented
by the warping invariance that is being considered to
the body of time series but not for the head and tails.
In this vein, the authors have considered more points
in the head and tails to be involved in the
computation of the DTW in order to provide more
accurate resemble of the time series.
3. MATERIALS AND METHOD
Hierarchical clustering algorithms work by
aggregating the objects into a tree of clusters
(Aghagolzadeh et al., 2007). Hierarchical clustering
can be categorized into two types; agglomerative and
divisive. Such categorization is inspired from the
mechanism of grouping the objects whether bottom-
up or top-down approach. Agglomerative
hierarchical clustering (AHC) is considered as a
 Journal of Theoretical and Applied Information Technology
XXst Month 201x. Vol. x No.x
© 2005 - 2012 JATIT & LLS. All rights reserved.

ISSN: 1992-8645 www.jatit.org E-ISSN: 1817-3195

bottom-up hierarchical approach where each object minimum distance/similarity between the two series
set in a separated cluster then AHC will merge such is of interest. Hence, the DTW can be computed as
clusters into larger clusters (Rani and Sikka, 2012). follows:
Such process is continuing until a specific
∑𝐾𝑘=1 𝑝𝐾
termination has been reached. Complete linkage 𝑑𝐷𝑇𝑊 = 𝑚𝑖𝑛 (3)
algorithm aims to identify the similarity between two 𝐾
clusters by measure two nearest data points that are
located in different clusters. Hence, the merge will 3.3. Modified Dynamic Time Warping (M-
be done between the clusters that have minimum DTW)
distance -most similar- between each other. In this
Let A and B are two time series that consist of data
paper, AHC has been applied with multiple distance
points as A = {𝑃𝐴1 , 𝑃𝐴2 , 𝑃𝐴3 , 𝑃𝐴4 , 𝑃𝐴5 , 𝑃𝐴6 }, and B
measures including Euclidean distance, Minkowski
distance, standard DTW and the modified DTW as = {𝑃𝐵1 , 𝑃𝐵2 , 𝑃𝐵3 , 𝑃𝐵4 , 𝑃𝐵5 , 𝑃𝐵6 , 𝑃𝐵7 }. DTW will
similarity measures. establish the similarity matrix between the two time
series by computing the Euclidean distance between
3.1. Euclidean and Minkowski Distance each corresponding pair of the data points as shown
Measures in Table 1.
Let 𝑥𝑖 and 𝑣𝑗 be a P-dimensional vector, then the Table 1. Similarity matrix
Euclidean distance can be measured as (Liao, 2005):
B PA1 PA2 PA3 PA4 PA5 PA6
A
𝑃
2
PB1 0 0 1 4 1 1
𝑑𝐸 = √∑(𝑥𝑖𝑘 − 𝑣𝑗𝑘 ) (1)
PB2 1 1 0 0 0 4
𝑘=1
PB3 4 4 1 0 0 9
Minkowski distance is a generalization of
Euclidean distance, which is computed as follows PB4 1 1 0 1 0 4
(Liao, 2005): PB5 1 0 1 4 1 1

𝑃 PB6 0 1 1 4 1 1
𝑞
𝑞
𝑑𝑀 = √∑(𝑥𝑖𝑘 − 𝑣𝑗𝑘 ) (2) PB7 1 1 4 9 4 0
𝑘=1

Where q is a positive integer.
3.2. Dynamic Time Warping (DTW)
DTW has been widely used to compare between
discrete sequences and sequences of continuous
values (Liao, 2005). Let 𝑆 = {𝑠1 , 𝑠2 , … , 𝑠𝑖 , … , 𝑠𝑛 }
and 𝑇 = {𝑡1 , 𝑡2 , … , 𝑡𝑗 , … , 𝑡𝑛 } be a two time series
sequences. DTW will minimize the differences
among these series by representing a matrix of 𝑛 ×
𝑚. In such matrix, the distance/similarity between 𝑠𝑖
and 𝑡𝑗 will be calculated using Euclidean distance.
However, a warping path 𝑃=
{𝑝1 , 𝑝2 , … , 𝑝𝑘 , … , 𝑝𝐾 } where max(𝑚, 𝑛) ≤ 𝐾 ≤ 𝑚 +
𝑛 − 1 will be elements from the matrix that meet
three constraints including boundary condition,
continuity and monotonicity. The boundary
condition constraint requires the warping path to
start and finish in diagonally opposite corner cells of
the matrix. That is 𝑝1 = (1,1) and 𝑝𝐾 = (𝑚, 𝑛). The
continuity constraint restricts the allowable steps to
adjacent cells. The monotonicity constraint forces
the points in the warping path to be monotonically
spaced in time. The warping path that has the
The objective of this matrix is to find the shortest
path by starting from the top most right corner
𝑃(𝑃𝐴6 , 𝑃𝐵1 ) and using dynamic programming to
reach the point of origin 𝑃(𝑃𝐴1 , 𝑃𝐵7 ) accumulating
the sum of the similarity between the went thru
points (accumulated path).
On 𝑃(𝑃𝐴6 , 𝑃𝐵1 ), DTW will pick the minimum
between three points 𝑃(𝑖 − 1, 𝑗) = 𝑃(𝑃𝐴5 , 𝑃𝐵1 ),
𝑃(𝑖, 𝑗 − 1) = 𝑃(𝑃𝐴6 , 𝑃𝐵2 ) or 𝑃(𝑖 − 1, 𝑗 − 1) =
𝑃(𝑃𝐴5 , 𝑃𝐵2 ). Since 𝑃(𝑃𝐴5 , 𝑃𝐵2 ) = 0 which is the
minimum value thus, it was selected and the
accumulated cost was increment by its value. And so
on until the point P(𝑃𝐴1 , 𝑃𝐵7 ) is reached.
On point 𝑃(𝑃𝐴5 , 𝑃𝐵2 ), all the neighboring cells
have equivalent values, here the randomization is
taking a place in which the movement will be
selected randomly as shown in Fig. 1 (a). Similarly,
in the points 𝑃(𝑃𝐴3 , 𝑃𝐵2 ) the selection has been
performed randomly.
Hence, the modification of DTW has been
conducted by setting the value of 𝑃(𝑖 − 1, 𝑗 − 1)
when handling neighbors with similar values, this
can be represented in Fig. 1 (b).

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 Journal of Theoretical and Applied Information Technology
XXst Month 201x. Vol. x No.x
© 2005 - 2012 JATIT & LLS. All rights reserved.

ISSN: 1992-8645 www.jatit.org E-ISSN: 1817-3195

(a) Standard DTW (b) Modified DTW

Figure 1. Obtaining the shortest path

As shown in Fig. 1, the summation of the path for 0 + 0 + 0 + 0 + 1} = 2. Apparently, the results of
the standard DTW can be expressed as 𝑆𝑢𝑚 = both applications shown variant values. Such
{1 + 0 + 0 + 0 + 1 + 0 + 0 + 0 + 1} = 3, whereas difference may have a potential impact on the final
for the modified DTW 𝑆𝑢𝑚 = {1 + 0 + 0 + 0 + outcome of the time series clustering. Fig. 2 depicts
the pseudo code of the modified DTW.
Algorithm 1. Modified Dynamic Time Warping
1 Input:
2 S // is a 2-dimensional matrix with 𝑚 × 𝑛
3 𝑉1 = {𝑠1 , 𝑠2 , … . , 𝑠𝑛 } //is the first vector with n time points
4 𝑉2 = {𝑠1 , 𝑠2 , … . , 𝑠𝑚 } // is the second vector with m time points
5 𝑖, 𝑗 // are loop index, cost is an integer
6
7 Steps:
8 Initialize the matrix
9 S[0,0] = 0;
10 FOR i = 1 to m DO LOOP
11 S[0 , i ] = ∞
12 END
13 FOR i = 1 to n DO LOOP
14 S[i , 0 ] = ∞
15 END
16 Populating the similarity matrix
17 FOR i = 1 to n DO LOOP
18 FOR j = 1 to m DO LOOP
19 Cost = d(V1[i], V2[j])//Euclidean distance
20 S[i , j] = cost + MINI
21 MINI = IF S[I-1, J-1] equals S[i, j-1]
22 MINI = S[i-1, j-1]
23 OR if S[i-1, j-1] equals S[i-1, j]
24 MINI = S[i-1, j-1]
25 ELSE MINI = Minimum ( S[i-1 , j] , //increment
26 S[i , j-1] , //decrement
27 S[i-1, j-1] ) //match
28 END
29 END
30 Return S[n , m]
31
32
33

Figure 2, Modified DTW pseudo code

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 Journal of Theoretical and Applied Information Technology
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© 2005 - 2012 JATIT & LLS. All rights reserved.

ISSN: 1992-8645 www.jatit.org E-ISSN: 1817-3195

4. EXPERIMENTAL RESULTS
Twenty time series datasets have been used in this
study from UCR time series data archive (Keogh and
Folias, 2002). Such archive contains several time
series datasets that are related to multiple domains
with different lengths.
Basically, the evaluation has been conducted
based on the distribution of members within the
cluster in which the majority will be considered as
the class label. Consequentially, the common
information retrieval metrics precision, recall and f-
measure are being used to evaluate the clusters. Such
metrics can be computed as follows:
|𝑇𝑃|
𝑃𝑟𝑒𝑐𝑖𝑠𝑖𝑜𝑛 =
|𝑇𝑃| + |𝐹𝑃|
|𝑇𝑃|
𝑅𝑒𝑐𝑎𝑙𝑙 =
|𝑇𝑃| + |𝐹𝑁|
𝑃×𝑅
𝐹 − 𝑚𝑒𝑎𝑠𝑢𝑟𝑒 = 2 ×
𝑃+𝑅
where TP is the instance that has been affiliated
within a cluster and related to this cluster, FP is the
instance that has been affiliated within a cluster but
not related, TN is the instance that is not affiliated
within a cluster but it is related to it, and finally FN
Table 2. Results of the four distance measures based on Precision, Recall and F-measure for all datasets
is the instance that is not affiliated within a cluster
and it is not related to it.
Based on the mentioned evaluation metrics, Table
2 depicts the results of Minkowski, Euclidean, DTW
and modified DTW for all datasets.
As shown in Table 2, for Minkowski, the results
were relatively similar to Euclidean except for
datasets 18 and 19 where Minkowski has shown
relatively higher performance. Vice versa, for
datasets 17 and 20 Minkowski shown poor
performance compared to Euclidean.
For DTW, the results were relatively higher than
Euclidean’s results especially for datasets 11, 16, 18
and 19 where the superiority of DTW was
(4)
remarkable.
For the modified DTW, the results of all the
(5)
datasets were better than Euclidean’s results
(6) especially for datasets 11, 13, 17, 18, 19 and 20
where the performance has significantly increased.
Fig. 3 depicts the performances for each distance
measure respectively, while Fig. 4 shows the
comparison among the distance measures based on
f-measure.

Dataset Euclidean Minkowski DTW Modified DTW

P R F P R F P R F P R F
1 TwoLeadECG 0 0 0 +1 +1 +1 -3 +6 +3 -5 +12 +6
2 OSU Leaf 0 0 0 -4 -2 -3 14 +7 +10 +4 +1 +4
3 Phoneme 0 0 0 0 0 0 -9 +3 +11 -3 +8 +11
4 ArrowHead 0 0 0 0 0 +2 -7 0 0 +16 +1 +8
5 DistalPhalanxTW 0 0 0 +9 +7 +8 10 +1 +3 +5 +12 +10
6 FordA 0 0 0 +2 0 +1 2 +1 +1 +1 +4 +2
7 FISH 0 0 0 +5 -3 0 20 +5 +10 +19 -1 +12
8 50Words 0 0 0 0 -1 -2 -1 +8 +7 +4 +14 +10
9 Beef 0 0 0 -19 +19 +1 2 +4 -1 +1 +19 +7
10 Swedish Leaf 0 0 0 -5 +1 0 6 +7 +8 +12 +10 +12
11 Face (all) 0 0 0 +4 +6 +5 30 +23 +25 +34 +10 +27
12 Computers 0 0 0 +21 0 +8 3 +1 +2 +11 +12 +12
13 Lightning-7 0 0 0 +11 -6 0 1 +9 +9 +10 +18 +17
14 Gun-Point 0 0 0 -4 -2 -3 +12 +8 +10 +14 +4 +6
15 MiddlePhalanxOutlineAgeGroup 0 0 0 +1 +3 -1 +7 17 +9 +6 +7 +7
16 ProximalPhalanxOutlineCorrect 0 0 0 +11 0 +3 +10 30 +20 +10 +21 +16
17 DistalPhalanxOutlineAgeGroup 0 0 0 -10 -20 -19 +20 0 +3 +9 +8 +6
18 BeetleFly 0 0 0 +35 +25 +30 +25 19 +21 +25 +21 +24
19 ProximalPhalanxOutlineAgeGroup 0 0 0 +30 +17 +23 +33 36 +34 +36 +39 +37
20 CBF 0 0 0 -30 -10 -19 -7 6 +1 +11 +31 +22

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Euclidean Minkowski
100 100

50 50

0 0
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

P R F P R F

DTW Modified DTW

100 100
80 80
60 60
40 40
20 20
0 0
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

P R F P R F

Figure 3. Results of precision, recall and f-measure for the four distance measures

F-measure
100

80

60

40

20

0
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

Euclidean Minkowski DTW Modified DTW

Figure 4. Comparison among the four distance measures based on f-measure

As shown in Fig 4, The result shows that DTW has
outperformed both of Minkowski and Euclidean
distance measures in terms of f-measure for 14 out
of 20 data sets including ‘1, 2, 3, 7, 8, 10, 11, 13, 14,
15, 16, 17, 19, 20’. In contrast, Minkowski has
outperformed the other distance functions in terms of
f-measure for 6 datasets including '4, 5, 6, 9, 12, 18'.
Apparently, Euclidean distance function has
obtained the lowest f-measure values for all datasets.

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 Journal of Theoretical and Applied Information Technology
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© 2005 - 2012 JATIT & LLS. All rights reserved.
ISSN: 1992-8645 www.jatit.org
In contrast between DTW and the modified DTW,
DTW has outperformed the modified DTW in terms
of F-measure for five datasets including ‘2, 10, 14,
15, 16’. This is due to the limitation of AHC in which
the clusters merging process cannot be undone (Gao
et al., 2010). In this manner, the modification of
DTW will lead to merge irrelevant clusters. Similar
to incorrect rejection of true in which the error may
lead to better results, the randomization of acquiring
the shortest path using DTW will avoid such
limitation of AHC.
On the other hand, the modified DTW has
outperformed DTW for the remaining 15 datasets. In
this manner, the modification of DTW to acquire the
shortest path has successfully enhanced the quality
of clustering results. Figure 3 shows both
performances of DTW and modified DTW.
The superiority of DTW compared to Euclidean
and Minkowski distance measures was expected
from the literature where several clustering
approaches have been proposed for time series using
DTW for various domains (Al-Naymat et al., 2009;
Niennattrakul and Ratanamahatana, 2007; Petitjean,
et al., 2011; Yuan, et al., 2011; Zhu, et al., 2012).
Multiple comparative analysis studies have been
presented to compare different distance measures
with clustering technique. For instance, Ferreira &
Zhao (Ferreira and Zhao, 2016) have proposed a
clustering approach for time series community
detection in social network using multiple distance
measures including ED, Infinite Norm, DTW,
Person Correlation, Wavelet Transform, and
Integrated Periodogram. Among these distance
functions, DTW has the superior performance
compared to other measures.
However, several researchers attempted to modify
DTW for instance, Zhu et al. (2012) have modified
DTW in terms of time-consuming. Whereas, Yuan
et al. (2011) have attempted to make DTW suitable
for specific domain specifically Gene expressions.
Furthermore, Petitjean et al. (2011) have modified
DTW to be able to identify similarity via global
averaging mechanism rather than the pair-wise
sequence matching. Similar to the mentioned
modifications, this study has proposed a modified
DTW by optimizing the acquired shortest path.
Results shown a superior performance compared to
the standard DTW.
5. CONCLUSION
This study has proposed a modification for
Dynamic Time Warping (DTW) in terms of
acquiring the shortest path for hierarchical time
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E-ISSN: 1817-3195
series clustering applications. Twenty UCR
benchmark datasets have been used in the
experiments. The clustering has been performed
using Agglomerative Hierarchical Clustering (AHC)
using multiple distance measures including
Euclidean distance, Minkowski distance, standard
DTW and the proposed modified DTW. Results
shown that the proposed DTW has outperformed the
other distance measures. This can demonstrate the
impact of acquiring the shortest path on the
clustering results. However, this study has not
addressed the impact of the modified DTW on the
efficiency thus; future researches could be examine
the time and memory consuming using the proposed
DTW.
ACKNOWLEDGEMENT
This study is supported by the University
Kebangsaan Malaysia (UKM) and funded by
research grant (AP2013-007).
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